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Rosso F, Rebellón-Sánchez DE, Llanos-Torres J, Hurtado-Bermudez LJ, Ayerbe L, Suárez JH, Orozco-Echeverri N, Rojas-Perdomo CC, Zapata-Vasquez IL, Patiño-Niño J, Parra-Lara LG. Clinical and microbiological characterization of Salmonella spp. isolates from patients treated in a university hospital in South America between 2012-2021: a cohort study. BMC Infect Dis 2023; 23:625. [PMID: 37749501 PMCID: PMC10519077 DOI: 10.1186/s12879-023-08589-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/06/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Salmonellosis is a major cause of morbidity and mortality and one of the most frequent etiologies of diarrhea in the world. Mortality due to Salmonellosis in Latin America still poorly understood, and there is a lack of studies that evaluate resistance and clinical manifestations. The aims of this study were to characterize patients infected with Salmonella spp. seen in a university hospital in Colombia between 2012 and 2021, to evaluate trends in antibiotic resistance and to determine the proportion of overall mortality and related factors. METHODS Retrospective observational study. All patients with microbiological diagnosis of Salmonella spp. were included. The sociodemographic, clinical and microbiological characteristics were described, and the proportion of antibiotic resistant isolates per year was estimated. The prevalence of mortality according to age groups was calculated. Log binomial regression models were used to establish factors associated with mortality. RESULTS Five hundred twenty-two patients were analyzed. Salmonellosis accounted for 0.01% of all medical consultations. The median age was 16 years old. The most common clinical presentation was gastroenteric syndrome (77.1%) and symptoms included diarrhea (79.1%), fever (66.7%), abdominal pain (39.6%) and vomiting (35.2%). Of the Salmonella spp. isolates, 78.2% were not classified, 19.1% corresponded to non-typhoidal Salmonella and 2.7% to Salmonella typhi. Mortality occurs in 4.02% of the patients and was higher in patients with hematologic malignancy (11.6%). When analyzing by age group, the proportion of deaths was 2.8% in patients aged 15 years or younger, while in those older than 15 years it was 5.4%. Factors associated to mortality where bacteremia (aPR = 3.41 CI95%: 1.08-10.76) and to require treatment in the ICU (aPR = 8.13 CI95%: 1.82-37.76). In the last 10 years there has been a steady increase in resistance rates to ciprofloxacin, ampicillin, ampicillin/sulbactam and ceftriaxone, reaching rates above 60% in recent years. CONCLUSIONS Despite improved availability of antibiotics for the treatment of salmonellosis in the past decades, mortality due to salmonellosis continues occurring in children and adults, mainly in patients with hematological malignancies and bacteremia. Antibiotic resistance rates have increased significantly over the last 10 years. Public health strategies for the control of this disease should be strengthened, especially in vulnerable populations.
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Affiliation(s)
- Fernando Rosso
- Fundación Valle del Lili, Centro de Investigaciones Clínicas (CIC), Carrera 98 #18-49, 760031, Cali, Colombia.
- Fundación Valle del Lili, Cali, Departamento de Medicina Interna, Servicio de Enfermedades Infecciosas, Carrera 98 #18-49, 760031, Cali, Colombia.
- Universidad Icesi, Facultad de Ciencias de la Salud, Calle 18 No. 122-135, Cali, 760031, Colombia.
| | - David E Rebellón-Sánchez
- Fundación Valle del Lili, Centro de Investigaciones Clínicas (CIC), Carrera 98 #18-49, 760031, Cali, Colombia.
- Fundación Valle del Lili, Cali, Departamento de Medicina Interna, Servicio de Enfermedades Infecciosas, Carrera 98 #18-49, 760031, Cali, Colombia.
| | - Julio Llanos-Torres
- Fundación Valle del Lili, Centro de Investigaciones Clínicas (CIC), Carrera 98 #18-49, 760031, Cali, Colombia
- Fundación Valle del Lili, Cali, Departamento de Medicina Interna, Servicio de Enfermedades Infecciosas, Carrera 98 #18-49, 760031, Cali, Colombia
| | - Leidy Johanna Hurtado-Bermudez
- Fundación Valle del Lili, Centro de Investigaciones Clínicas (CIC), Carrera 98 #18-49, 760031, Cali, Colombia
- Universidad Icesi, Facultad de Ciencias de la Salud, Calle 18 No. 122-135, Cali, 760031, Colombia
| | - Laura Ayerbe
- Universidad Icesi, Facultad de Ciencias de la Salud, Calle 18 No. 122-135, Cali, 760031, Colombia
| | - John Harold Suárez
- Universidad Icesi, Facultad de Ciencias de la Salud, Calle 18 No. 122-135, Cali, 760031, Colombia
| | - Nicolás Orozco-Echeverri
- Universidad Icesi, Facultad de Ciencias de la Salud, Calle 18 No. 122-135, Cali, 760031, Colombia
| | | | - Isabel Lucia Zapata-Vasquez
- Fundación Valle del Lili, Centro de Investigaciones Clínicas (CIC), Carrera 98 #18-49, 760031, Cali, Colombia
| | - Jaime Patiño-Niño
- Fundación Valle del Lili, Cali, Departamento de Pediatría, Servicio de Enfermedades Infecciosas, Carrera 98 #18-49, 760031, Cali, Colombia
| | - Luis Gabriel Parra-Lara
- Fundación Valle del Lili, Centro de Investigaciones Clínicas (CIC), Carrera 98 #18-49, 760031, Cali, Colombia
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Ragueh AA, Aboubaker MH, Mohamed SI, Rolain JM, Diene SM. Emergence of Carbapenem-Resistant Gram-Negative Isolates in Hospital Settings in Djibouti. Antibiotics (Basel) 2023; 12:1132. [PMID: 37508230 PMCID: PMC10376901 DOI: 10.3390/antibiotics12071132] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Introduction: The antimicrobial resistance (AMR) of bacteria is increasing rapidly against all classes of antibiotics, with the increasing detection of carbapenem-resistant isolates. However, while growing prevalence has been reported around the world, data on the prevalence of carbapenem resistance in developing countries are fairly limited. In this study, we investigated and determined the resistance rate to carbapenems among multidrug-resistant Gram-negative bacteria (MDR-GNB) isolated in Djibouti and characterized their resistance mechanisms. Results: Of the 256 isolates, 235 (91.8%) were identified as Gram-negative bacteria (GNB). Of these GNBs, 225 (95.7%) isolates exhibited a multidrug resistance phenotype, and 20 (8.5%) isolates were resistant to carbapenems, including 13 Escherichia coli, 4 Acinetobacter baumannii, 2 Klebsiella pneumoniae and 1 Proteus mirabilis. The most predominant GNB in this hospital setting were E. coli and K. pneumoniae species. Carbapenemase genes such as blaOXA-48 and blaNDM-5 were identified, respectively, in six and four E. coli isolates, whereas the carbapenemase blaNDM-1 was identified in three E. coli, two K. pneumoniae, one P. mirabilis and one A. baumannii. Moreover, three A. baumannii isolates co-hosted blaOXA-23 and blaNDM-1. Materials and Methods: A total of 256 clinical strains collected between 2019 and 2020 were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). Antibiotic susceptibility testing was performed using disk diffusion and E-test methods. Real-time polymerase chain reaction (RT-PCR), standard PCR and sequencing were used to investigate genes encoding for extended-spectrum-β-lactamases, carbapenemases and colistin resistance genes. Conclusions: We report, for the first time, the presence of MDR-GNB clinical isolates and the emergence of carbapenem-resistant isolates in Djibouti. In addition to performing antimicrobial susceptibility testing, we recommend phenotypic and molecular screening to track the spread of carbapenemase genes among clinical GNB isolates.
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Affiliation(s)
- Ayan Ali Ragueh
- Campus Balbala Croisement RN2-RN5, Université de Djibouti, Djibouti 1904, Djibouti
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Faculté de Pharmacie, Aix-Marseille Universite, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France
| | | | - Sitani Idriss Mohamed
- Laboratoire de Biologie et de Biochimie Clinique de L'hôpital Général Peltier, 1323, Avenue Maréchal, Djibouti 1119, Djibouti
| | - Jean-Marc Rolain
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Faculté de Pharmacie, Aix-Marseille Universite, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France
| | - Seydina M Diene
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Faculté de Pharmacie, Aix-Marseille Universite, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France
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Zhang Y, Yazid NBM, Ho PY, Hu X, Chen S, Vasoo S, Kanitthamniyom P. DropCarba - An automated magnetic digital microfluidic platform for rapid phenotypic testing of carbapenemase-producing Gram-negative bacilli. Biosens Bioelectron 2023; 225:115099. [PMID: 36709588 DOI: 10.1016/j.bios.2023.115099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
Carbapenemase-producing Gram-negative bacilli (CPGNB) is a type of antibiotic-resistant pathogens that often lead to severe clinical consequences. Phenotypic tests, such as Carba NP and blue Carba, are able to detect the resistant mechanism and provide rapid detection of carbapenemase producers to potentially guide personalized therapy. However, these tests require relatively tedious hands-on fluidic operations, and the assay format is ill-suited for automation and parallelization for improved throughput. In this study, we report an automated magnetic digital microfluidics-based platform, known as DropCarba, for parallel CPGNB detection in droplets. It automates the entire carbapenemase testing process and eliminates the need for almost all hands-on fluidic operations, which ensures high consistency and minimizes human errors with a simple "press-and-go" operation. DropCarba was validated with a large number of bacterial isolates of various Enterobacterales species (200 strains in total with 100 CPGNB and 100 non-resistant strains) in a blinded manner, and the results agree well with the benchmark Carba NP. DropCarba, with its full automation, simple operation, reduced reagent consumption, parallelization processing, and scalable manufacturing, will greatly improve CPGNB screening and make a valuable contribution to our fight against antibiotic resistance.
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Affiliation(s)
- Yi Zhang
- School of Electronic and Electrical Engineering, University of Electronic Science and Technology of China, China.
| | | | - Pei-Yun Ho
- National Center for Infectious Disease, Tan Tock Seng Hospital, Singapore
| | - Xuyang Hu
- China-Singapore International Joint Research Institute, China
| | - Songlin Chen
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore
| | - Shawn Vasoo
- National Center for Infectious Disease, Tan Tock Seng Hospital, Singapore
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Development of Microfluidic Chip-Based Loop-Mediated Isothermal Amplification (LAMP) Method for Detection of Carbapenemase Producing Bacteria. Microbiol Spectr 2022; 10:e0032222. [PMID: 35980298 PMCID: PMC9603548 DOI: 10.1128/spectrum.00322-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid and accurate diagnostic methods to identify carbapenemase-producing organisms (CPO) is of great importance for controlling the CPO infection. Herein, we have developed a microfluidic chip-based technique to detect CPO and assessed its clinical value in detecting CPO directly from blood cultures (BCs). The detection performance of the microfluidic chip-based LAMP amplification method was analyzed retrospectively on a collection of 192 isolates including molecularly characterized 108 CPO and 84 non-CPO and prospectively on a collection of 133 positive BCs with or without CPO suspicion, respectively. In the retrospective study, the microfluidic chip-based LAMP amplification method exhibited 87.5% accuracy (95% CI [82.0–91.5]), 97.7% sensitivity (95% CI [91.2–99.6]), 78.8% specificity (95% CI [69.5–86.0]), 79.6% positive predictive value (PPV) (95% CI [70.6–86.5]) and 97.6% negative predictive value (NPV) (95% CI [90.9–99.6]). Among the 192 isolates, 22 (11.5%) false-positives (FP) and 2 (1.0%) false negatives (FN) were observed. In the prospective study, the 133 routine isolates of positive BCs including 18 meropenem-resistant CPO and 115 non-CPO were assessed, and 4 FP were observed in non-CPO and CPO, respectively. The current method showed a total detection performance of 94.0% accuracy (95% CI [88.4–97.1]), 100.0% sensitivity (95% CI [73.2–100.0]), 93.2% specificity (95% CI [86.7–96.8]), 63.6% PPV (95% CI [40.8–82.0]) and 100.0% NPV (95% CI [95.8–100.0]). In summary, the microfluidic chip-based LAMP amplification method is reliable for the rapid screening and detection of CPO with high accuracy, sensitivity, and specificity, and could easily be implemented in clinical microbiology laboratories. IMPORTANCE Rapid and accurate identification of CPO may reduce the genetic exchanges among bacteria and prevent further dissemination of carbapenemases to non-CPO. The current method had designed microfluidic chip-based LAMP amplification method for multiplex detection of carbapenemase genes and evaluated the detection performance of the newly method. The current method can rapidly screen and detect CPO with high accuracy, sensitivity, and specificity, and could easily be implemented in clinical microbiology laboratories, as this will reduce the carbapenem resistance issues worldwide.
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Companion Animals—An Overlooked and Misdiagnosed Reservoir of Carbapenem Resistance. Antibiotics (Basel) 2022; 11:antibiotics11040533. [PMID: 35453284 PMCID: PMC9032395 DOI: 10.3390/antibiotics11040533] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 12/19/2022] Open
Abstract
The dissemination of antimicrobial-resistance is a major global threat affecting both human and animal health. Carbapenems are human use β-lactams of last resort; thus. the dissemination of carbapenemase-producing (CP) bacteria creates severe limitations for the treatment of multidrug-resistant bacteria in hospitalized patients. Even though carbapenems are not routinely used in veterinary medicine, reports of infection or colonization by carbapenemase-producing Enterobacterales in companion animals are being reported. NDM-5 and OXA-48-like carbapenemases are among the most frequently reported in companion animals. Like in humans, Escherichia coli and Klebsiella pneumoniae are the most represented CP Enterobacterales found in companion animals, alongside with Acinetobacter baumannii. Considering that the detection of carbapenemase-producing Enterobacterales presents several difficulties, misdiagnosis of CP bacteria in companion animals may lead to important animal and public-health consequences. It is of the upmost importance to ensure an adequate monitoring and detection of CP bacteria in veterinary microbiology in order to safeguard animal health and minimise its dissemination to humans and the environment. This review encompasses an overview of the carbapenemase detection methods currently available, aiming to guide veterinary microbiologists on the best practices to improve its detection for clinical or research purposes.
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Furniss RCD, Kaderabkova N, Barker D, Bernal P, Maslova E, Antwi AA, McNeil HE, Pugh HL, Dortet L, Blair JM, Larrouy-Maumus GJ, McCarthy RR, Gonzalez D, Mavridou DA. Breaking antimicrobial resistance by disrupting extracytoplasmic protein folding. eLife 2022; 11:57974. [PMID: 35025730 PMCID: PMC8863373 DOI: 10.7554/elife.57974] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/11/2022] [Indexed: 11/24/2022] Open
Abstract
Antimicrobial resistance in Gram-negative bacteria is one of the greatest threats to global health. New antibacterial strategies are urgently needed, and the development of antibiotic adjuvants that either neutralize resistance proteins or compromise the integrity of the cell envelope is of ever-growing interest. Most available adjuvants are only effective against specific resistance proteins. Here, we demonstrate that disruption of cell envelope protein homeostasis simultaneously compromises several classes of resistance determinants. In particular, we find that impairing DsbA-mediated disulfide bond formation incapacitates diverse β-lactamases and destabilizes mobile colistin resistance enzymes. Furthermore, we show that chemical inhibition of DsbA sensitizes multidrug-resistant clinical isolates to existing antibiotics and that the absence of DsbA, in combination with antibiotic treatment, substantially increases the survival of Galleria mellonella larvae infected with multidrug-resistant Pseudomonas aeruginosa. This work lays the foundation for the development of novel antibiotic adjuvants that function as broad-acting resistance breakers. Antibiotics, like penicillin, are the foundation of modern medicine, but bacteria are evolving to resist their effects. Some of the most harmful pathogens belong to a group called the 'Gram-negative bacteria', which have an outer layer – called the cell envelope – that acts as a drug barrier. This envelope contains antibiotic resistance proteins that can deactivate or repel antibiotics or even pump them out of the cell once they get in. One way to tackle antibiotic resistance could be to stop these proteins from working. Proteins are long chains of building blocks called amino acids that fold into specific shapes. In order for a protein to perform its role correctly, it must fold in the right way. In bacteria, a protein called DsbA helps other proteins fold correctly by holding them in place and inserting links called disulfide bonds. It was unclear whether DsbA plays a role in the folding of antibiotic resistance proteins, but if it did, it might open up new ways to treat antibiotic resistant infections. To find out more, Furniss, Kaderabkova et al. collected the genes that code for several antibiotic resistance proteins and put them into Escherichia coli bacteria, which made the bacteria resistant to antibiotics. Furniss, Kaderabkova et al. then stopped the modified E. coli from making DsbA, which led to the antibiotic resistance proteins becoming unstable and breaking down because they could not fold correctly. Further experiments showed that blocking DsbA with a chemical inhibitor in other pathogenic species of Gram-negative bacteria made these bacteria more sensitive to antibiotics that they would normally resist. To demonstrate that using this approach could work to stop infections by these bacteria, Furniss, Kaderabkova et al. used Gram-negative bacteria that produced antibiotic resistance proteins but could not make DsbA to infect insect larvae. The larvae were then treated with antibiotics, which increased their survival rate, indicating that blocking DsbA may be a good approach to tackling antibiotic resistant bacteria. According to the World Health Organization, developing new treatments against Gram-negative bacteria is of critical importance, but the discovery of new drugs has ground to a halt. One way around this is to develop ways to make existing drugs work better. Making drugs that block DsbA could offer a way to treat resistant infections using existing antibiotics in the future.
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Affiliation(s)
| | - Nikol Kaderabkova
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
| | - Declan Barker
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Patricia Bernal
- Department of Microbiology, Universidad de Sevilla, Seville, Spain
| | - Evgenia Maslova
- Department of Life Sciences, Brunel University London, London, United Kingdom
| | - Amanda Aa Antwi
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Helen E McNeil
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Hannah L Pugh
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Paris-Sud University, Paris, France
| | - Jessica Ma Blair
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | | | - Ronan R McCarthy
- Department of Life Sciences, Brunel University London, London, United Kingdom
| | - Diego Gonzalez
- Department of Biology, University of Neuchatel, Neuchatel, Switzerland
| | - Despoina Ai Mavridou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, United States
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Humphrey M, Larrouy-Maumus GJ, Furniss RCD, Mavridou DAI, Sabnis A, Edwards AM. Colistin resistance in Escherichia coli confers protection of the cytoplasmic but not outer membrane from the polymyxin antibiotic. MICROBIOLOGY-SGM 2021; 167. [PMID: 34723787 PMCID: PMC8743629 DOI: 10.1099/mic.0.001104] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Colistin is a polymyxin antibiotic of last resort for the treatment of infections caused by multi-drug-resistant Gram-negative bacteria. By targeting lipopolysaccharide (LPS), the antibiotic disrupts both the outer and cytoplasmic membranes, leading to bacterial death and lysis. Colistin resistance in Escherichia coli occurs via mutations in the chromosome or the acquisition of mobilized colistin-resistance (mcr) genes. Both these colistin-resistance mechanisms result in chemical modifications to the LPS, with positively charged moieties added at the cytoplasmic membrane before the LPS is transported to the outer membrane. We have previously shown that MCR-1-mediated LPS modification protects the cytoplasmic but not the outer membrane from damage caused by colistin, enabling bacterial survival. However, it remains unclear whether this observation extends to colistin resistance conferred by other mcr genes, or resistance due to chromosomal mutations. Using a panel of clinical E. coli that had acquired mcr −1, –1.5, −2, –3, −3.2 or −5, or had acquired polymyxin resistance independently of mcr genes, we found that almost all isolates were susceptible to colistin-mediated permeabilization of the outer, but not cytoplasmic, membrane. Furthermore, we showed that permeabilization of the outer membrane of colistin-resistant isolates by the polymyxin is in turn sufficient to sensitize bacteria to the antibiotic rifampicin, which normally cannot cross the LPS monolayer. These findings demonstrate that colistin resistance in these E. coli isolates is due to protection of the cytoplasmic but not outer membrane from colistin-mediated damage, regardless of the mechanism of resistance.
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Affiliation(s)
- Madeleine Humphrey
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.,Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Gerald J Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - R Christopher D Furniss
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91 Stockholm, Sweden
| | - Despoina A I Mavridou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, 78712, Texas, USA
| | - Akshay Sabnis
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Andrew M Edwards
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
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Detection of Multidrug-Resistant Enterobacterales-From ESBLs to Carbapenemases. Antibiotics (Basel) 2021; 10:antibiotics10091140. [PMID: 34572722 PMCID: PMC8465816 DOI: 10.3390/antibiotics10091140] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/03/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022] Open
Abstract
Multidrug-resistant Enterobacterales (MDRE) are an emerging threat to global health, leading to rising health care costs, morbidity and mortality. Multidrug-resistance is commonly caused by different β-lactamases (e.g., ESBLs and carbapenemases), sometimes in combination with other resistance mechanisms (e.g., porin loss, efflux). The continuous spread of MDRE among patients in hospital settings and the healthy population require adjustments in healthcare management and routine diagnostics. Rapid and reliable detection of MDRE infections as well as gastrointestinal colonization is key to guide therapy and infection control measures. However, proper implementation of these strategies requires diagnostic methods with short time-to-result, high sensitivity and specificity. Therefore, research on new techniques and improvement of already established protocols is inevitable. In this review, current methods for detection of MDRE are summarized with focus on culture based and molecular techniques, which are useful for the clinical microbiology laboratory.
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Hovan MR, Narayanan N, Cedarbaum V, Bhowmick T, Kirn TJ. Comparing mortality in patients with carbapenemase-producing carbapenem resistant Enterobacterales and non-carbapenemase-producing carbapenem resistant Enterobacterales bacteremia. Diagn Microbiol Infect Dis 2021; 101:115505. [PMID: 34399381 DOI: 10.1016/j.diagmicrobio.2021.115505] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/08/2021] [Accepted: 07/18/2021] [Indexed: 12/30/2022]
Abstract
Carbapenem-resistant Enterobacterales (CRE) are classified as either carbapenemase-producing CRE (CP-CRE) or non-carbapenemase-producing CRE (non-CP-CRE) based on their mechanism of carbapenem resistance. Few studies have compared outcomes associated with each type of infection. We attempted to determine if either CRE subset is associated with increased mortality. We performed a retrospective observational study to collect demographic, clinical and outcomes data to compare patients with CP-CRE and non-CP-CRE bacteremia. Of 146 cases analyzed, 88/146 (60%) were CP-CRE and 58/146 (40%) were non-CP-CRE. Patients with CP-CRE bacteremia were less likely to receive active empiric or targeted antibiotic therapy. Non-CP-CRE bacteremia was associated with a 2.4 times higher hazard of death at 30 days after bacteremia onset compared to CP-CRE (HR, 2.4; 95% CI, 1.2, 4.6). Patients with non-CP-CRE bacteremia had a higher hazard of death at 30 days after bacteremia onset compared to those with CP-CRE bacteremia.
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Affiliation(s)
- Michael R Hovan
- Department of Medicine, New-York Presbyterian/Weill Cornell Medicine, Weill Department of Medicine, New York, NY, USA.
| | - Navaneeth Narayanan
- Department of Medicine, Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, Medical Education Building, NJ, USA; Rutgers University Ernest Mario School of Pharmacy, NJ, USA
| | - Vanessa Cedarbaum
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Medical Education Building, New Brunswick, NJ, USA; Department of Medicine, Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, Medical Education Building, NJ, USA
| | - Tanaya Bhowmick
- Department of Medicine, Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, Medical Education Building, NJ, USA
| | - Thomas J Kirn
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Medical Education Building, New Brunswick, NJ, USA; Department of Medicine, Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, Medical Education Building, NJ, USA.
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Mukherjee S, Mitra S, Dutta S, Basu S. Neonatal Sepsis: The Impact of Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae. Front Med (Lausanne) 2021; 8:634349. [PMID: 34179032 PMCID: PMC8225938 DOI: 10.3389/fmed.2021.634349] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/26/2021] [Indexed: 01/12/2023] Open
Abstract
The convergence of a vulnerable population and a notorious pathogen is devastating, as seen in the case of sepsis occurring during the first 28 days of life (neonatal period). Sepsis leads to mortality, particularly in low-income countries (LICs) and lower-middle-income countries (LMICs). Klebsiella pneumoniae, an opportunistic pathogen is a leading cause of neonatal sepsis. The success of K. pneumoniae as a pathogen can be attributed to its multidrug-resistance and hypervirulent-pathotype. Though the WHO still recommends ampicillin and gentamicin for the treatment of neonatal sepsis, K. pneumoniae is rapidly becoming untreatable in this susceptible population. With escalating rates of cephalosporin use in health-care settings, the increasing dependency on carbapenems, a "last resort antibiotic," has led to the emergence of carbapenem-resistant K. pneumoniae (CRKP). CRKP is reported from around the world causing outbreaks of neonatal infections. Carbapenem resistance in CRKP is largely mediated by highly transmissible plasmid-encoded carbapenemase enzymes, including KPC, NDM, and OXA-48-like enzymes. Further, the emergence of a more invasive and highly pathogenic hypervirulent K. pneumoniae (hvKP) pathotype in the clinical context poses an additional challenge to the clinicians. The deadly package of resistance and virulence has already limited therapeutic options in neonates with a compromised defense system. Although there are reports of CRKP infections, a review on neonatal sepsis due to CRKP/ hvKP is scarce. Here, we discuss the current understanding of neonatal sepsis with a focus on the global impact of the CRKP, provide a perspective regarding the possible acquisition and transmission of the CRKP and/or hvKP in neonates, and present strategies to effectively identify and combat these organisms.
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Affiliation(s)
- Subhankar Mukherjee
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shravani Mitra
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Sulagna Basu
- Division of Bacteriology, Indian Council of Medical Research (ICMR)-National Institute of Cholera and Enteric Diseases, Kolkata, India
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11
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The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update. Infect Dis Clin North Am 2020; 34:659-676. [PMID: 33011047 DOI: 10.1016/j.idc.2020.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.
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12
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Mancini S, Bodendoerfer E, Kolensnik-Goldmann N, Herren S, Röthlin K, Courvalin P, Böttger EC. Evaluation of standardized automated rapid antimicrobial susceptibility testing of Enterobacterales-containing blood cultures: a proof-of-principle study. J Antimicrob Chemother 2020; 75:3218-3229. [DOI: 10.1093/jac/dkaa336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/01/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Rapid antimicrobial susceptibility testing (RAST) of bacteria causing bloodstream infections is critical for implementation of appropriate antibiotic regimens.
Objectives
We have established a procedure to prepare standardized bacterial inocula for Enterobacterales-containing clinical blood cultures and assessed antimicrobial susceptibility testing (AST) data generated with the WASPLabTM automated reading system.
Methods
A total of 258 blood cultures containing Enterobacterales were examined. Bacteria were enumerated by flow cytometry using the UF-4000 system and adjusted to an inoculum of 106 cfu/mL. Disc diffusion plates were automatically streaked, incubated for 6, 8 and 18 h and imaged using the fully automated WASPLabTM system. Growth inhibition zones were compared with those obtained with inocula prepared from primary subcultures following the EUCAST standard method. Due to time-dependent variations of the inhibition zone diameters, early AST readings were interpreted using time-adjusted tentative breakpoints and areas of technical uncertainty.
Results and conclusions
Inhibition zones obtained after 18 h incubation using an inoculum of 106 cfu/mL prepared directly from blood cultures were highly concordant with those of the EUCAST standard method based on primary subcultures, with categorical agreement (CA) of 95.8%. After 6 and 8 h incubation, 89.5% and 93.0% of the isolates produced interpretable results, respectively, with CA of >98.5% and very low numbers of clinical categorization errors for both the 6 h and 8 h readings. Overall, with the standardized and automated RAST method, consistent AST data from blood cultures containing Enterobacterales can be generated after 6–8 h of incubation and subsequently confirmed by standard reading of the same plate after 18 h.
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Affiliation(s)
- Stefano Mancini
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Elias Bodendoerfer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Sebastian Herren
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | - Kim Röthlin
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
| | | | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Schweiz
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13
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Lucena Baeza L, Hamprecht A. A profile of the GenePOC Carba C assay for the detection and differentiation of gene sequences associated with carbapenem-non-susceptibility. Expert Rev Mol Diagn 2020; 20:757-769. [PMID: 32567412 DOI: 10.1080/14737159.2020.1785287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The novel GenePOC/Revogene Carba C assay (GenePOC, Québec, Canada; now Meridian Bioscience, Cincinnati, OH, USA) is a CE-IVD marked, FDA-approved qualitative in vitro diagnostic test for the detection of genes associated with carbapenem-non-susceptibility. Colonies of Enterobacterales can be directly tested without prior DNA isolation. The test consists of a fluorescent-based real-time PCR assay that runs on the centripetal microfluidic revogene platform, providing results within 70 minutes. The assay was evaluated in two studies comprising a total of 294 molecularly characterized clinical Enterobacterales isolates. The overall sensitivity for the detection of carbapenemase gene sequences with the GenePOC assay was 100% (95% CI, 98.4% to 100). Besides the common KPC, VIM, NDM and OXA-48-like carbapenemase genes, also the very variable IMP variants were all detected. The specificity of the assay was 100% (95% CI, 98.8% to 100%). In this article the performance of the GenePOC/Revogene Carba C assay is evaluated and other currently available methods for the detection of carbapenemases are reviewed.
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Affiliation(s)
- Luis Lucena Baeza
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne , Cologne, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne , Cologne, Germany.,University of Cologne , Cologne, Germany.,German Centre for Infection Research , Partner Site Bonn-Cologne, Cologne, Germany.,University of Oldenburg , Institute for Medical Microbiology and Virology, Oldenburg, Germany
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14
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Park M, Park YJ, Yu J, Lee J, Ahn DR, Min SJ. Performance of a novel fluorogenic probe assay for the detection of extended-spectrum-β-lactamase or plasmid AmpC β-lactamase-producing Enterobacterales directly from simulated blood culture bottles. J Microbiol Methods 2020; 175:105988. [PMID: 32598975 DOI: 10.1016/j.mimet.2020.105988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 05/29/2020] [Accepted: 06/18/2020] [Indexed: 10/24/2022]
Abstract
Resistance to third generation cephalosporins is widely disseminated in Enterobacteriaceae mainly because of extended-spectrum-β-lactamases (ESBL), plasmid AmpC β-lactamases (PABL), and hyper-production of chromosomal AmpC β-lactamases. Here, we evaluated the performance of rapid test using novel fluorogenic probe assay in simulated blood cultures and compared the results with the phenol red assay using a total of 172 characterized isolates (39 ESBL producers, 13 PABL producers, and 120 susceptible isolates). We prepared a pellet by centrifugation and washing, which can also be used for identification with MALDI-TOF directly from positive blood cultures. After that, we mixed the pellet with fluorogenic probe and measured the fluorescent signal using fluorometer. The fluorogenic probe assay showed higher sensitivity than the phenol red assay (96.2% vs. 71.2%, p < .0001) in 172 simulated blood culture bottles especially in detecting PABL (84.6% vs. 0%, p = .0026) and the turnaround time was 1.5 h. This fluorogenic probe assay, combined with the direct identification of pathogens, could be very useful for rapid identification of isolates and detecting cephalosporin resistance caused by ESBL and PABL directly from positive blood cultures.
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Affiliation(s)
- MiJung Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Laboratory Medicine, Green Cross Laboratories, Yongin, Republic of Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Jinkyung Yu
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Department of Infectious Disease Team, Seoul Metropolitan Government Research Institute of Public Health and Environment, Gwacheon, Republic of Korea
| | - Jieun Lee
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dae-Ro Ahn
- Department of Biological Chemistry, KIST campus, University of Science and Technology (UST), Seoul, Republic of Korea
| | - Sun-Joon Min
- Department of Chemical & Molecular Engineering / Applied Chemistry, Hanyang University, Ansan, Gyeonggi-do, Republic of Korea
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15
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Accuracy and applicability of different phenotypic methods for carbapenemase detection in Enterobacteriaceae: A systematic review and meta-analysis. J Glob Antimicrob Resist 2020; 21:138-147. [DOI: 10.1016/j.jgar.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 11/23/2022] Open
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16
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Swathi C, Sudhaharan S, Lakshmi V, Suguna Ratnakar K, Sritharan V. Direct Detection and Discrimination of Carbapenemases of Acinetobacter baumannii from Uncultured Tracheal Aspirates. Microb Drug Resist 2020; 26:1153-1162. [PMID: 32364821 DOI: 10.1089/mdr.2019.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carbapenemases play important roles in conferring resistance to beta-lactam antibiotics, including the carbapenems. Detection of carbapenemase activity helps to understand the possible mechanism(s) of carbapenem resistance. Identification of carbapenemases is currently being done by various phenotypic methods and molecular methods. However, innovative biochemical and spectrophotometric methods are desirable as they will be easy to perform, affordable, and rapid. A novel chromogenic method called Carba NP test was introduced recently to screen for carbapenemases in clinical isolates of gram-negative pathogens. We adopted this assay (1) to detect the total carbapenemase activity, (2) to discriminate Class A, B, and D carbapenemases with inhibitors, (3) to compare with carbapenemase genotype, and (4) for direct differential diagnosis of carbapenemases in uncultured clinical sample such as tracheal aspirate. The study included 132 purulent tracheal aspirates. All samples were processed and screened by a protocol optimized in our laboratory, which showed good sensitivity and correlation with genotyping and conventional phenotyping. Our protocol not only offers the fastest way to identify the pathogen but also its carbapenemase profile, directly from uncultured clinical samples in less than 4 hr. Our protocol is currently being validated on other types of clinical specimens in our laboratory.
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Affiliation(s)
- Cheguri Swathi
- Department of Molecular Diagnostics & Biomarkers, Global Medical Education and Research Foundation (GMERF), Hyderabad, India
| | - Sukanya Sudhaharan
- Department of Microbiology, Nizam's Institute of Medical Sciences (NIMS), Hyderabad, India
| | - Vemu Lakshmi
- Department of Microbiology, Nizam's Institute of Medical Sciences (NIMS), Hyderabad, India
| | - Kamaraju Suguna Ratnakar
- Department of Molecular Diagnostics & Biomarkers, Global Medical Education and Research Foundation (GMERF), Hyderabad, India
| | - Venkataraman Sritharan
- Department of Molecular Diagnostics & Biomarkers, Global Medical Education and Research Foundation (GMERF), Hyderabad, India
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17
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Saliba R, Aho-Glélé LS, Karam-Sarkis D, Zahar JR. Evaluation of polymerase chain reaction assays for direct screening of carbapenemase-producing Enterobacteriaceae from rectal swabs: a diagnostic meta-analysis. J Hosp Infect 2020; 104:381-389. [DOI: 10.1016/j.jhin.2019.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 01/08/2023]
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18
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Blood-Modified Carbapenem Inactivation Method: a Phenotypic Method for Detecting Carbapenemase-Producing Enterobacteriaceae Directly from Positive Blood Culture Broths. J Clin Microbiol 2020; 58:JCM.01377-19. [PMID: 31748319 DOI: 10.1128/jcm.01377-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/11/2019] [Indexed: 11/20/2022] Open
Abstract
A variant of the modified carbapenem inactivation method (mCIM) was developed to detect carbapenemase activity directly from positive blood culture broths. The method, termed "Blood-mCIM," was evaluated using Bactec blood culture bottles (Becton, Dickinson and Company, Franklin Lakes, NJ) inoculated with 27 different carbapenemase-producing Enterobacteriaceae (CPE) isolates and 34 different non-CPE isolates. The assay was positive for all blood culture broths inoculated with CPE isolates and negative for all blood culture broths inoculated with non-CPE isolates, corresponding to a diagnostic sensitivity and specificity of 100%, respectively. This assay is inexpensive using "off the shelf" reagents, does not require centrifugation or mechanical lysis, and can be readily implemented in any clinical microbiology laboratory. The Blood-mCIM should facilitate expedient administration of antimicrobial therapy targeted toward CPE bloodstream infections and assist infection control and public health surveillance.
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19
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Performance of a Novel Fluorogenic Assay for Detection of Carbapenemase-Producing Enterobacteriaceae from Bacterial Colonies and Directly from Positive Blood Cultures. J Clin Microbiol 2019; 58:JCM.01026-19. [PMID: 31666362 DOI: 10.1128/jcm.01026-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Rapid and accurate detection of carbapenemase-producing Enterobacteriaceae (CPE) is critical for appropriate treatment and infection control. We compared a rapid fluorogenic assay using a carbapenem-based fluorogenic probe with other phenotypic assays: modified carbapenem inactivation method (mCIM), Carba NP test (CNP), and carbapenemase inhibition test (CIT). A total of 217 characterized isolates of Enterobacteriaceae were included as follows: 63 CPE; 48 non-carbapenemase-producing carbapenem-resistant Enterobacteriaceae (non-CP-CRE); 53 extended-spectrum β-lactamase producers; and 53 third-generation-cephalosporin-susceptible isolates. The fluorogenic assay using bacterial colonies (Fluore-C) was conducted by lysing the isolates followed by centrifugation and mixing the supernatant with fluorogenic probe. In addition, for the fluorogenic assay using spiked blood culture bottles (Fluore-Direct), pellets were obtained via the saponin preparation method, which can directly identify the pathogens using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The fluorescence signal was measured over 50 min using a fluorometer. The fluorescent signal of CPE was significantly higher than that of non-CPE in both Fluore-C (median relative fluorescence units [RFU] [range], 5,814 [240 to 32,009] versus 804 [36 to 2,480], respectively; P < 0.0001) and Fluore-Direct (median RFU [range], 10,355 [1,689 to 31,463] versus 1,068 [428 to 2,155], respectively; P < 0.0001) tests. Overall, positive and negative percent agreements of Fluore-C, mCIM, CNP, CIT, and Fluore-Direct were 100% and 98.7%, 98.3% and 97.5%, 88.1% and 100%, 96.4% and 98.7%, and 98.3% and 98.1%, respectively. The relatively lower positive percent agreement (PPA) of CNP was mainly observed in OXA-type CPE. The fluorogenic assay showed excellent performance with bacterial colonies and also directly from positive blood cultures. We included many non-CP-CRE isolates for strict evaluation. The fluorogenic assay will be a useful tool for clinical microbiology laboratories.
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20
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Bianco G, Boattini M, Iannaccone M, Fossati L, Cavallo R, Costa C. Direct β-Lactam Inactivation Method: a New Low-Cost Assay for Rapid Detection of Carbapenemase- or Extended-Spectrum-β-Lactamase-Producing Enterobacterales Directly from Positive Blood Culture Bottles. J Clin Microbiol 2019; 58:e01178-19. [PMID: 31694972 PMCID: PMC6935928 DOI: 10.1128/jcm.01178-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/31/2019] [Indexed: 01/05/2023] Open
Abstract
We validate and evaluate a new phenotypic assay, named the direct β-lactam inactivation method (dBLIM), for the rapid and simultaneous detection of carbapenemase or extended-spectrum-cephalosporinase activity directly from Enterobacterales (EB)-positive blood cultures (BCs). It originates from the carbapenem inactivation method (CIM), an inexpensive and highly sensitive assay for carbapenemase activity detection. dBLIM cutoff values to detect extended-spectrum β-lactamase (ESBL) and carbapenemase activities resulted in diameters of ≤12 mm for a 5-μg-cefotaxime disk and for a 10-μg-meropenem disk. dBLIM assessment was determined with both aerobic and anaerobic BC bottles spiked with 422 characterized EB strains, classifiable into the following 4 phenotypic groups: (i) ESBL/AmpC-type β-lactamase (ACBL)/carbapenemase (CARB)-nonproducing (np-ESBL/ACBL/CARB) EB (n = 116), (ii) ESBL-producing EB (n = 111), (iii) AmpC-β-lactamase-producing EB (n = 33), and (iv) carbapenemase-producing EB (n = 162). No false-positive results were obtained in any of the np-ESBL/ACBL/CARB EB, ESBL, and AmpC groups, demonstrating an overall assay specificity of 100%. There were no significant discrepancies in dBLIM performance between aerobic and anaerobic BCs across all groups, except with VIM-type carbapenemase-expressing EB. Interestingly, among BCs spiked with blaVIM-harboring EB, the sensitivity rates of the assay in anaerobic and aerobic bottles were 53.6% and 100%, respectively. In contrast, dBLIM performance was deemed excellent for the KPC, OXA-48, and NDM carbapenemase producers regardless of the type of bottle being tested, with a sensitivity rate ranging between 99% and 100%. Concerning the detection of the extended-spectrum cephalosporinases of the ESBL-producing and AmpC types, dBLIM sensitivities was 100% and 84 to 87%, respectively. dBLIM may be a cost-effective and highly robust phenotypic screening method for the reliable detection of carbapenemases or extended-spectrum cephalosporinases directly from BCs on the same day of bottle positivity detection.
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Affiliation(s)
- Gabriele Bianco
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Matteo Boattini
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Marco Iannaccone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Lucina Fossati
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
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21
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Systematic Comparison of Four Methods for Detection of Carbapenemase-Producing Enterobacterales Directly from Blood Cultures. J Clin Microbiol 2019; 57:JCM.00709-19. [PMID: 31413083 PMCID: PMC6813004 DOI: 10.1128/jcm.00709-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/07/2019] [Indexed: 01/30/2023] Open
Abstract
Early identification of infections caused by carbapenemase-producing Enterobacterales (CPE) can help to optimize patient treatment and improve outcome. In this study, protocols for rapid detection of carbapenemase production directly from positive blood cultures were developed applying a concentration and hemolysis step before a test for carbapenemase production was performed. Early identification of infections caused by carbapenemase-producing Enterobacterales (CPE) can help to optimize patient treatment and improve outcome. In this study, protocols for rapid detection of carbapenemase production directly from positive blood cultures were developed applying a concentration and hemolysis step before a test for carbapenemase production was performed. Four different methods (three modified colorimetric assays [β-Carba, bcCarba NP, and NeoRapid Carb] and a variation of the carbapenem inactivation method [CIM] test with blood cultures [bcCIM]) were assessed on blood cultures spiked with 185 different molecularly characterized Enterobacterales isolates. The challenge collection included 81 carbapenemase-negative isolates and 104 CPEs (OXA-48 [n = 25], NDM [n = 20], KPC [n = 18], VIM [n = 25], GIM [n = 5], OXA-48-like [n = 9], and OXA-48-like plus NDM [n = 2]). The sensitivity/specificity was 99.0%/95.1% for bcCarba NP, 99.0%/91.4% for NeoRapid Carb, 100%/95.1% for β-Carba and 100%/100% for bcCIM. Weakly hydrolyzing carbapenemases (e.g., OXA-48-like) were also well detected by the assays. The time to result was 20 to 45 min for β-Carba, 2 to 3 h for bcCarba NP, 2.5 to 2 h for NeoRapid Carb, and 18 to 24 h for bcCIM. In conclusion, all assays demonstrated good detection of CPE. The protocols can be easily implemented in any clinical microbiology laboratory and could help to optimize therapy early in bloodstream infections by CPE.
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22
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Cointe A, Walewski V, Hobson CA, Doit C, Bidet P, Dortet L, Bonacorsi S, Birgy A. Rapid Carbapenemase Detection With Xpert Carba-R V2 Directly On Positive Blood Vials. Infect Drug Resist 2019; 12:3311-3316. [PMID: 31695450 PMCID: PMC6815938 DOI: 10.2147/idr.s204436] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/05/2019] [Indexed: 12/03/2022] Open
Abstract
The rapid detection of carbapenemase allows implementation of infection control measures and adaptation of antibiotic therapy. We evaluated the performances of the Xpert Carba-R V2® assay for the direct detection and identification of carbapenemase on positive blood cultures. We focused our evaluation on its detection capacity and on the risks of interference due to the patient’s blood. Isolates of several variants of OXA-48-like (n=10), KPC (n=10), NDM (n=11), VIM (n=7), IMP-1 (n=1) carbapenemases and 14 non carbapenemase-producing Enterobacteriaceae were tested. For each isolate (n=53), an aerobic vial was seeded, and incubated in Bactec Fx (Becton Dickinson®) automate. When positive, the Xpert® Carba-R-V2 assay was assessed for carbapenemase detection using 40 µl aliquot. Reproducibility tests were performed on a subset of 23 isolates using aerobic and anaerobic vials. Longer incubation time was also evaluated on 6 isolates. A complementary prospective study in real-time testing of patient-derived clinical samples on 20 additional positive blood vials with Gram negative bacilli on direct examination was performed. Perfect sensitivity and specificity (100%) were observed regardless of the carbapenemase type, the blood vials used and the time of incubation. Xpert® Carba-R-V2 assay is suitable for the rapid detection of the main carbapenemase genes directly on positive blood vials. Its performances and rapid time analysis allow its use in routine to guide therapeutic choices and to implement infection control measures.
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Affiliation(s)
- Aurélie Cointe
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France.,Service de Microbiologie, Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Violaine Walewski
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France.,Service de Microbiologie, Hôpitaux Universitaires de Paris Seine Denis (HUPSSD), site Avicenne, AP-HP, Bobigny, France
| | - Claire Amaris Hobson
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Catherine Doit
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France.,Service de Microbiologie, Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Philippe Bidet
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France.,Service de Microbiologie, Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - Laurent Dortet
- EA7361, Université Paris-Sud, Université Paris-Saclay, LabEx Lermit, Service de Bactériologie-Hygiène, Hôpital Bicêtre, AP-HP, Le Kremlin-Bicêtre, France.,Centre National de Référence associé de la résistance aux antibiotiques: Entérobactéries productrices de carbapénémases, Le Kremlin-Bicêtre, France.,Evolution et Ecologie de la résistance aux antibiotiques, Institut Pasteur - APHP -Université Paris Sud, Paris, France
| | - Stéphane Bonacorsi
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France.,Service de Microbiologie, Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
| | - André Birgy
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Service de Microbiologie, Hôpital Robert-Debré, AP-HP, Paris, France.,Service de Microbiologie, Centre National de Référence associé Escherichia coli, Hôpital Robert-Debré, AP-HP, Paris, France
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Alvim ALS, Couto BRGM, Gazzinelli A. Epidemiological profile of healthcare-associated infections caused by Carbapenemase-producing Enterobacteriaceae. Rev Esc Enferm USP 2019; 53:e03474. [PMID: 31291394 DOI: 10.1590/s1980-220x2018001903474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 12/06/2018] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To study the epidemiological profile of Healthcare-associated Infections caused by Enterobacteria which carry the Klebsiella pneumoniae Carbapenemase gene (blaKPC) in the hospital environment. METHOD A descriptive study was conducted in a private hospital in Belo Horizonte, MG, Brazil, which included all patients with infections caused by Enterobacteriaceae which carry the Klebsiella pneumoniae Carbapenemase gene. The data were collected by the Automated System of Hospital Infection Control and analyzed by descriptive statistics by the Epi Info 7 program. RESULTS Eighty-two (82) patients participated in the study. Klebsiella pneumoniae was the most frequent species (68%) isolated in blood (30%), bronchoalveolar lavage (22%) and urine (18%), while catheter-associated bloodstream infection (30%) predominated regarding topography. A case fatality rate of 62% is highlighted in evaluating the outcome. CONCLUSION The resistance genes spread rapidly, limiting the antimicrobial options for treating infectious diseases. The epidemiological profile of Healthcare-Associated Infections found in this study can be prevented by prevention and infection control programs.
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Affiliation(s)
- André Luiz Silva Alvim
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Enfermagem, Belo Horizonte, MG, Brazil
| | | | - Andrea Gazzinelli
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Enfermagem, Belo Horizonte, MG, Brazil
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Anantharajah A, Tossens B, Olive N, Kabamba-Mukadi B, Rodriguez-Villalobos H, Verroken A. Performance Evaluation of the MBT STAR ®-Carba IVD Assay for the Detection of Carbapenemases With MALDI-TOF MS. Front Microbiol 2019; 10:1413. [PMID: 31281303 PMCID: PMC6596351 DOI: 10.3389/fmicb.2019.01413] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/05/2019] [Indexed: 11/13/2022] Open
Abstract
Objectives: The increasing rate of carbapenem resistance in Gram-negative bacteria is a major public health problem and rapid detection is essential for infection management. We evaluated the performances of the MBT STAR®-Carba IVD assay (Bruker Daltonics) to detect carbapenemase-producing organisms (CPO) from bacterial colonies and directly from positive blood culture bottles with MALDI-TOF MS. Methods: We analyzed 130 strains with a reduced susceptibility to at least one carbapenem including 109 CPO (6 KPC, 27 NDM, 21 VIM, 1 IMP, 41 OXA-48-like, 8 OXA-23, 2 OXA-24/-40, and 2 OXA-58) and 21 non-CPO. The assay on colonies was performed with all 130 strains while the assay on spiked blood cultures was performed with 45 strains. Samples were prepared with the MBT STAR®-CARBA IVD kit and imipenem hydrolysis by the potential carbapenemase was analyzed with the MBT STAR®-BL module (Bruker Daltonics) on MALDI-TOF MS. Results: Performed on colonies, the assay detected all carbapenemase-producing Enterobacteriaceae (n = 78), Pseudomonas spp. (n = 19) and Acinetobacter spp. (n = 12). All 21 tested non-CPO remained negative resulting in sensitivity and specificity of 100%. Performed on positive blood cultures, the assay detected all carbapenemase-producing Enterobacteriaceae (n = 23) and Pseudomonas spp. (n = 4) but missed 9/12 carbapenemase-producing Acinetobacter spp. However, a prolonged imipenem-incubation time of the strain pellet improved carbapenemase detection. Non-CPO from positive blood culture bottles remained negative (n = 5) with the assay with the exception of one Klebsiella pneumoniae isolate. Conclusion: The MBT STAR®-Carba IVD assay is a highly reliable method for the detection of carbapenemase activity in Gram-negative bacteria. However, time-consuming sample preparation steps and reagent costs need to be considered before implementation in a routine clinical microbiology laboratory.
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Affiliation(s)
- Ahalieyah Anantharajah
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Bastien Tossens
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Nathalie Olive
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Benoit Kabamba-Mukadi
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Hector Rodriguez-Villalobos
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Alexia Verroken
- Department of Microbiology, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
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Ombelet S, Barbé B, Affolabi D, Ronat JB, Lompo P, Lunguya O, Jacobs J, Hardy L. Best Practices of Blood Cultures in Low- and Middle-Income Countries. Front Med (Lausanne) 2019; 6:131. [PMID: 31275940 PMCID: PMC6591475 DOI: 10.3389/fmed.2019.00131] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/29/2019] [Indexed: 12/25/2022] Open
Abstract
Bloodstream infections (BSI) have a substantial impact on morbidity and mortality worldwide. Despite scarcity of data from many low- and middle-income countries (LMICs), there is increasing awareness of the importance of BSI in these countries. For example, it is estimated that the global mortality of non-typhoidal Salmonella bloodstream infection in children under 5 already exceeds that of malaria. Reliable and accurate diagnosis of these infections is therefore of utmost importance. Blood cultures are the reference method for diagnosis of BSI. LMICs face many challenges when implementing blood cultures, due to financial, logistical, and infrastructure-related constraints. This review aims to provide an overview of the state-of-the-art of sampling and processing of blood cultures, with emphasis on its use in LMICs. Laboratory processing of blood cultures is relatively straightforward and can be done without the need for expensive and complicated equipment. Automates for incubation and growth monitoring have become the standard in high-income countries (HICs), but they are still too expensive and not sufficiently robust for imminent implementation in most LMICs. Therefore, this review focuses on "manual" methods of blood culture, not involving automated equipment. In manual blood cultures, a bottle consisting of a broth medium supporting bacterial growth is incubated in a normal incubator and inspected daily for signs of growth. The collection of blood for blood culture is a crucial step in the process, as the sensitivity of blood cultures depends on the volume sampled; furthermore, contamination of the blood culture (accidental inoculation of environmental and skin bacteria) can be avoided by appropriate antisepsis. In this review, we give recommendations regarding appropriate blood culture sampling and processing in LMICs. We present feasible methods to detect and speed up growth and discuss some challenges in implementing blood cultures in LMICs, such as the biosafety aspects, supply chain and waste management.
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Affiliation(s)
- Sien Ombelet
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KULeuven, Leuven, Belgium
| | - Barbara Barbé
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dissou Affolabi
- Centre National Hospitalier Universitaire—Hubert Koutoucou Maga, Cotonou, Benin
| | | | - Palpouguini Lompo
- Clinical Research Unit of Nanoro, Institut de Recherche en Science de la Santé, Nanoro, Burkina Faso
| | - Octavie Lunguya
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
- Department of Medical Biology, Cliniques Universitaires, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KULeuven, Leuven, Belgium
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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NG-Test Carba 5 for Rapid Detection of Carbapenemase-Producing Enterobacterales from Positive Blood Cultures. Antimicrob Agents Chemother 2019; 63:AAC.00011-19. [PMID: 30803973 DOI: 10.1128/aac.00011-19] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/17/2019] [Indexed: 12/30/2022] Open
Abstract
The immunochromatographic assay, NG-test Carba 5 (NG Biotech), has been evaluated for detection of carbapenemase-producing Enterobacterales (CPE) from spiked blood cultures (n = 205). It detected and discriminated in less than 30 minutes KPC, IMP, VIM, NDM, and OXA-48-like producers with a sensitivity and specificity of 97.7% and 96.1%, respectively. Thus, it might help the rapid optimization of treatment of bloodstream infections due to CPE.
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Bhaskar BH, Mulki SS, Joshi S, Adhikary R, Venkatesh BM. Molecular Characterization of Extended Spectrum β-lactamase and Carbapenemase Producing Klebsiella pneumoniae from a Tertiary Care Hospital. Indian J Crit Care Med 2019; 23:61-66. [PMID: 31086448 PMCID: PMC6487608 DOI: 10.5005/jp-journals-10071-23118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Objective The extended-spectrum beta-lactamase (ESBL) and carbapenemase producing gram-negative bacteria among the members of Enterobacteriaceae are of major health concern globally. The present study was carried out to determine proportion and genetic characterization of ESBL and carbapenemase producing Klebsiella pneumoniae strains isolated from intensive care units of a tertiary care hospital. Materials and methods A total of 250 non-duplicate K. pneumoniae isolates were recovered from various clinical specimens from our intensive care units from May 2014 to May 2015. Antibiotic susceptibility testing was performed as recommended by Clinical and Laboratory Standard Institute. Phenotypic identification of ESBL and carbapenemase producing isolates were confirmed by the double-disk synergy test, modified Hodge test, imipenem and imipenem-EDTA combined test, respectively. Molecular characterization of β-lactamase genes were performed by polymerase chain reaction. Results Out of 250 Klebsiella pneumonaie, 84% isolates were ESBL producers, 66% were carbapenem resistant based on their reduced susceptibility to imipenem, meropenem and ertapenem. Among these 165 carbapenem resistant isolates, 9.7% were positive for blaNDM-1 and these isolates were also found to be positive for one or more bla genes. Co-carriage of AmpC in ESBL and carbapenem resistant isolates were 7.8% and 3.6%, respectively and were negative for blaKPC genes. Conclusion The study indicated the prevalence of ESBLs and blaNDM-1, with additional bla genes and AmpC among the K. pneumoniae isolates in our intensive care units. NDM-1 producing Enterobacteriaceae is a growing health care problem. Detection of the prevalence of antibacterial resistance pattern helps towards improved antibiotic policy and empirical antibiotic treatment. How to cite this article Beena HB, Shenoy SM, et al. Molecular Characterization of Extended Spectrum β-lactamase and Carbapenemase Producing Klebsiella pneumoniae from a Tertiary Care Hospital. Indian J of Crit Care Med 2019;23(2):61-66.
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Affiliation(s)
| | - Shalini Shenoy Mulki
- Department of Microbiology, Kasturba Medical College, Mangaluru, Karnataka, India
| | - Sangeetha Joshi
- Department of Microbiology, Manipal Hospital, Bengaluru, Karnataka, India
| | - Ranjeeta Adhikary
- Department of Microbiology, Manipal Hospital, Bengaluru, Karnataka, India
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Seco BMS, Campos JC, da Costa Rocha DA, de Lima AV, de Oliveira FF, Lemo MEB, Sampaio SCF, Sampaio JLM. Improved blood culture workflow for faster identification of KPC-producing Enterobacterales. Braz J Microbiol 2018; 50:127-132. [PMID: 30637648 DOI: 10.1007/s42770-018-0037-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/04/2018] [Indexed: 11/26/2022] Open
Abstract
Carba-NP original report for blood cultures described the need of subculture and mechanical lysis before testing, reaching the turnaround time of approximately 4 hours for sample preparation. We tested 100 consecutive blood cultures positive for Gram-negative bacilli on the Gram stain from a large clinical laboratory. Bacterial pellets were prepared by centrifugation and submitted to Carba-NP and Blue-Carba tests and used further to prepare smears for Vitek MS. Results obtained with colonies grown on sheep blood agar using the same methodologies were used as the gold standard. Carbapenemase genes were confirmed by PCR and DNA sequencing. Vitek MS identified correctly 86% of the samples. Of note, 7% of the samples were incorrectly reported by the instrument as containing a single isolate. KPC-2 was the predominant carbapenemase detected. There was 100% concordance for both negative and positive results for Carba-NP. In contrast, for Blue-Carba the concordance for positive results was 92.8%, and 41% of strains negative for carbapenemases presented a yellowish color on control well turning the test non-interpretable. The turnaround time for sample preparation for preparing the pellet was 13 min, and no subculture or mechanical lysis is needed when detecting KPC production in Enterobacterales.
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Affiliation(s)
- Bruna Mara Silva Seco
- School of Pharmacy, Clinical Microbiology and Antimicrobial Resistance Laboratory, University of São Paulo, Av. Professor Lineu Prestes, 580, São Paulo, SP, Zip code 05508-900, Brazil
- Fleury Medicine and Health, Microbiology Section, São Paulo, Brazil
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Arnimallee 22, 14195, Berlin, Germany
| | - Juliana Coutinho Campos
- School of Pharmacy, Clinical Microbiology and Antimicrobial Resistance Laboratory, University of São Paulo, Av. Professor Lineu Prestes, 580, São Paulo, SP, Zip code 05508-900, Brazil
| | - Darlan Augusto da Costa Rocha
- School of Pharmacy, Clinical Microbiology and Antimicrobial Resistance Laboratory, University of São Paulo, Av. Professor Lineu Prestes, 580, São Paulo, SP, Zip code 05508-900, Brazil
| | - Aline Valerio de Lima
- School of Pharmacy, Clinical Microbiology and Antimicrobial Resistance Laboratory, University of São Paulo, Av. Professor Lineu Prestes, 580, São Paulo, SP, Zip code 05508-900, Brazil
| | | | | | | | - Jorge Luiz Mello Sampaio
- School of Pharmacy, Clinical Microbiology and Antimicrobial Resistance Laboratory, University of São Paulo, Av. Professor Lineu Prestes, 580, São Paulo, SP, Zip code 05508-900, Brazil.
- Fleury Medicine and Health, Microbiology Section, São Paulo, Brazil.
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Bardet L, Rolain JM. Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2018; 2018:3095249. [PMID: 30631384 PMCID: PMC6305056 DOI: 10.1155/2018/3095249] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/11/2018] [Indexed: 12/27/2022]
Abstract
The recent discovery of the plasmid-mediated mcr-1 gene conferring resistance to colistin is of clinical concern. The worldwide screening of this resistance mechanism among samples of different origins has highlighted the urgent need to improve the detection of colistin-resistant isolates in clinical microbiology laboratories. Currently, phenotypic methods used to detect colistin resistance are not necessarily suitable as the main characteristic of the mcr genes is the low level of resistance that they confer, close to the clinical breakpoint recommended jointly by the CLSI and EUCAST expert systems (S ≤ 2 mg/L and R > 2 mg/L). In this context, susceptibility testing recommendations for polymyxins have evolved and are becoming difficult to implement in routine laboratory work. The large number of mechanisms and genes involved in colistin resistance limits the access to rapid detection by molecular biology. It is therefore necessary to implement well-defined protocols using specific tools to detect all colistin-resistant bacteria. This review aims to summarize the current clinical microbiology diagnosis techniques and their ability to detect all colistin resistance mechanisms and describe new tools specifically developed to assess plasmid-mediated colistin resistance. Phenotyping, susceptibility testing, and genotyping methods are presented, including an update on recent studies related to the development of specific techniques.
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Affiliation(s)
- Lucie Bardet
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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Tadros M, Goneau L, Romaschin A, Jarvis M, Matukas L. Rapid detection of resistance to carbapenems and cephalosporins in Enterobacteriaceae using liquid chromatography tandem mass spectrometry. PLoS One 2018; 13:e0206842. [PMID: 30412608 PMCID: PMC6226185 DOI: 10.1371/journal.pone.0206842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 10/19/2018] [Indexed: 12/20/2022] Open
Abstract
Carbapenemase producing Enterobacteriaceae (CPE) are becoming a global healthcare concern. Current laboratory methods for the detection of CPE include screening followed by confirmatory phenotypic and genotypic tests. These processes would generally take ≥72 hours, which could negatively impact patient care and Infection Control practices. To this end, we developed a protocol for rapid resistance testing (RRT) to detect hydrolysis in a panel of beta lactam antibiotics consisting of ampicillin, cefazolin, cefotaxime and imipenem, using liquid chromatography tandem mass spectrometry. Ninety—nine beta lactamase producing Enterobacteriaceae isolates were used to evaluate the RRT method, 54 isolates were CPE and 45 isolates were Class A or AmpC beta lactamase producing Enterobacteriaceae but not carbapenemase producers. We also tested 10 E.coli isolates that were susceptible to ampicillin, cefazolin, cefotaxime and imipenem. Receiver Operating Characteristic (ROC) Curves analysis showed that imipenem had a sensitivity and a specificity of 100% for crabapenemase detection at hydrolysis cut off values that are greater than 50% and less than or equal to 80%. The RRT protocol can be conducted in a time frame of less than 2 hours. This preliminary study shows that the rapid resistance testing protocol might have utility for the rapid detection of CPE. Additional work with a greater number and variety of beta- lactamase producing Enterobacteriaceae isolates is required to validate these preliminary findings.
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Affiliation(s)
- Manal Tadros
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Microbiology, St. Michael’s Hospital, Toronto, Ontario, Canada
- * E-mail:
| | - Lee Goneau
- Department of Microbiology, Public Health Ontario, Toronto, Ontario, Canada
| | | | | | - Larissa Matukas
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Microbiology, St. Michael’s Hospital, Toronto, Ontario, Canada
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Meier M, Hamprecht A. Rapid detection of carbapenemases directly from positive blood cultures by the β-CARBA test. Eur J Clin Microbiol Infect Dis 2018; 38:259-264. [PMID: 30411220 DOI: 10.1007/s10096-018-3422-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/05/2018] [Indexed: 11/25/2022]
Abstract
The rapid detection of blood stream infections (BSI) by carbapenemase-producing Enterobacterales (CPE) is indispensable to early optimize antibiotic treatment and to improve survival. While phenotypic tests are time-consuming and PCR is expensive and not available in many routine laboratories, colorimetric tests (e.g., Carba NP test) can provide rapid results at moderate cost. However, up to now, the detection of CPE-BSI requires a further 3-h incubation in broth supplemented with zinc sulfate and imipenem after a blood culture has become positive, thereby causing delay and additional hands-on time. The purpose of this study was to develop and evaluate a new method for the detection of CPE directly from positive blood culture without the need for incubation in broth, based on the commercially available colorimetric β-CARBA test. For the evaluation, blood cultures spiked with 140 different Enterobacterales isolates producing diverse beta-lactamases were tested with the new method. Of these, 70 were CPE (OXA-48-like, NDM, KPC, VIM, and GIM). After blood cultures turned positive, blood culture fluid was drawn, and erythrocytes were hemolyzed with SDS, washed, and equilibrated before the β-CARBA was performed on the bacterial pellet. All carbapenemases were reliably detected, including weak carbapenemases of the OXA-48 group. The sensitivity was 100% (95% CI 94.9-100) and the specificity 94.3% (95% CI 89.2-99.4). The time to result was 20 to 45 min. Carbapenemases can rapidly and reliably be detected directly from blood cultures using the new method, which could help to improve the outcome of these difficult-to-treat infections.
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Affiliation(s)
- Maria Meier
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Goldenfelsstrasse 19-21, 50935, Cologne, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Goldenfelsstrasse 19-21, 50935, Cologne, Germany.
- DZIF (German Centre for Infection Research), Partner Site Bonn-Cologne, Cologne, Germany.
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Hamprecht A, Vehreschild JJ, Seifert H, Saleh A. Rapid detection of NDM, KPC and OXA-48 carbapenemases directly from positive blood cultures using a new multiplex immunochromatographic assay. PLoS One 2018; 13:e0204157. [PMID: 30216371 PMCID: PMC6138386 DOI: 10.1371/journal.pone.0204157] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/04/2018] [Indexed: 11/18/2022] Open
Abstract
Bloodstream infections caused by carbapenemase-producing Enterobacteriaceae (CPE) are associated with treatment failure and increased mortality. Detection of CPE from blood cultures (BC) by standard methods takes 16–72 hours, which can delay the initiation of appropriate antimicrobial therapy and compromise patient outcome. In the present study, we developed and evaluated a new method for the rapid detection of carbapenemases directly from positive BC using a new multiplex immunochromatographic test (ICT). The new ICT was assessed using 170 molecularly characterized Enterobacteriaceae clinical isolates including 126 CPE (OXA-48-like (N = 79), KPC (N = 18) and NDM (N = 29)). After spiking with bacteria and incubation in a BC system, blood from positive BC bottles was hemolyzed, bacteria concentrated by centrifugation and lysed. The lysate was transferred to the RESIST-3 O.K.N. ICT (Coris BioConcept, Gembloux, Belgium), which detects OXA-48-like, KPC and NDM carbapenemases. The final results of the ICT were read when they became positive, at the latest after 15 min. All CPE isolates (126/126) were correctly detected with the new protocol (100% sensitivity, 100% specificity). There was perfect concordance between ICT results and molecular characterization. Total time to result was 20–45 min. Conclusions: This proof-of-principle study demonstrates that with the newly developed method, OXA-48-like, KPC and NDM carbapenemases can be reliably detected directly from positive BC bottles. The new method is more rapid than other currently available assays and can be performed in any routine microbiology laboratory. This can help to rapidly identify patients with CPE BSI and optimize the management of patients with these difficult-to-treat infections. Further studies are needed to assess the performance of the ICT in routine diagnostics.
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Affiliation(s)
- Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
- DZIF (German Centre for Infection Research), partner site Bonn-Cologne, Germany
- * E-mail:
| | - Jörg Janne Vehreschild
- DZIF (German Centre for Infection Research), partner site Bonn-Cologne, Germany
- Department I for Internal Medicine, University Hospital of Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
- DZIF (German Centre for Infection Research), partner site Bonn-Cologne, Germany
| | - Ahmad Saleh
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
- DZIF (German Centre for Infection Research), partner site Bonn-Cologne, Germany
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Performance of rapid tests for carbapenemase detection among Brazilian Enterobacteriaceae isolates. Braz J Microbiol 2018; 49:914-918. [PMID: 30145262 PMCID: PMC6175730 DOI: 10.1016/j.bjm.2018.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 06/07/2018] [Accepted: 07/07/2018] [Indexed: 01/04/2023] Open
Abstract
The global emergence of carbapenemases led to the need of developing new methods for their rapid detection. The aim of this study was to evaluate the performance of the rapid tests for carbapenemase-producing and non-producing Enterobacteriaceae. Carbapenem non-susceptible Enterobacteriaceae from a surveillance study submitted to a multiplex real time PCR for carbapenemase detection were included in this study. The isolates were subjected to the rapid phenotypic tests Carba NP, Blue-Carba and Carbapenem Inactivation Method (CIM). A total of 83 carbapenemase-producing (43) and non-producing (40) isolates were included in the study. The sensitivity/specificity were 62.7%/97.5%, 95.3%/100%, and 74.4%/97.5% for Carba NP, Blue-Carba and CIM, respectively. Both Carba NP and Blue-Carba presented their final results after 75 min of incubation; the final results for CIM were obtained only after 8 h. Failure to detect OXA-370 carbapenemase was the main problem for Carba NP and CIM assays. As the Blue-Carba presented the highest sensitivity, it can be considered the best screening test. Conversely, CIM might be the easiest to perform, as it does not require special reagents. The early detection of carbapenemases aids to establish infection control measures and prevent carbapenemases to spread reducing the risk of healthcare associated infections and therapeutic failure.
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Rapid Detection of Carbapenemase Production Directly from Blood Culture by Colorimetric Methods: Evaluation in a Routine Microbiology Laboratory. J Clin Microbiol 2018; 56:JCM.00325-18. [PMID: 29950338 DOI: 10.1128/jcm.00325-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/22/2018] [Indexed: 01/21/2023] Open
Abstract
The aim of this study was to evaluate the two rapid colorimetric methods (CNPt-Direct and Blue-Carba) for the detection of carbapenemase production directly from blood culture in a routine microbiology laboratory. The methods were initially evaluated on spiked blood cultures with 61 carbapenemase-positive isolates. Afterwards, they were used in blood cultures (314 samples were evaluated) obtained from patients in a routine microbiology laboratory during a period of 6 months. The colorimetric methods were compared to the conventional culture of blood. The results of the spiked blood cultures indicated that both colorimetric methods presented positive results for the vast majority (95%) of the isolates harboring KPC, NDM, and IMP genes. However, the assay failed to detect many GES- and OXA-48-like-positive isolates (65% positive results). In the second part of the study, a total of 314 blood cultures from patients were evaluated, and 33 yielded Enterobacteriaceae isolates resistant to meropenem (30 isolates were positive for carbapenemases according to PCR). The colorimetric tests correctly detected 24 out of the 30 carbapenemase-positive isolates directly from the blood vial (80% positive results). Overall positive percent agreement and negative percent agreement were 80% and 100%, respectively. The colorimetric assays are simple and cost-effective methods that can be implemented in a routine microbiology laboratory, diminishing the time necessary to detect carbapenemase-producing isolates from 24 to 48 h to 3 to 5 h. Moreover, according to our results, the positive colorimetric test results do not need to be confirmed and can be immediately provided to the attending physician.
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Bir R, Mohapatra S, Kumar A, Tyagi S, Sood S, Das BK, Kapil A. Comparative evaluation of in-house Carba NP test with other phenotypic tests for rapid detection of carbapenem-resistant Enterobacteriaceae. J Clin Lab Anal 2018; 33:e22652. [PMID: 30129058 DOI: 10.1002/jcla.22652] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/28/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is alarming worldwide causing serious infections. Rapid and accurate identification of CRE is crucial to reduce the mortality and morbidity. In this study, we tried to develop an in-house Carba NP test for detection of CRE and evaluate its performance with others. METHODS A prospective study was conducted with 40 nonrepeating Enterobacteriaceae isolates over a period of 3 months. All the isolates were screened for carbapenem resistance as per CLSI 2016 guidelines followed by PCR for blaNDM-1, blaOXA-48, blaKPC, blaVIM, and blaIMP genes. All the isolates were subjected to five phenotypic tests, that is, in-house Carba NP (iCarba NP), commercial Carba NP (cCarba NP), Blue-Carba, modified Hodge test (MHT), and CHROMagar. RESULTS Among the 40 isolates, 87.5% were identified as Escherichia coli, 7.5% were Klebsiella pneumoniae, 2.5% were Enterobacter cloacae, and 2.5% were Citrobacter freundii. Thirty-three of 40 (82.5%) isolates were found to harbor one or more resistant genes. Considering PCR to be the gold standard test, sensitivity of the phenotypic methods for CRE detection ranged from 63.6% (MHT) to 96.9% (CHROMagar). Both cCarba NP and iCarba NP observed to have highest specificity. The performance of iCarba NP was found comparable with cCarba NP by kappa score 1 and found approximately 10 times less expensive than cCarba NP. CONCLUSION CHROMagar was observed most sensitive assay for detection of CRE followed by both Carba NP tests. iCarba NP was proved cheaper and equally good as cCarba NP for detection of CRE.
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Affiliation(s)
- Raunak Bir
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sarita Mohapatra
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Amarjeet Kumar
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sonu Tyagi
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Seema Sood
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Ku Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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Périllaud C, Pilmis B, Diep J, Péan de Ponfilly G, Vidal B, Couzigou C, Mizrahi A, Lourtet-Hascoët J, Le Monnier A, Nguyen Van JC. Prospective evaluation of rapid antimicrobial susceptibility testing by disk diffusion on Mueller-Hinton rapid-SIR directly on blood cultures. Diagn Microbiol Infect Dis 2018; 93:14-21. [PMID: 30149988 DOI: 10.1016/j.diagmicrobio.2018.07.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 11/15/2022]
Abstract
BACKGROUND With the worldwide spread of antibiotic resistance, delivering antibiotic susceptibility test (AST) results in a timely manner represents a major challenge. In cases of sepsis, rapid AST may facilitate early optimization of empiric antibiotic therapy. Disc diffusion is a well-standardized AST method, however 16 to 24 h are required to achieve an overall AST profile according to antimicrobial societies. METHODS In this prospective pilot study, we evaluated the performance of Mueller-Hinton-Rapid-SIR (MHR-SIR) agar after 6-8 h of incubation in comparison with standard MH agar after 16 h of incubation directly on positive blood cultures caused by Enterobacteriaceae and Staphylococcus aureus from routine clinical microbiology. A total of 133 positive blood samples including 110 Enterobacteriaceae (83%) and 23 Staphylococcus aureus (17%) were tested in parallel by two direct AST methods, each using EUCAST breakpoints. For each combination bacterium and antibiotic, we compared the categorical agreement and the correlation between the diameters obtained by MHR-SIR and by standard MH. RESULTS Our results showed 97.7% categorical agreement for Enterobacteriaceae, with 1.4% minor errors, 0.4% major errors and 0.5% very major errors. For S. aureus, we observed 97.8% categorical agreement, 1.9% minor errors, 0.3% major errors and no very major errors. CONCLUSION Our results showed excellent categorical agreement and correlations between diameters for MHR-SIR and standard MH methods. MHRSIR can predict the result of overall AST profile within 6-8 h with reliable results. AST is obtained on the same day the blood culture becomes positive, with a very moderate cost.
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Affiliation(s)
- Claire Périllaud
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Benoît Pilmis
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Julien Diep
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | | | - Barbara Vidal
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Carine Couzigou
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Assaf Mizrahi
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Julie Lourtet-Hascoët
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Alban Le Monnier
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Jean-Claude Nguyen Van
- Service de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France.
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Betelli L, Neuwirth C, Solanas S, Chantemesse B, Vienney F, Hartmann A, Rochelet M. A voltammetric test for the rapid discrimination of β-lactamase-producing Enterobacteriaceae in blood cultures. Talanta 2018; 184:210-218. [DOI: 10.1016/j.talanta.2018.02.092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/21/2018] [Accepted: 02/24/2018] [Indexed: 01/22/2023]
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Descours G, Desmurs L, Hoang TLT, Ibranosyan M, Baume M, Ranc AG, Fuhrmann C, Dauwalder O, Salka W, Vandenesch F. Evaluation of the Accelerate Pheno™ system for rapid identification and antimicrobial susceptibility testing of Gram-negative bacteria in bloodstream infections. Eur J Clin Microbiol Infect Dis 2018; 37:1573-1583. [PMID: 29808350 DOI: 10.1007/s10096-018-3287-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/16/2018] [Indexed: 12/22/2022]
Abstract
Identification and antimicrobial susceptibility testing (AST) are critical steps in the management of bloodstream infections. Our objective was to evaluate the performance of the Accelerate Pheno™ System, CE v1.2 software, for identification and AST of Gram-negative pathogens from positive blood culture bottles. A total of 104 bottles positive for Gram-negative bacteria collected from inpatients throughout our institution were randomly selected after Gram staining. The time-to-identification and AST results, and the raw AST results obtained by the Accelerate Pheno™ system and routine techniques (MALDI-TOF MS and VITEK®2, EUCAST guidelines) were compared. Any discrepant AST result was tested by microdilution. The Pheno™ significantly improved turn-around times for identification (5.3 versus 23.7 h; p < 0.0001) and AST (10.7 versus 35.1 h; p < 0.0001). Complete agreement between the Accelerate Pheno™ system and the MALDI-TOF MS for identification was observed for 96.2% of samples; it was 99% (98/99) for monomicrobial samples versus 40% (3/5) for polymicrobial ones. The overall categorical agreement for AST was 93.7%; it was notably decreased for beta-lactams (cefepime 84.4%, piperacillin-tazobactam 86.5%, ceftazidime 87.6%) or Pseudomonas aeruginosa (71.9%; with cefepime 33.3%, piperacillin-tazobactam 77.8%, ceftazidime 0%). Analysis of discrepant results found impaired performance of the Accelerate Pheno™ system for beta-lactams (except cefepime) in Enterobacteriales (six very major errors) and poor performance in P. aeruginosa. The Accelerate Pheno™ system significantly improved the turn-around times for bloodstream infection diagnosis. Nonetheless, improvements in the analysis of polymicrobial samples and in AST algorithms, notably beta-lactam testing in both P. aeruginosa and Enterobacteriales, are required for implementation in routine workflow.
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Affiliation(s)
- Ghislaine Descours
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France. .,Inserm, U1111, CNRS, UMR5308, École Normale Supérieure de Lyon, Université Lyon 1, Lyon, France. .,Université Lyon 1, Lyon, France.
| | - Laurent Desmurs
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France
| | - Thi Lam Thuy Hoang
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France
| | - Marine Ibranosyan
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France
| | - Maud Baume
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France
| | - Anne-Gaëlle Ranc
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France
| | - Christine Fuhrmann
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France.,Department of Hygiene, Centre Léon Bérard, Lyon, France
| | - Olivier Dauwalder
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France.,Inserm, U1111, CNRS, UMR5308, École Normale Supérieure de Lyon, Université Lyon 1, Lyon, France
| | - Waël Salka
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France
| | - François Vandenesch
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Microbiology Laboratory, Institute for Infectious Agents, Lyon, France.,Inserm, U1111, CNRS, UMR5308, École Normale Supérieure de Lyon, Université Lyon 1, Lyon, France.,Université Lyon 1, Lyon, France
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Spread of Plasmid-Encoded NDM-1 and GES-5 Carbapenemases among Extensively Drug-Resistant and Pandrug-Resistant Clinical Enterobacteriaceae in Durban, South Africa. Antimicrob Agents Chemother 2018; 62:AAC.02178-17. [PMID: 29507063 DOI: 10.1128/aac.02178-17] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/23/2018] [Indexed: 01/09/2023] Open
Abstract
Whole-genome sequence analyses revealed the presence of blaNDM-1 (n = 31), blaGES-5 (n = 8), blaOXA-232 (n = 1), or blaNDM-5 (n = 1) in extensively drug-resistant and pandrug-resistant Enterobacteriaceae organisms isolated from in-patients in 10 private hospitals (2012 to 2013) in Durban, South Africa. Two novel NDM-1-encoding plasmids from Klebsiella pneumoniae were circularized by PacBio sequencing. In p19-10_01 [IncFIB(K); 223.434 bp], blaNDM-1 was part of a Tn1548-like structure (16.276 bp) delineated by IS26 The multireplicon plasmid p18-43_01 [IncR_1/IncFIB(pB171)/IncFII(Yp); 212.326 bp] shared an 80-kb region with p19-10_01, not including the blaNDM-1-containing region. The two plasmids were used as references for tracing NDM-1-encoding plasmids in the other genome assemblies. The p19-10_01 sequence was detected in K. pneumoniae (n = 7) only, whereas p18-43_01 was tracked to K. pneumoniae (n = 4), Klebsiella michiganensis (n = 1), Serratia marcescens (n = 11), Enterobacter spp. (n = 7), and Citrobacter freundii (n = 1), revealing horizontal spread of this blaNDM-1-bearing plasmid structure. Global phylogeny showed clustering of the K. pneumoniae (18/20) isolates together with closely related carbapenemase-negative ST101 isolates from other geographical origins. The South African isolates were divided into three phylogenetic subbranches, where each group had distinct resistance and replicon profiles, carrying either p19-10_01, p18-10_01, or pCHE-A1 (8,201 bp). The latter plasmid carried blaGES-5 and aacA4 within an integron mobilization unit. Our findings imply independent plasmid acquisition followed by local dissemination. Additionally, we detected blaOXA-232 carried by pPKPN4 in K. pneumoniae (ST14) and blaNDM-5 contained by a pNDM-MGR194-like genetic structure in Escherichia coli (ST167), adding even more complexity to the multilayer molecular mechanisms behind nosocomial spread of carbapenem-resistant Enterobacteriaceae in Durban, South Africa.
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Bayraktar B, Barış A, Malkoçoğlu G, Erdemir D, Kına N. Comparison of Carba NP-Direct, Carbapenem Inactivation Method, and β-CARBA Tests for Detection of Carbapenemase Production in Enterobacteriaceae. Microb Drug Resist 2018; 25:97-102. [PMID: 29694266 DOI: 10.1089/mdr.2017.0427] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Rapid and accurate detection of carbapenemase-producing isolates are extremely important for management of antimicrobial therapy and the implementation of infection control measures. We evaluated the performance of Carba NP-direct, carbapenem inactivation method (CIM), and the commercial β-CARBA tests for detection of carbapenemase production in Enterobacteriaceae. Enterobacteriaceae isolates with previously characterized carbapenemase types (n = 110) and non-carbapenemase-producing Escherichia coli (n = 15) isolates were tested. Sensitivities of Carba NP-direct, CIM, and β-CARBA tests were 99.0%, 92.7%, and 93.6%, respectively, while specificity was 100% for all three tests. For β-CARBA test, a 60-min incubation time instead of 30 increased the sensitivity to 98.1%, and lessened false negativity, particularly with OXA-48-like producers. Our results showed that Carba NP-direct, CIM, and β-CARBA tests are useful tools for the reliable detection of carbapenemase activity in enterobacterial isolates. Carba NP-direct is a simple, rapid, and low-cost test for routine use.
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Affiliation(s)
- Banu Bayraktar
- 1 Clinical Microbiology Laboratory, Şişli Hamidiye Etfal Training and Research Hospital , Istanbul, Turkey
| | - Ayşe Barış
- 1 Clinical Microbiology Laboratory, Şişli Hamidiye Etfal Training and Research Hospital , Istanbul, Turkey
| | | | - Duygu Erdemir
- 1 Clinical Microbiology Laboratory, Şişli Hamidiye Etfal Training and Research Hospital , Istanbul, Turkey
| | - Nur Kına
- 1 Clinical Microbiology Laboratory, Şişli Hamidiye Etfal Training and Research Hospital , Istanbul, Turkey
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Bonomo RA, Burd EM, Conly J, Limbago BM, Poirel L, Segre JA, Westblade LF. Carbapenemase-Producing Organisms: A Global Scourge. Clin Infect Dis 2018; 66:1290-1297. [PMID: 29165604 PMCID: PMC5884739 DOI: 10.1093/cid/cix893] [Citation(s) in RCA: 410] [Impact Index Per Article: 58.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 10/13/2017] [Indexed: 12/21/2022] Open
Abstract
The dramatic increase in the prevalence and clinical impact of infections caused by bacteria producing carbapenemases is a global health concern. Carbapenemase production is especially problematic when encountered in members of the family Enterobacteriaceae. Due to their ability to readily spread and colonize patients in healthcare environments, preventing the transmission of these organisms is a major public health initiative and coordinated international effort are needed. Central to the treatment and control of carbapenemase-producing organisms (CPOs) are phenotypic (growth-/biochemical-dependent) and nucleic acid-based carbapenemase detection tests that identify carbapenemase activity directly or their associated molecular determinants. Importantly, bacterial isolates harboring carbapenemases are often resistant to multiple antibiotic classes, resulting in limited therapy options. Emerging agents, novel antibiotic combinations and treatment regimens offer promise for management of these infections. This review highlights our current understanding of CPOs with emphasis on their epidemiology, detection, treatment, and control.
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Affiliation(s)
- Robert A Bonomo
- Medical Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
- Departments of Medicine, Pharmacology, Molecular Biology, and Microbiology, Case Western Reserve University and Research Service, CWRU-VA Center for Antimicrobial Resistance and Epidemiology (CARES), Cleveland, Ohio
| | - Eileen M Burd
- Department of Pathology and Laboratory Medicine, Atlanta, Georgia
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
| | - John Conly
- Departments of Medicine, Pathology and Laboratory Medicine, Microbiology, Calgary, Alberta, Canada
- Immunology and Infectious Diseases, Synder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, and Alberta Health Services, Calgary, Alberta, Canada
| | - Brandi M Limbago
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Laurent Poirel
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science, University of Fribourg, Switzerland
| | - Julie A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, New York, New York
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
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Candevir Ulu A, Güven Gökmen T, Kibar F, Kurtaran B, Önlen C, Kuşçu F, İnal AS, Kömür S, Yaman A, Aksu HSZ, Taşova Y. Molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae at a Turkish centre: Is the increase of resistance a threat for Europe? J Glob Antimicrob Resist 2017; 11:10-16. [DOI: 10.1016/j.jgar.2017.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/15/2017] [Accepted: 06/21/2017] [Indexed: 12/18/2022] Open
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The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives. Infect Dis Clin North Am 2017; 30:323-345. [PMID: 27208762 DOI: 10.1016/j.idc.2016.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens.
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Nodari CS, Gales AC, Barth AL, Magagnin CM, Zavascki AP, Carvalhaes CG. Detection of OXA-370 directly from rectal swabs and blood culture vials using an immunochromatographic assay. J Microbiol Methods 2017; 139:92-94. [PMID: 28483549 DOI: 10.1016/j.mimet.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/03/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
We evaluated the performance of OXA-48 K-SeT assay for detecting OXA-370 directly from spiked rectal swabs and blood culture vials. The limit of detection of this test was 104UFC/mL for rectal swabs. Detection of the OXA-370-producing isolates was successfully achieved directly from positive blood culture vials independent of growing conditions.
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Affiliation(s)
- Carolina Silva Nodari
- Laboratório Alerta, Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, 781 Pedro de Toledo St, São Paulo, Brazil.
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, 781 Pedro de Toledo St, São Paulo, Brazil
| | - Afonso Luís Barth
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil
| | - Cibele Massotti Magagnin
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil; Programa de Pós-Graduação em Ciências Médicas, Universidade Federal do Rio Grande do Sul, 2400 Ramiro Barcelos St, Porto Alegre, Brazil
| | - Alexandre Prehn Zavascki
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil; Infectious Diseases Service, Hospital de Clínicas de Porto Alegre, 2350 Ramiro Barcelos St, Porto Alegre, Brazil
| | - Cecília Godoy Carvalhaes
- Laboratório Alerta, Division of Infectious Diseases, Department of Medicine, Escola Paulista de Medicina, Universidade Federal de São Paulo, 781 Pedro de Toledo St, São Paulo, Brazil; Clinical Microbiology Section, Disciplina de Medicina Laboratorial, Universidade Federal de São Paulo, 715 Napoleão de Barros St, São Paulo, Brazil
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Sakarikou C, Ciotti M, Dolfa C, Angeletti S, Favalli C. Rapid detection of carbapenemase-producing Klebsiella pneumoniae strains derived from blood cultures by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS). BMC Microbiol 2017; 17:54. [PMID: 28274205 PMCID: PMC5343375 DOI: 10.1186/s12866-017-0952-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/09/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Carbapenemase-producing Enterobacteriaceae (CPE), particularly carbapenemase-producing Klebsiella pneumoniae isolates, are important causative agents of nosocomial infections associated with significant mortality rates mostly in critical wards. The rapid detection and typing of these strains is critical either for surveillance purposes and to prevent outbreaks and optimize antibiotic therapy. In this study, the MALDI-TOF MS method was used to detect rapidly these isolates from blood cultures (BCs) and to obtain proteomic profiles enable to discriminate between carbapenemase-producing and non-carbapenemase-producing strains. RESULTS Fifty-five K. pneumoniae strains were tested. Identification and carbapenemase-production detection assay using Ertapenem were performed both from bacterial pellets extracted directly from BCs flasks and from subcultures of these strains. For all isolates, a complete antimicrobial susceptibility testing and a genotypic characterization were performed. We found 100% agreement between the carbapenemase-producing profile generated by MALDI TOF MS and that obtained using conventional methods. The assay detected and discriminated different carbapenemase-producing K. pneumoniae isolates within 30 min to 3 h after incubation with Ertapenem. CONCLUSIONS MALDI-TOF MS is a promising, rapid and economical method for the detection of carbapenemase-producing K. pneumoniae strains that could be successfully introduced into the routine diagnostic workflow of clinical microbiology laboratories.
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Affiliation(s)
- Christina Sakarikou
- Department of Experimental Medicine and Surgery, “Tor Vergata” University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Marco Ciotti
- Laboratory of Clinical Microbiology and Virology, Polyclinic “Tor Vergata” Foundation, V.le Oxford 81, 00133 Rome, Italy
| | - Camilla Dolfa
- Department of Experimental Medicine and Surgery, “Tor Vergata” University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Silvia Angeletti
- Clinical Pathology and Microbiology Laboratory, University Hospital Campus Bio-Medico, Via Alvaro del Portillo 200, 00128 Rome, Italy
| | - Cartesio Favalli
- Department of Experimental Medicine and Surgery, “Tor Vergata” University of Rome, Via Montpellier 1, 00133 Rome, Italy
- Laboratory of Clinical Microbiology and Virology, Polyclinic “Tor Vergata” Foundation, V.le Oxford 81, 00133 Rome, Italy
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Williams MR, Stedtfeld RD, Waseem H, Stedtfeld T, Upham B, Khalife W, Etchebarne B, Hughes M, Tiedje JM, Hashsham SA. Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:1229-1241. [PMID: 29657581 PMCID: PMC5898395 DOI: 10.1039/c6ay03405e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.
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Affiliation(s)
- M R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - R D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - H Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - T Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - B Upham
- Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - W Khalife
- Department of Microbiology, Sparrow Laboratories, Sparrow Health System, Lansing, MI 48912, USA
| | - B Etchebarne
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - M Hughes
- Osteopathic Medical Specialties, Section of Emergency Medicine, Michigan State University, East Lansing, MI 4882, USA
| | - J M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - S A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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47
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Decousser JW, Poirel L, Nordmann P. Recent advances in biochemical and molecular diagnostics for the rapid detection of antibiotic-resistant Enterobacteriaceae: a focus on ß-lactam resistance. Expert Rev Mol Diagn 2017; 17:327-350. [DOI: 10.1080/14737159.2017.1289087] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jean-Winoc Decousser
- Department of Virology, Bacteriology - Infection Control, Parasitology - Mycology, Assistance Publique - Hôpitaux de Paris, University Hospital Henri Mondor, Créteil, France
- IAME, UMR 1137, INSERM, Paris, France
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland
- French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland
- National Reference Center for Emerging Antibiotic Resistance, University of fribourg, fribourg, switzerland
- Institute for Microbiology, University of Lausanne and University hospital Center, Lausanne, Switzerland
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Bialvaei AZ, Kafil HS, Asgharzadeh M, Yousef Memar M, Yousefi M. Current methods for the identification of carbapenemases. J Chemother 2017; 28:1-19. [PMID: 26256147 DOI: 10.1179/1973947815y.0000000063] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Detection of carbapenemases in clinical microbiology labs is a challenging issue. Comparison of the results of susceptibility testing with the breakpoint values of carbapenems is the first step in the screening of carbapenemase producers. To date, screening of carbapenemase-producing (CP) bacteria has been mostly performed by a selective medium. Although these media are practical for the detection of most CP isolates, the inoculated plates have to be incubated overnight. Subsequently, we need the confirmation of the carbapenemase producers present in the culture medium by additional testing [e.g. inhibition studies with liquid or solid media, modified Hodge test (MHT), or gradient strips], which can take up to another 48 hours. Despite the lack of discrimination between the three different classes of carbapenemases (KPC, MBL and OXA) and difficulties in the interpretation of the results, the MHT is usually deemed as the phenotypic reference method for the confirmation of carbapenemase production. Molecular techniques, such as real-time polymerase chain reaction (PCR) assays, in contrast to phenotypic methods that are very time consuming, are faster and allow for the quick identification of carbapenemase genes. These techniques can detect and characterize carbapenemases, including NDM- and KPC-mediated resistance, which is critical for epidemiological investigations. The aim of this review is to gather a summary of the available methods for carbapenemase detection and describe the strengths and weaknesses of each method.
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Affiliation(s)
- Abed Zahedi Bialvaei
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | - Hossein Samadi Kafil
- a Drug Applied Research Center, Faculty of Medical Sciences , Tabriz University of Medical Sciences , Iran
| | | | - Mohammad Yousef Memar
- c Infectious Disease and Tropical Medicine Research Center , Tabriz University of Medical Sciences , Iran
| | - Mehdi Yousefi
- d Immunology Research Center , Tabriz University of Medical Sciences , Iran
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Aguirre-Quiñonero A, Martínez-Martínez L. Non-molecular detection of carbapenemases in Enterobacteriaceae clinical isolates. J Infect Chemother 2017; 23:1-11. [DOI: 10.1016/j.jiac.2016.09.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/28/2016] [Accepted: 09/28/2016] [Indexed: 01/11/2023]
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50
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Utilizing the Carba NP test as an indicator of expression level of carbapenemase genes in Enterobacteriaceae. J Microbiol Methods 2016; 133:35-39. [PMID: 28007530 DOI: 10.1016/j.mimet.2016.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/17/2016] [Accepted: 12/17/2016] [Indexed: 11/22/2022]
Abstract
The Carba NP test was developed to detect carbapenemase-producing Enterobacteriaceae, and uses imipenem as the reaction substrate. In Japan, IMP-6 metallo-β-lactamase (MBL) producers, which are usually resistant to meropenem but susceptible to imipenem, and IMP-1 MBL producers, which are usually resistant to both carbapenems are prevalent. We performed the Carba NP test with IMP-6 and IMP-1 MBL producers, and both types were detected by the Carba NP test with high sensitivity. All IMP-1 MBL producers were detected by the Carba NP test, but the minimum inhibitory concentrations (MICs) of imipenem varied from 0.25 to >32μg/mL, and the time to positivity varied from 0 to 30min. Time to positivity was significantly correlated with expression levels of blaIMP-1, but not with MICs of imipenem. These results suggested that the Carba NP test can be used as a screening assay for carbapenemase gene expression levels among producers of the same type of carbapenemase. Using this approach, it is possible to determine whether the carbapenem resistance of each carbapenemase-producing Enterobacteriaceae isolate is primarily due to carbapenemase production, or to another mechanism such as outer membrane impermeability.
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