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Duan B, Zeng X, Peng J. Advances in genotypic antimicrobialresistance testing: a comprehensive review. SCIENCE CHINA. LIFE SCIENCES 2025; 68:130-143. [PMID: 39300049 DOI: 10.1007/s11427-023-2570-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/15/2024] [Indexed: 09/22/2024]
Abstract
Antimicrobial resistance (AMR) represents a substantial threat to global public health, complicating the treatment of common infections and leading to prolonged illness and escalated healthcare expenses. To effectively combat AMR, timely and accurate detection is crucial for AMR surveillance and individual-based therapy. Phenotypic antibiotic resistance testing (AST) has long been considered the gold standard in clinical applications, serving as the foundation for clinical AMR diagnosis and optimized therapy. It has significantly contributed to ensuring patients' health and the development of novel antimicrobials. Despite advancements in automated culture-based AST technologies, inherent limitations impede the widespread use of phenotypic AST in AMR surveillance. Genotypic AST technologies offer a promising alternative option, exhibiting advantages of rapidity, high sensitivity, and specificity. With the continuous advancement and expanding applications of genotypic AST technologies, such as microfluidics, mass spectrometry, and high-resolution melting curve analysis, new vigor has been injected into the development and clinical implementation of genotypic AST technologies. In this narrative review, we discuss the principles, applications, and advancements of emerging genotypic AST methods in clinical settings. The comprehensive review aims to highlight the significant scientific potential of emerging genotypic AST technologies in clinical AMR diagnosis, providing insights to enhance existing methods and explore novel approaches.
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Affiliation(s)
- Boheng Duan
- Huan Kui College of Nanchang University, Nanchang, 330031, China
| | - Xianjun Zeng
- Department of Imaging, The Second Affiliated Hospital of Nanchang University, Nanchang, 330038, China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
- Key Laboratory of Pathogen Infection Prevention and Control (Ministry of Education), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 102629, China.
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Deng QM, Zhang J, Zhang YY, Jia M, Ding DS, Fang YQ, Wang HZ, Gu HC. Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology: Three case reports. World J Clin Cases 2024; 12:5208-5216. [DOI: 10.12998/wjcc.v12.i22.5208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/29/2024] [Accepted: 06/17/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Infectious diseases are still one of the greatest threats to human health, and the etiology of 20% of cases of clinical fever is unknown; therefore, rapid identification of pathogens is highly important. Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming; serologic detection has window periods, false-positive and false-negative problems; and nucleic acid molecular detection methods can detect several known pathogens only once. Three-generation nanopore sequencing technology provides new options for identifying pathogens.
CASE SUMMARY Case 1: The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days, accompanied by cough and sputum. Nanopore sequencing of the drainage fluid revealed the presence of oral-like bacteria, leading to a clinical diagnosis of bronchopleural fistula. Cefoperazone sodium sulbactam treatment was effective. Case 2: The patient was admitted to the hospital with fever and headache, and CT revealed lung inflammation. Antibiotic treatment for Streptococcus pneumoniae, identified through nanopore sequencing of cerebrospinal fluid, was effective. Case 3: The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months. Despite antibacterial treatment, her symptoms worsened. The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii. The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.
CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.
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Affiliation(s)
- Qing-Mei Deng
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Jian Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yi-Yong Zhang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Min Jia
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Du-Shan Ding
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Yu-Qin Fang
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
| | - Hong-Zhi Wang
- Science Island Branch, Graduate School of University of Science and Technology of China, Hefei 230031, Anhui Province, China
| | - Hong-Cang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei 230031, Anhui Province, China
- Medical Pathology Center, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, Anhui Province, China
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Guillén R, Salinas C, Mendoza-Álvarez A, Rubio Rodríguez LA, Díaz-de Usera A, Lorenzo-Salazar JM, González-Montelongo R, Flores C, Rodríguez F. Genomic epidemiology of the primary methicillin-resistant Staphylococcus aureus clones causing invasive infections in Paraguayan children. Microbiol Spectr 2024; 12:e0301223. [PMID: 38415665 PMCID: PMC10986618 DOI: 10.1128/spectrum.03012-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/22/2024] [Indexed: 02/29/2024] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the major human pathogens. It could carry numerous resistance genes and virulence factors in its genome, some of which are related to the severity of the infection. An observational, descriptive, cross-sectional study was designed to molecularly analyze MRSA isolates that cause invasive infections in Paraguayan children from 2009 to 2013. Ten representative MRSA isolates of the main clonal complex identified were analyzed with short-read paired-end sequencing and assessed for the virulome, resistome, and phylogenetic relationships. All the genetically linked MRSA isolates were recovered from diverse clinical sources, patients, and hospitals at broad gap periods. The pan-genomic analysis of these clones revealed three major and different clonal complexes (CC30, CC5, and CC8), each composed of clones closely related to each other. The CC30 genomes prove to be a successful clone, strongly installed and disseminated throughout our country, and closely related to other CC30 public genomes from the region and the world. The CC5 shows the highest genetic variability, and the CC8 carried the complete arginine catabolic mobile element (ACME), closely related to the USA300-NAE-ACME+, identified as the major cause of CA-MRSA infections in North America. Multiple virulence and resistance genes were identified for the first time in this study, highlighting the complex virulence profiles of MRSA circulating in the country. This study opens a wide range of new possibilities for future projects and trials to improve the existing knowledge on the epidemiology of MRSA circulating in Paraguay. IMPORTANCE The increasing prevalence of methicillin-resistant Staphylococcus aureus (MRSA) is a public health problem worldwide. The most frequent MRSA clones identified in Paraguay in previous studies (including community and hospital acquired) were the Pediatric (CC5-ST5-IV), the Cordobes-Chilean (CC5-ST5-I), the SouthWest Pacific (CC30-ST30-IV), and the Brazilian (CC8-ST239-III) clones. In this study, the pan-genomic analysis of the most representative MRSA clones circulating in invasive infection in Paraguayan children over the years 2009-2013, such as the CC30-ST30-IV, CC5-ST5-IV, and CC8-ST8-IV, was carried out to evaluate their genetic diversity, their repertoire of virulence factors, and antimicrobial resistance determinants. This revealed multiple virulence and resistance genes, highlighting the complex virulence profiles of MRSA circulating in Paraguay. Our work is the first genomic study of MRSA in Paraguay and will contribute to the development of genomic surveillance in the region and our understanding of the global epidemiology of this pathogen.
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Affiliation(s)
- Rosa Guillén
- Microbiology Department, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción (IICS-UNA), San Lorenzo, Paraguay
| | - Claudia Salinas
- Microbiology Department, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción (IICS-UNA), San Lorenzo, Paraguay
| | | | - Luis A. Rubio Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Carlos Flores
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Fátima Rodríguez
- Microbiology Department, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción (IICS-UNA), San Lorenzo, Paraguay
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Bai HJ, Geng QF, Jin F, Yang YL. Epidemiologic analysis of antimicrobial resistance in hospital departments in China from 2022 to 2023. JOURNAL OF HEALTH, POPULATION, AND NUTRITION 2024; 43:39. [PMID: 38449053 PMCID: PMC10918933 DOI: 10.1186/s41043-024-00526-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/13/2024] [Indexed: 03/08/2024]
Abstract
Bacterial drug resistance monitoring in hospitals is a crucial aspect of healthcare management and a growing concern worldwide. In this study, we analysed the bacterial drug resistance surveillance in our hospital from 2022 Q1 to 2023 Q2. The main sampling sources were respiratory, blood, and urine-based, and the main clinical infections were respiratory and genitourinary in nature. Specimens were inoculated and cultured; bacterial strains were isolated using a VITEK® 2 Compact 60-card automatic microorganism identifier (bioMerieux, Paris, France) and their matching identification cards were identified, and manual tests were supplemented for strain identification. The most common Gram-positive bacteria detected were Staphylococcus aureus, followed by Enterococcus faecalis (E. faecalis), Staphylococcus epidermidis (S. epidermidis), and Staphylococcus haemolyticus (S. haemolyticus). The most common Gram-negative bacteria detected were Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The most prevalent multidrug-resistant bacteria were those producing extended-spectrum beta-lactamases, followed by methicillin-resistant Staphylococcus aureus, followed by carbapenem-resistant Enterobacterales. This study suggests that the prevention and control of infections in the respiratory and genitourinary systems should be the focus of anti-infective work and that the use of antimicrobials should be reduced and regulated to prevent the emergence and spread of resistant bacteria.
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Affiliation(s)
- Hui-Jun Bai
- Department of Clinical Pharmacy, The Seventh People's Hospital of Hebei Province, 389 Jungong Road, Xicheng District, Dingzhou, 073000, China
| | - Qing-Feng Geng
- Department of Hospital Office, The Seventh People's Hospital of Hebei Province, 389 Jungong Road, Xicheng District, Dingzhou, 073000, China
| | - Fang Jin
- Department of Clinical Laboratory, The Seventh People's Hospital of Hebei Province, 389 Jungong Road, Xicheng District, Dingzhou, 073000, China
| | - Yong-Li Yang
- Department of Hospital Office, The Seventh People's Hospital of Hebei Province, 389 Jungong Road, Xicheng District, Dingzhou, 073000, China.
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