1
|
Xiang Y, Zhu K, Min K, Zhang Y, Liu J, Liu K, Han Y, Li X, Du X, Wang X, Huang Y, Li X, Peng Y, Yang C, Liu H, Liu H, Li X, Wang H, Wang C, Wang Q, Jia H, Yang M, Wang L, Wu Y, Cui Y, Chen F, Yang H, Baker S, Xu X, Yang J, Song H, Qiu S. Characterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance. Nat Commun 2024; 15:6123. [PMID: 39033143 DOI: 10.1038/s41467-024-50331-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 07/03/2024] [Indexed: 07/23/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants. Characterized by macro, red, dry, and rough (mrdar) colonies, these variants demonstrate enhanced biofilm formation at 28 °C and 37 °C compared to typical rdar colonies. The mrdar variants exhibit extensive multidrug resistance, with significantly higher resistance to at least five classes of antimicrobial agents compared to non-mrdar variants. This resistance is primarily conferred by an IncHI2 plasmid harboring 19 antimicrobial resistance genes. Phylogenomic analysis divides the global collections into six lineages. The majority of mrdar variants belong to sublineage L6.5, which originated from Chinese smooth colony strains and possibly emerged circa 1977. Among the mrdar variants, upregulation of the csgDEFG operons is observed, probably due to a distinct point mutation (-44G > T) in the csgD gene promoter. Pangenome and genome-wide association analyses identify 87 specific accessory genes and 72 distinct single nucleotide polymorphisms associated with the mrdar morphotype.
Collapse
Affiliation(s)
- Ying Xiang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Kunpeng Zhu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
- Kaifeng Center for Disease Control and Prevention, Kaifeng, China
| | - Kaiyuan Min
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yaowen Zhang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
- Daxing Center for Disease Control and Prevention, Beijing, China
| | - Jiangfeng Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Kangkang Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yiran Han
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinge Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinying Du
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xin Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Ying Huang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xinping Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yuqian Peng
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Chaojie Yang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hongbo Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hongbo Liu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Xiaoying Li
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Hui Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Chao Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Qi Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Huiqun Jia
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Mingjuan Yang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Ligui Wang
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, China
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.
| | - Juntao Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
| | - Hongbin Song
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China.
| | - Shaofu Qiu
- Center for Disease Control and Prevention of Chinese PLA, Beijing, China.
| |
Collapse
|
2
|
Shen Z, Zhang CY, Gull T, Zhang S. Comparison of genotypic and phenotypic antimicrobial resistance profiles of Salmonella enterica isolates from poultry diagnostic specimens. J Vet Diagn Invest 2024; 36:529-537. [PMID: 38571400 PMCID: PMC11185115 DOI: 10.1177/10406387241242118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The spread of antimicrobial-resistant bacteria is a significant concern, as it can lead to increased morbidity and mortality in both humans and animals. Whole-genome sequencing (WGS) is a powerful tool that can be used to conduct a comprehensive analysis of the genetic basis of antimicrobial resistance (AMR). We compared the phenotypic and genotypic AMR profiles of 97 Salmonella isolates derived from chicken and turkey diagnostic samples. We focused AMR analysis on 5 antimicrobial classes: aminoglycoside, beta-lactam, phenicol, tetracycline, and trimethoprim. The overall sensitivity and specificity of WGS in predicting phenotypic antimicrobial resistance in the Salmonella isolates were 93.4% and 99.8%, respectively. There were 16 disagreement instances, including 15 that were phenotypically resistant but genotypically susceptible; the other instance involved phenotypic susceptibility but genotypic resistance. Of the isolates examined, 67 of 97 (69%) carried at least 1 resistance gene, with 1 isolate carrying as many as 12 resistance genes. Of the 31 AMR genes analyzed, 16 were identified as aminoglycoside-resistance genes, followed by 4 beta-lactam-resistance, 3 tetracycline-resistance, 2 sulfonamide-resistance, and 1 each of fosfomycin-, quinolone-, phenicol-, trimethoprim-, bleomycin-, and colistin-resistance genes. Most of the resistance genes found were located on plasmids.
Collapse
Affiliation(s)
- Zhenyu Shen
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri–Columbia, Columbia, MO, USA
| | - C. Y. Zhang
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri–Columbia, Columbia, MO, USA
| | - Tamara Gull
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri–Columbia, Columbia, MO, USA
| | - Shuping Zhang
- Veterinary Medical Diagnostic Laboratory and Department of Veterinary Pathobiology, College Veterinary Medicine, University of Missouri–Columbia, Columbia, MO, USA
| |
Collapse
|
3
|
Huang J, Yue H, Wei W, Shan J, Zhu Y, Feng L, Ma Y, Zou B, Wu H, Zhou G. FARPA-based tube array coupled with quick DNA extraction enables ultra-fast bedside detection of antibiotic-resistant pathogens. Analyst 2024; 149:3607-3614. [PMID: 38767613 DOI: 10.1039/d4an00185k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rapid and accurate detection of pathogens and antimicrobial-resistant (AMR) genes of the pathogens are crucial for the clinical diagnosis and effective treatment of infectious diseases. However, the time-consuming steps of conventional culture-based methods inhibit the precise and early application of anti-infection therapy. For the prompt treatment of pathogen-infected patients, we have proposed a novel tube array strategy based on our previously reported FARPA (FEN1-aided recombinase polymerase amplification) principle for the ultra-fast detection of antibiotic-resistant pathogens on site. The entire process from "sample to result" can be completed in 25 min by combining quick DNA extraction from a urine sample with FARPA to avoid the usually complicated DNA extraction step. Furthermore, a 36-tube array made from commercial 384-well titre plates was efficiently introduced to perform FARPA in a portable analyser, achieving an increase in the loading sample throughput (from several to several tens), which is quite suitable for the point-of-care testing (POCT) of multiple pathogens and multiple samples. Finally, we tested 92 urine samples to verify the performance of our proposed method. The sensitivities for the detection of E. coli, K. pneumoniae, E. faecium, and E. faecalis were 92.7%, 93.8%, 100% and 88.9%, respectively. The specificities for the detection of the four pathogens were 100%. Consequently, our rapid, low-cost and user-friendly POCT method holds great potential for guiding the rational use of antibiotics and reducing bacterial resistance.
Collapse
Affiliation(s)
- Jinling Huang
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Huijie Yue
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Wei Wei
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Jingwen Shan
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Yue Zhu
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Liying Feng
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Yi Ma
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| |
Collapse
|
4
|
Xing Z, Jiang H, Liu X, Chai Q, Xin Z, Zhu C, Bao Y, Chen H, Gao H, Ma D. Integrating DNA/RNA microbe detection and host response for accurate diagnosis, treatment and prognosis of childhood infectious meningitis and encephalitis. J Transl Med 2024; 22:583. [PMID: 38902725 PMCID: PMC11191231 DOI: 10.1186/s12967-024-05370-w] [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: 07/18/2023] [Accepted: 06/02/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Infectious meningitis/encephalitis (IM) is a severe neurological disease that can be caused by bacterial, viral, and fungal pathogens. IM suffers high morbidity, mortality, and sequelae in childhood. Metagenomic next-generation sequencing (mNGS) can potentially improve IM outcomes by sequencing both pathogen and host responses and increasing the diagnosis accuracy. METHODS Here we developed an optimized mNGS pipeline named comprehensive mNGS (c-mNGS) to monitor DNA/RNA pathogens and host responses simultaneously and applied it to 142 cerebrospinal fluid samples. According to retrospective diagnosis, these samples were classified into three categories: confirmed infectious meningitis/encephalitis (CIM), suspected infectious meningitis/encephalitis (SIM), and noninfectious controls (CTRL). RESULTS Our pipeline outperformed conventional methods and identified RNA viruses such as Echovirus E30 and etiologic pathogens such as HHV-7, which would not be clinically identified via conventional methods. Based on the results of the c-mNGS pipeline, we successfully detected antibiotic resistance genes related to common antibiotics for treating Escherichia coli, Acinetobacter baumannii, and Group B Streptococcus. Further, we identified differentially expressed genes in hosts of bacterial meningitis (BM) and viral meningitis/encephalitis (VM). We used these genes to build a machine-learning model to pinpoint sample contaminations. Similarly, we also built a model to predict poor prognosis in BM. CONCLUSIONS This study developed an mNGS-based pipeline for IM which measures both DNA/RNA pathogens and host gene expression in a single assay. The pipeline allows detecting more viruses, predicting antibiotic resistance, pinpointing contaminations, and evaluating prognosis. Given the comparable cost to conventional mNGS, our pipeline can become a routine test for IM.
Collapse
Affiliation(s)
- Zhihao Xing
- Biobank & Clinical laboratory & Department of Respiratory Medicine, Shenzhen Children's Hospital of Shantou University Medical College, Shenzhen, Guangdong, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Hanfang Jiang
- Clinical laboratory, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Xiaorong Liu
- Biobank & Clinical laboratory & Department of Respiratory Medicine, Shenzhen Children's Hospital of Shantou University Medical College, Shenzhen, Guangdong, China
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Qiang Chai
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Zefeng Xin
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Chunqing Zhu
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
- Clinical laboratory, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Yanmin Bao
- Department of Respiratory Medicine, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Hongyu Chen
- Clinical laboratory, Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Hongdan Gao
- Medical Testing, Bengbu Medical College, Bengbu, Anhui, China
| | - Dongli Ma
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong, China.
| |
Collapse
|
5
|
Sharma MK, Stobart M, Akochy PM, Adam H, Janella D, Rabb M, Alawa M, Sekirov I, Tyrrell GJ, Soualhine H. Evaluation of Whole Genome Sequencing-Based Predictions of Antimicrobial Resistance to TB First Line Agents: A Lesson from 5 Years of Data. Int J Mol Sci 2024; 25:6245. [PMID: 38892433 PMCID: PMC11172968 DOI: 10.3390/ijms25116245] [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: 04/13/2024] [Revised: 05/24/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Phenotypic susceptibility testing of the Mycobacterium tuberculosis complex (MTBC) isolate requires culture growth, which can delay rapid detection of resistant cases. Whole genome sequencing (WGS) and data analysis pipelines can assist in predicting resistance to antimicrobials used in the treatment of tuberculosis (TB). This study compared phenotypic susceptibility testing results and WGS-based predictions of antimicrobial resistance (AMR) to four first-line antimicrobials-isoniazid, rifampin, ethambutol, and pyrazinamide-for MTBC isolates tested between the years 2018-2022. For this 5-year retrospective analysis, the WGS sensitivity for predicting resistance for isoniazid, rifampin, ethambutol, and pyrazinamide using Mykrobe was 86.7%, 100.0%, 100.0%, and 47.8%, respectively, and the specificity was 99.4%, 99.5%, 98.7%, and 99.9%, respectively. The predictive values improved slightly using Mykrobe corrections applied using TB Profiler, i.e., the WGS sensitivity for isoniazid, rifampin, ethambutol, and pyrazinamide was 92.31%, 100%, 100%, and 57.78%, respectively, and the specificity was 99.63%. 99.45%, 98.93%, and 99.93%, respectively. The utilization of WGS-based testing addresses concerns regarding test turnaround time and enables analysis for MTBC member identification, antimicrobial resistance prediction, detection of mixed cultures, and strain genotyping, all through a single laboratory test. WGS enables rapid resistance detection compared to traditional phenotypic susceptibility testing methods using the WHO TB mutation catalog, providing an insight into lesser-known mutations, which should be added to prediction databases as high-confidence mutations are recognized. The WGS-based methods can support TB elimination efforts in Canada and globally by ensuring the early start of appropriate treatment, rapidly limiting the spread of TB outbreaks.
Collapse
Affiliation(s)
- Meenu Kaushal Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| | - Michael Stobart
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
| | - Pierre-Marie Akochy
- Laboratoire de Santé Publique du Québec-Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada
| | - Heather Adam
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Diagnostic Services, Shared Health, Winnipeg, MB R3C 3H8, Canada
| | - Debra Janella
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
| | - Melissa Rabb
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
| | - Mohey Alawa
- Regina Qu’Appelle Health Region, Regina, SK S4T 1A5, Canada;
| | - Inna Sekirov
- Public Health Laboratory, B.C. Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada;
| | - Gregory J. Tyrrell
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 2J2, Canada
- Alberta Precision Laboratories Public Health, Edmonton, AB T6G 2J2, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada (M.S.)
- Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
| |
Collapse
|
6
|
Hinić V, Seth-Smith HMB, Stammler S, Egli A. Rapid detection of plasmid-mediated AmpC-producers by eazyplex® SuperBug AmpC assay compared to whole-genome sequencing. J Microbiol Methods 2024; 221:106938. [PMID: 38642781 DOI: 10.1016/j.mimet.2024.106938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/11/2024] [Accepted: 04/18/2024] [Indexed: 04/22/2024]
Abstract
Current methods for plasmid-mediated AmpC β-lactamase (pAmpC) detection in routine microbiological laboratories are based on various phenotypic tests. Eazyplex®SuperBug AmpC assay is a molecular assay based on isothermal amplification for rapid detection of the most common pAmpC types from bacterial culture: CMY-2 group, DHA, ACC and MOX. Our aim was to evaluate the diagnostic performance of this assay. The assay was evaluated on 64 clinical isolates of Enterobacterales without chromosomal inducible AmpC, and with phenotypically confirmed AmpC production. The results were confirmed, and isolates further characterized by whole-genome sequencing (WGS). eazyplex®SuperBug AmpC assay correctly detected the two most common pAmpC types CMY-2 group (16/16) and DHA (19/19). Detection of ACC and MOX could not be evaluated on our set of isolates since there was only one isolate harbouring ACC and none with MOX. pAmpC encoding genes could be detected in only eight of 36 investigated Escherichia coli isolates. The remaining 28 E. coli isolates harboured previously described mutations in the blaEC promoter, leading to the overexpression of chromosomally encoded E. coli specific AmpC β-lactamase. All results were 100% concordant with the results of WGS. eazyplex®SuperBug AmpC assay enabled rapid and reliable detection of pAmpC-encoding genes in Enterobacterales like Klebsiella spp. and Proteus spp. and the distinction between plasmid-mediated and chromosomally encoded AmpC in E. coli.
Collapse
Affiliation(s)
- Vladimira Hinić
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
| | - Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sabrina Stammler
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| |
Collapse
|
7
|
Riester O, Kaiser L, Laufer S, Deigner HP. Rapid Phenotypic Antibiotics Susceptibility Analysis by a 3D Printed Prototype. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308806. [PMID: 38528800 DOI: 10.1002/advs.202308806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/31/2024] [Indexed: 03/27/2024]
Abstract
One of the most important public health concerns is the increase in antibiotic-resistant pathogens and corresponding treatment of associated infections. Addressing this challenge requires more efficient use of antibiotics, achievable by the use of evidence-based, effective antibiotics identified by antibiotic susceptibility testing (AST). However, the current standard method of phenotypic AST used for this purpose requires 48 h or more from sample collection to result. Until results are available, broad-spectrum antibiotics are used to avoid delaying treatment. The turnaround time must therefore be shortened in order for the results to be available before the second administration of antibiotics. The phenotypic electrochemical AST method presented here identifies effective antibiotics within 5-10 h after sampling. Spiked serum samples, including polymicrobial samples, with clinically relevant pathogens and respective concentrations commonly found in bloodstream infections (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Pseudomonas aeruginosa) are used. Direct loading of the test with diluted serum eliminates the need for a pre-culture, as required by existing methods. Furthermore, by combining several electrochemical measurement procedures with computational analysis, allowing the method to be used both online and offline, the AST achieves a sensitivity of 94.44% and a specificity of 95.83% considering each replicate individually.
Collapse
Affiliation(s)
- Oliver Riester
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054, Villingen-Schwenningen, Germany
- Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054, Villingen-Schwenningen, Germany
| | - Stefan Laufer
- Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
- Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany
- IFIT Cluster of Excellence EXC 2180 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, 72076, Tuebingen, Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Strasse 17, 78054, Villingen-Schwenningen, Germany
- Faculty of Science, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
- EXIM Department, Fraunhofer Institute IZI (Leipzig), Schillingallee 68, 18057, Rostock, Germany
| |
Collapse
|
8
|
Gopikrishnan M, Haryini S, C GPD. Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review. J Basic Microbiol 2024; 64:e2300579. [PMID: 38308076 DOI: 10.1002/jobm.202300579] [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: 10/03/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/04/2024]
Abstract
In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life-threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post-COVID era compared to the pre-COVID era has raised global concern. The prevalence of nosocomial-related infections, especially outbreaks of drug-resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next-generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug-resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug-resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host-directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug-resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.
Collapse
Affiliation(s)
- Mohanraj Gopikrishnan
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Sree Haryini
- Department of Biomedical Sciences, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - George Priya Doss C
- Department of Integrative Biology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| |
Collapse
|
9
|
Karampatakis T. Molecular Characterization of Gram-Negative Bacteria: Antimicrobial Resistance, Virulence and Epidemiology. Antibiotics (Basel) 2024; 13:402. [PMID: 38786131 PMCID: PMC11117266 DOI: 10.3390/antibiotics13050402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Multidrug-resistant (MDR), extensively drug-resistant (XDR) and pan-drug-resistant (PDR) Gram-negative bacteria constitute a huge public health problem [...].
Collapse
|
10
|
Robillard DW, Sundermann AJ, Raux BR, Prinzi AM. Navigating the network: a narrative overview of AMR surveillance and data flow in the United States. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e55. [PMID: 38655022 PMCID: PMC11036423 DOI: 10.1017/ash.2024.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
The antimicrobial resistance (AMR) surveillance landscape in the United States consists of a data flow that starts in the clinical setting and is maintained by a network of national and state public health laboratories. These organizations are well established, with robust methodologies to test and confirm antimicrobial susceptibility. Still, the bridge that guides the flow of data is often one directional and caught in a constant state of rush hour that can only be refined with improvements to infrastructure and automation in the data flow. Moreover, there is an absence of information in the literature explaining the processes clinical laboratories use to coalesce and share susceptibility test data for AMR surveillance, further complicated by variability in testing procedures. This knowledge gap limits our understanding of what is needed to improve and streamline data sharing from clinical to public health laboratories. Successful models of AMR surveillance display attributes like 2-way communication between clinical and public health laboratories, centralized databases, standardized data, and the use of electronic health records or data systems, highlighting areas of opportunity and improvement. This article explores the roles and processes of the organizations involved in AMR surveillance in the United States and identifies current knowledge gaps and opportunities to improve communication between them through standardization, communication, and modernization of data flow.
Collapse
Affiliation(s)
- Darin W. Robillard
- Division of Public Health, University of Utah School of Medicine, Salt Lake City, UT, USA
- Corporate Program Management, bioMérieux, Salt Lake City, UT, USA
| | - Alexander J. Sundermann
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Brian R. Raux
- US Medical Affairs, bioMérieux, Salt Lake City, UT, USA
| | | |
Collapse
|
11
|
Phu DH, Wongtawan T, Wintachai P, Nhung NT, Yen NTP, Carrique-Mas J, Turni C, Omaleki L, Blackall PJ, Thomrongsuwannakij T. Molecular characterization of Campylobacter spp. isolates obtained from commercial broilers and native chickens in Southern Thailand using whole genome sequencing. Poult Sci 2024; 103:103485. [PMID: 38335668 PMCID: PMC10869288 DOI: 10.1016/j.psj.2024.103485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
Chickens are the primary reservoirs of Campylobacter spp., mainly C. jejuni and C. coli, that cause human bacterial gastrointestinal infections. However, genomic characteristics and antimicrobial resistance of Campylobacter spp. in low- to middle-income countries need more comprehensive exploration. This study aimed to characterize 21 C. jejuni and 5 C. coli isolates from commercial broilers and native chickens using whole genome sequencing and compare them to 28 reference Campylobacter sequences. Among the 26 isolates, 13 sequence types (ST) were identified in C. jejuni and 5 ST in C. coli. The prominent ST was ST 2274 (5 isolates, 19.2%), followed by ST 51, 460, 2409, and 6455 (2 isolates in each ST, 7.7%), while all remaining ST (464, 536, 595, 2083, 6736, 6964, 8096, 10437, 828, 872, 900, 8237, and 13540) had 1 isolate per ST (3.8%). Six types of antimicrobial resistance genes (ant(6)-Ia, aph(3')-III, blaOXA, cat, erm(B), and tet(O)) and one point mutations in the gyrA gene (Threonine-86-Isoleucine) and another in the rpsL gene (Lysine-43-Arginine) were detected. The blaOXA resistance gene was present in all isolates, the gyrA mutations was in 95.2% of C. jejuni and 80.0% of C. coli, and the tet(O) resistance gene in 76.2% of C. jejuni and 80.0% of C. coli. Additionally, 203 virulence-associated genes linked to 16 virulence factors were identified. In terms of phenotypic resistance, the C. jejuni isolates were all resistant to ciprofloxacin, enrofloxacin, and nalidixic acid, with lower levels of resistance to tetracycline (76.2%), tylosin (52.3%), erythromycin (23.8%), azithromycin (22.2%), and gentamicin (11.1%). Most C. coli isolates were resistant to all tested antimicrobials, while 1 C. coli was pan-susceptible except for tylosin. Single-nucleotide polymorphisms concordance varied widely, with differences of up to 13,375 single-nucleotide polymorphisms compared to the reference Campylobacter isolates, highlighting genetic divergence among comparative genomes. This study contributes to a deeper understanding of the molecular epidemiology of Campylobacter spp. in Thai chicken production systems.
Collapse
Affiliation(s)
- Doan Hoang Phu
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Doctoral Program in Health Sciences, College of Graduate Studies, Walailak University, Nakhon Si Thammarat 80160, Thailand; Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City 70000, Vietnam
| | - Tuempong Wongtawan
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | | | - Nguyen Thi Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City 70000, Vietnam
| | | | - Juan Carrique-Mas
- Food and Agriculture Organization of the United Nations, Ha Noi 10000, Vietnam
| | - Conny Turni
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Lida Omaleki
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Thotsapol Thomrongsuwannakij
- Akkhraratchakumari Veterinary College, Walailak University, Nakhon Si Thammarat 80160, Thailand; Centre for One Health, Walailak University, Nakhon Si Thammarat 80160, Thailand.
| |
Collapse
|
12
|
Kals M, Mancini L, Kotar J, Donald A, Cicuta P. Multipad agarose plate: a rapid and high-throughput approach for antibiotic susceptibility testing. J R Soc Interface 2024; 21:20230730. [PMID: 38531408 PMCID: PMC10973877 DOI: 10.1098/rsif.2023.0730] [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: 12/09/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
We describe a phenotypic antibiotic susceptibility testing (AST) method that can provide an eightfold speed-up in turnaround time compared with the current clinical standard by leveraging advances in microscopy and single-cell imaging. A newly developed growth plate containing 96 agarose pads, termed the multipad agarose plate (MAP), can be assembled at low cost. Pads can be prepared with dilution series of antibiotics. Bacteria are seeded on the pads and automatically imaged using brightfield microscopy, with a fully automated segmentation pipeline quantifying microcolony formation and growth rate. Using a test set of nine antibiotics with very different targets, we demonstrate that accurate minimum inhibitory concentration (MIC) measurements can be performed based on the growth rate of microcolonies within 3 h of incubation with the antibiotic when started from exponential phase. Faster, reliable and high-throughput methods for AST, such as MAP, could improve patient care by expediting treatment initiation and alleviating the burden of antimicrobial resistance.
Collapse
Affiliation(s)
- Morten Kals
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
- Synoptics Ltd, Cambridge CB4 1TF, UK
| | - Leonardo Mancini
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Jurij Kotar
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | | | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| |
Collapse
|
13
|
Cardenas-Arias AR, Sano E, Cardoso B, Fuga B, Sellera FP, Esposito F, Aravena-Ramírez V, Huaman DC, Gonzales CD, Espinoza LL, Hernández LM, Lincopan N. Genomic data of global clones of CTX-M-65-producing Escherichia coli ST10 from South American llamas inhabiting the Andean Highlands of Peru. J Glob Antimicrob Resist 2024; 36:135-138. [PMID: 38072242 DOI: 10.1016/j.jgar.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND The global spread of extended-spectrum β-lactamase (ESβL)-producing Escherichia coli has been considered a One Health issue that demands continuous genomic epidemiology surveillance in humans and non-human hosts. OBJECTIVES To report the occurrence and genomic data of ESβL-producing E. coli strains isolated from South American llamas inhabiting a protected area with public access in the Andean Highlands of Peru. METHODS Two ESβL-producing E. coli strains (E. coli L1LB and L2BHI) were identified by MALDI-TOF. Genomic DNAs were extracted and sequenced using the Illumina NextSeq platform. De novo assembly was performed by CLC Genomic Workbench and in silico prediction was accomplished by curated bioinformatics tools. SNP-based phylogenomic analysis was performed using publicly available genomes of global E. coli ST10. RESULTS Escherichia coli L1LB generated a total of 4 000 11 and L2BHI a total of 4 002 54 paired-end reads of ca.164 × and ca. 157 ×, respectively. Both E. coli strains were assigned to serotype O8:H4, fimH41, and ST10. The blaCTX-M-65 ESβL gene, along with other medically important antimicrobial resistance genes, was predicted. Broad virulomes, including the presence of the astA gene, were confirmed. The phylogenomic analysis revealed that E. coli L1LB and L2BHI strains are closely related to isolates from companion animals and human hosts, as well as environmental strains, previously reported in North America, South America, Africa, and Asia. CONCLUSION Presence of ESβL-producing E. coli ST10 in South American camelids with historical and cultural importance supports successful expansion of international clones of priority pathogens in natural areas with public access.
Collapse
Affiliation(s)
- Adriana R Cardenas-Arias
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Elder Sano
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Brenda Cardoso
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Valentina Aravena-Ramírez
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Dennis Carhuaricra Huaman
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carla Duran Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Luis Luna Espinoza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Lenin Maturrano Hernández
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Nilton Lincopan
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
14
|
Bhatia M, Shamanna V, Nagaraj G, Gupta P, Omar BJ, Diksha, Rohilla R, Ravikumar KL. Assessment of in vitro colistin susceptibility of carbapenem-resistant clinical Gram-negative bacterial isolates using four commercially available systems & Whole-genome sequencing: A diagnostic accuracy study. Diagn Microbiol Infect Dis 2024; 108:116155. [PMID: 38219381 DOI: 10.1016/j.diagmicrobio.2023.116155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024]
Abstract
AIM To analyze the diagnostic utility of commercially available platforms and Whole-genome sequencing (WGS) for accurate determination of colistin susceptibility test results. MATERIAL & METHODS An exploratory diagnostic accuracy study was conducted in which sixty carbapenem-resistant Gram-negative bacteria were subjected to identification and AST using MALDI-TOF MS & MicroScan walkaway 96 Plus. Additional AST was performed using the BD Phoenix system and Mikrolatest colistin kit. The test isolates were subjected to Vitek-2 and WGS at CRL, Bengaluru. RESULTS There was no statistically significant agreement between the colistin susceptibility results obtained by WGS, with those of commercial phenotypic platforms. The MicroScan 96 Plus had the highest sensitivity (31 %) & NPV (77 %), and the BD Phoenix system had the highest specificity (97 %) and PPV (50 %), respectively, for determining colistin resistance. CONCLUSION The utility of WGS as a tool in AMR surveillance and validation of phenotypic AST methods should be explored further.
Collapse
Affiliation(s)
- Mohit Bhatia
- Department of Microbiology, Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi, 110029, India.
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India; Department of Biotechnology, NMAM Institute of Technology, Nitte, Udupi, Karnataka 574110, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences Deoghar, Jharkhand 814152, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Diksha
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Ranjana Rohilla
- Department of Microbiology, Sri Guru Ram Rai Institute of Medical & Health Science, Dehradun, Uttarakhand 248001, India
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| |
Collapse
|
15
|
Verma N, Sharma T, Bhardwaj A, Vemuluri VR. Comparative genomics and characterization of a multidrug-resistant Acinetobacter baumannii VRL-M19 isolated from a crowded setting in India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 118:105549. [PMID: 38181886 DOI: 10.1016/j.meegid.2023.105549] [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: 07/31/2023] [Revised: 12/17/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024]
Abstract
A crowded vegetable market serves as a mass gathering, posing a potential risk for infection transmission. In this study, we isolated a multidrug-resistant Acinetobacter baumannii strain, VRL-M19, from the air of such a market and conducted comparative genomics and phenotypic characterization. Antimicrobial susceptibility testing, genome sequencing using Illumina HiSeq X10, and pan-genome analysis with 788 clinical isolates identified core, accessory, and unique drug-resistant determinants. Mutational analysis of drug-resistance genes, virulence factor annotation, in vitro pathogenicity assessment, subsystem analysis, Multilocus sequence typing, and whole genome phylogenetic analysis were performed. VRL-M19 exhibited multidrug resistance with 69 determinants, and analysis across 788 clinical isolates and 350 Indian isolates revealed more accessory genes (52 out of 69) in the Indian isolates. Multiple mutations were observed in drug target modification genes, and the strain was identified as a moderate biofilm-former with 55 virulence factors. Whole genome phylogenetics indicated a close relationship between VRL-M19 and clinical A. baumannii strains. In conclusion, our comprehensive study suggests that VRL-M19 is a multidrug-resistant, potential pathogen with biofilm-forming capabilities, closely associated with clinical A. baumannii strains.
Collapse
Affiliation(s)
- Neha Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Tina Sharma
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anshu Bhardwaj
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Venkata Ramana Vemuluri
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160036, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
16
|
Costales C, Dien Bard J. The Report Says What?: How the Medical Microbiologist can aid in the Interpretation of Next-Generation Sequencing Results. Clin Lab Med 2024; 44:75-84. [PMID: 38280799 DOI: 10.1016/j.cll.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Abstract
The applications of next-generation sequencing (NGS) in the clinical microbiology laboratory are expanding at a rapid pace. The medical microbiologist thus plays a key role in translating the results of these emerging technologies to the practicing clinician. Here we discuss the factors to consider to successfully develop standardized reporting for microbial targeted or metagenomic NGS testing in the clinical laboratory.
Collapse
Affiliation(s)
- Cristina Costales
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
17
|
Klaper K, Tlapák H, Selb R, Jansen K, Heuer D. Integrated molecular, phenotypic and epidemiological surveillance of antimicrobial resistance in Neisseria gonorrhoeae in Germany. Int J Med Microbiol 2024; 314:151611. [PMID: 38309143 DOI: 10.1016/j.ijmm.2024.151611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Numbers of infections with Neisseria gonorrhoeae are among the top three sexually transmitted infections (STI) worldwide. In addition, the emergence and spread of antimicrobial resistance (AMR) in Neisseria gonorrhoeae pose an important public-health issue. The integration of genomic, phenotypic and epidemiological data to monitor Neisseria gonorrhoeae fosters our understanding of the emergence and spread of AMR in Neisseria gonorrhoeae and helps to inform therapy guidelines and intervention strategies. Thus, the Gonococcal resistance surveillance (Go-Surv-AMR) was implemented at the Robert Koch Institute in Germany in 2021 to obtain molecular, phenotypic and epidemiological data on Neisseria gonorrhoeae isolated in Germany. Here, we describe the structure and aims of Go-Surv-AMR. Furthermore, we point out future directions of Go-Surv-AMR to improve the integrated genomic surveillance of Neisseria gonorrhoeae. In this context we discuss current and prospective sequencing approaches and the information derived from their application. Moreover, we highlight the importance of combining phenotypic and WGS data to monitor the evolution of AMR in Neisseria gonorrhoeae in Germany. The implementation and constant development of techniques and tools to improve the genomic surveillance of Neisseria gonorrhoeae will be important in coming years.
Collapse
Affiliation(s)
- Kathleen Klaper
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Hana Tlapák
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany
| | - Regina Selb
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Klaus Jansen
- Department of Infectious Disease Epidemiology, Unit 34 `'HIV/AIDS, STI and Blood-borne Infections´, Robert Koch Institute, Berlin, Germany
| | - Dagmar Heuer
- Department Infectious Diseases, Unit 18 `Sexually transmitted bacterial pathogens and HIV´, Robert Koch Institute, Berlin, Germany.
| |
Collapse
|
18
|
Padhi AK, Maurya S. Uncovering the secrets of resistance: An introduction to computational methods in infectious disease research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:173-220. [PMID: 38448135 DOI: 10.1016/bs.apcsb.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Antimicrobial resistance (AMR) is a growing global concern with significant implications for infectious disease control and therapeutics development. This chapter presents a comprehensive overview of computational methods in the study of AMR. We explore the prevalence and statistics of AMR, underscoring its alarming impact on public health. The role of AMR in infectious disease outbreaks and its impact on therapeutics development are discussed, emphasizing the need for novel strategies. Resistance mutations are pivotal in AMR, enabling pathogens to evade antimicrobial treatments. We delve into their importance and contribution to the spread of AMR. Experimental methods for quantitatively evaluating resistance mutations are described, along with their limitations. To address these challenges, computational methods provide promising solutions. We highlight the advantages of computational approaches, including rapid analysis of large datasets and prediction of resistance profiles. A comprehensive overview of computational methods for studying AMR is presented, encompassing genomics, proteomics, structural bioinformatics, network analysis, and machine learning algorithms. The strengths and limitations of each method are briefly outlined. Additionally, we introduce ResScan-design, our own computational method, which employs a protein (re)design protocol to identify potential resistance mutations and adaptation signatures in pathogens. Case studies are discussed to showcase the application of ResScan in elucidating hotspot residues, understanding underlying mechanisms, and guiding the design of effective therapies. In conclusion, we emphasize the value of computational methods in understanding and combating AMR. Integration of experimental and computational approaches can expedite the discovery of innovative antimicrobial treatments and mitigate the threat posed by AMR.
Collapse
Affiliation(s)
- Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.
| | - Shweata Maurya
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| |
Collapse
|
19
|
Benvenga V, Cuénod A, Purushothaman S, Dasen G, Weisser M, Bassetti S, Roloff T, Siegemund M, Heininger U, Bielicki J, Wehrli M, Friderich P, Frei R, Widmer A, Herzog K, Fankhauser H, Nolte O, Bodmer T, Risch M, Dubuis O, Pranghofer S, Calligaris-Maibach R, Graf S, Perreten V, Seth-Smith HMB, Egli A. Historic methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection. Genome Med 2024; 16:23. [PMID: 38317199 PMCID: PMC10840241 DOI: 10.1186/s13073-024-01292-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes. METHODS We accessed 451 historic (1965-1987) MRSA isolates stored in the Culture Collection of Switzerland, mostly collected from the Zurich region. We determined phenotypic antimicrobial resistance (AMR) and performed whole genome sequencing (WGS) using Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international assemblies from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes. RESULTS Among the 451 historic Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-III. Early MRSA were predominantly from clonal complex (CC)8. From 1980 to the end of the twentieth century, we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally. CONCLUSIONS The combined analysis of 1761 historic and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss-German and international MRSA across time.
Collapse
Affiliation(s)
- Vanni Benvenga
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
| | - Srinithi Purushothaman
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
| | | | - Maja Weisser
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Stefano Bassetti
- Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, Lausanne, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Martin Siegemund
- Intensive Care Medicine, University Hospital Basel, Basel, Switzerland
| | - Ulrich Heininger
- Infectious Diseases and Hospital Epidemiology, University of Basel Children's Hospital, Basel, Switzerland
| | - Julia Bielicki
- Infectious Diseases and Hospital Epidemiology, University of Basel Children's Hospital, Basel, Switzerland
| | - Marianne Wehrli
- Microbiology Department, Hospital of Schaffhausen, Schaffhausen, Switzerland
| | - Paul Friderich
- Medicinal microbiology department, Hospital of Lucerne, Lucerne, Switzerland
| | - Reno Frei
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Andreas Widmer
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Kathrin Herzog
- Clinical Microbiology, Cantonal Hospital Thurgau, Münsterlingen, Switzerland
| | - Hans Fankhauser
- Clinical Microbiology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Oliver Nolte
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
- Clinical Microbiology, Zentrum für Labormedizin St, Gallen, St. Gallen, Switzerland
| | | | | | - Olivier Dubuis
- Clinical Microbiology, Viollier AG, Allschwil, Switzerland
| | | | | | - Susanne Graf
- Clinical Microbiology, Cantonal Hospital Basellandschaft, Liestal, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
- Swiss Pathogen Surveillance Platform (SPSP), Lausanne, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland
- Swiss Institute of Bioinformatics, University of Basel, Lausanne, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, Zurich, 8006, Switzerland.
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.
- Swiss Pathogen Surveillance Platform (SPSP), Lausanne, Switzerland.
| |
Collapse
|
20
|
Chen J, Zhong J, Chang Y, Zhou Y, Koo SH, Tan TY, Lei H, Ai Y. Rapid and Accurate Antimicrobial Susceptibility Testing Using Label-Free Electrical Impedance-Based Microfluidic Platform. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2303352. [PMID: 37794624 DOI: 10.1002/smll.202303352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/01/2023] [Indexed: 10/06/2023]
Abstract
Antimicrobial resistance has become a serious threat to the global public health. Accurate and rapid antimicrobial susceptibility testing (AST) allows evidence-based prescribing of antibiotics to improve patient care and clinical outcomes. Current culture-based AST assays are inherently limited by the doubling time of bacterial reproduction, which require at least 24 h to have a decisive result. Herein, a label-free electrical impedance-based microfluidic platform designed to expedite and streamline AST procedure for clinical practice is presented. Following a 30-min exposure of bacterial samples to antibiotics, the presented high-throughput, single-bacterium level impedance characterization platform enables a rapid 2-min AST assay. The platform facilitates accurate analysis of individual bacterial viability, as indicated by changes in electrical characteristics, thereby enabling the determination of antimicrobial resistance. Moreover, the potential clinical applicability of this platform is demonstrated by testing different E. coli strains against five antibiotics, yielding 100% categorical agreements compared to standard culture methods.
Collapse
Affiliation(s)
- Jiahong Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety/National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Yifu Chang
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Avenida da Universidade, Taipa, Macau, 999078, China
| | - Yinning Zhou
- Joint Key Laboratory of the Ministry of Education, Institute of Applied Physics and Materials Engineering, University of Macau, Avenida da Universidade, Taipa, Macau, 999078, China
| | - Seok Hwee Koo
- Department of Laboratory Medicine, Changi General Hospital, Singapore, 529889, Singapore
| | - Thean Yen Tan
- Department of Laboratory Medicine, Changi General Hospital, Singapore, 529889, Singapore
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety/National-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, College of Food Science, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| |
Collapse
|
21
|
Nagel OG, Gasparotti ML, Machado SI, Althaus RL. Similarities of Geobacillus bacteria based on their profiles of antimicrobial susceptibility in milk samples. Rev Argent Microbiol 2024; 56:102-111. [PMID: 37704517 DOI: 10.1016/j.ram.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/29/2023] [Accepted: 07/03/2023] [Indexed: 09/15/2023] Open
Abstract
The genus Geobacillus is composed of thermophilic bacteria that exhibit diverse biotechnological potentialities. Specifically, Geobacillus stearothermophilus is included as a test bacterium in commercial microbiological inhibition methods, although it exhibits limited sensitivity to aminoglycosides, macrolides, and quinolones. Therefore, this article evaluates the antibiotic susceptibility profiles of five test bacteria (G. stearothermophilus subsp. calidolactis C953, Geobacillus thermocatenulatus LMG 19007, Geobacillus thermoleovorans LMG 9823, Geobacillus kaustophilus DSM 7263 and Geobacillus vulcani 13174). For that purpose, the minimum inhibitory concentrations (MICs) of 21 antibiotics were determined in milk samples for five test bacteria using the radial diffusion microbiological inhibition method. Subsequently, the similarities between bacteria and antibiotics were analyzed using cluster analysis. The dendrogram of this multivariate analysis shows an association between a group formed by G. thermocatenulatus and G. stearothermophilus and another by G. thermoleovorans, G. kaustophilus and G. vulcani. Finally, future microbiological methods could be developed in microtiter plates using G. thermocatenulatus as test bacterium, as it exhibits similar sensitivities to G. stearothermophilus. Conversely, G. vulcani, G. thermoleovorans and G. kaustophilus show higher MICs than G. thermocatenulatus.
Collapse
Affiliation(s)
- Orlando G Nagel
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina
| | - Maria L Gasparotti
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina
| | - Selva I Machado
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina
| | - Rafael L Althaus
- Facultad de Ciencias Veterinarias, Universidad Nacional del Litoral, R.P.L. Kreder 2805, 3080 Esperanza, Argentina.
| |
Collapse
|
22
|
Coenye T. Biofilm antimicrobial susceptibility testing: where are we and where could we be going? Clin Microbiol Rev 2023; 36:e0002423. [PMID: 37812003 PMCID: PMC10732061 DOI: 10.1128/cmr.00024-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/27/2023] [Indexed: 10/10/2023] Open
Abstract
Our knowledge about the fundamental aspects of biofilm biology, including the mechanisms behind the reduced antimicrobial susceptibility of biofilms, has increased drastically over the last decades. However, this knowledge has so far not been translated into major changes in clinical practice. While the biofilm concept is increasingly on the radar of clinical microbiologists, physicians, and healthcare professionals in general, the standardized tools to study biofilms in the clinical microbiology laboratory are still lacking; one area in which this is particularly obvious is that of antimicrobial susceptibility testing (AST). It is generally accepted that the biofilm lifestyle has a tremendous impact on antibiotic susceptibility, yet AST is typically still carried out with planktonic cells. On top of that, the microenvironment at the site of infection is an important driver for microbial physiology and hence susceptibility; but this is poorly reflected in current AST methods. The goal of this review is to provide an overview of the state of the art concerning biofilm AST and highlight the knowledge gaps in this area. Subsequently, potential ways to improve biofilm-based AST will be discussed. Finally, bottlenecks currently preventing the use of biofilm AST in clinical practice, as well as the steps needed to get past these bottlenecks, will be discussed.
Collapse
Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
23
|
Kahlmeter G, Turnidge J. Wild-type distributions of minimum inhibitory concentrations and epidemiological cut-off values-laboratory and clinical utility. Clin Microbiol Rev 2023; 36:e0010022. [PMID: 38038445 PMCID: PMC10732016 DOI: 10.1128/cmr.00100-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
The characterization of wild-type minimum inhibitory concentration (MIC) and zone diameter distributions with the setting of epidemiological cut-off values (ECOFFs or ECVs) provides a reference for the otherwise relative MIC values in the international system for antimicrobial susceptibility testing. Distributions of MIC values for a species and an agent follow a log-normal distribution, which in the absence of resistance mechanisms is monomodal and designated wild type (WT). The upper end of the WT distribution, the ECOFF, can be identified with statistical methods. In the presence of phenotypically detectable resistance, the distribution has at least one more mode (the non-WT), but despite this, the WT is most often identifiable using the same methods. The ECOFF provides the most sensitive measure of resistance development in a species against an agent. The WT and non-WT modes are independent of the organism´s response to treatment, but when the European Committee on Antimicrobial Susceptibility Testing (EUCAST) determines the clinical breakpoints, the committee avoids breakpoints that split WT distributions of target species. This is to avoid the poorer reproducibility of susceptibility categorization when breakpoints split major populations but also because the EUCAST has failed to identify different clinical outcomes for isolates with different MIC values inside the wild-type distribution. In laboratory practice, the ECOFF is used to screen for and exclude resistance and allows the comparison of resistance between systems with different breakpoints from different breakpoint organizations, breakpoints evolving over time, and different breakpoints between human and animal medicine. The EUCAST actively encourages colleagues to question MIC distributions as presented on the website (https://www.eucast.org/mic_and_zone_distributions_and_ecoffs) and to contribute MIC and inhibition zone diameter data.
Collapse
Affiliation(s)
- Gunnar Kahlmeter
- Technical Data Coordinator of the European Committee on Antimicrobial Susceptibility Testing (EUCAST), Växjö, Sweden
- Head of the Swedish Reference Laboratory for phenotypic susceptibility testing, Växjö, Sweden
- Head of the EUCAST Development Laboratory, Växjö, Sweden
| | - John Turnidge
- Document and Technical Support to the European Committee on Antimicrobial Susceptibility Testing (EUCAST), Växjö, Sweden
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
| |
Collapse
|
24
|
Sapula SA, Amsalu A, Whittall JJ, Hart BJ, Siderius NL, Nguyen L, Gerber C, Turnidge J, Venter H. The scope of antimicrobial resistance in residential aged care facilities determined through analysis of Escherichia coli and the total wastewater resistome. Microbiol Spectr 2023; 11:e0073123. [PMID: 37787536 PMCID: PMC10715142 DOI: 10.1128/spectrum.00731-23] [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: 02/16/2023] [Accepted: 08/07/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Antimicrobial resistance (AMR) is a global threat that imposes a heavy burden on our health and economy. Residential aged care facilities (RACFs), where frequent inappropriate antibiotic use creates a selective environment that promotes the development of bacterial resistance, significantly contribute to this problem. We used wastewater-based epidemiology to provide a holistic whole-facility assessment and comparison of antimicrobial resistance in two RACFs and a retirement village. Resistant Escherichia coli, a common and oftentimes problematic pathogen within RACFs, was isolated from the wastewater, and the phenotypic and genotypic AMR was determined for all isolates. We observed a high prevalence of an international high-risk clone, carrying an extended-spectrum beta-lactamase in one facility. Analysis of the entire resistome also revealed a greater number of mobile resistance genes in this facility. Finally, both facilities displayed high fluoroquinolone resistance rates-a worrying trend seen globally despite measures in place aimed at limiting their use.
Collapse
Affiliation(s)
- Sylvia A. Sapula
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Anteneh Amsalu
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Department of Medical Microbiology, University of Gondar, Gondar, Ethiopia
| | - Jon J. Whittall
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Bradley J. Hart
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Naomi L. Siderius
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Lynn Nguyen
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Cobus Gerber
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - John Turnidge
- Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Henrietta Venter
- Health and Biomedical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| |
Collapse
|
25
|
Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, Midega JT, Feasey NA, Peacock SJ. Genomics for public health and international surveillance of antimicrobial resistance. THE LANCET. MICROBE 2023; 4:e1047-e1055. [PMID: 37977162 DOI: 10.1016/s2666-5247(23)00283-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Historically, epidemiological investigation and surveillance for bacterial antimicrobial resistance (AMR) has relied on low-resolution isolate-based phenotypic analyses undertaken at local and national reference laboratories. Genomic sequencing has the potential to provide a far more high-resolution picture of AMR evolution and transmission, and is already beginning to revolutionise how public health surveillance networks monitor and tackle bacterial AMR. However, the routine integration of genomics in surveillance pipelines still has considerable barriers to overcome. In 2022, a workshop series and online consultation brought together international experts in AMR and pathogen genomics to assess the status of genomic applications for AMR surveillance in a range of settings. Here we focus on discussions around the use of genomics for public health and international AMR surveillance, noting the potential advantages of, and barriers to, implementation, and proposing recommendations from the working group to help to drive the adoption of genomics in public health AMR surveillance. These recommendations include the need to build capacity for genome sequencing and analysis, harmonising and standardising surveillance systems, developing equitable data sharing and governance frameworks, and strengthening interactions and relationships among stakeholders at multiple levels.
Collapse
Affiliation(s)
- Kate S Baker
- Department for Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Katie L Hopkins
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, UK; Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - Leonor Sánchez-Busó
- Genomics and Health Area, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO-Public Health), Valencia, Spain; CIBERESP, ISCIII, Madrid, Spain
| | - Maria Getino
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Benjamin P Howden
- The Centre for Pathogen Genomics, Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Lillian A Musila
- Department of Emerging Infectious Diseases, United States Army Medical Research Directorate - Africa, Nairobi, Kenya; Kenya Medical Research Institute, Nairobi, Kenya
| | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Daniel G Amoako
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa; School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Nuffield Department of Medicine, University of Oxford, Big Data Institute, Oxford, UK
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana, West Africa
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Malawi
| | | |
Collapse
|
26
|
Davies TJ, Swann J, Sheppard AE, Pickford H, Lipworth S, AbuOun M, Ellington MJ, Fowler PW, Hopkins S, Hopkins KL, Crook DW, Peto TEA, Anjum MF, Walker AS, Stoesser N. Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli. Microb Genom 2023; 9:001151. [PMID: 38100178 PMCID: PMC10763500 DOI: 10.1099/mgen.0.001151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Several bioinformatics genotyping algorithms are now commonly used to characterize antimicrobial resistance (AMR) gene profiles in whole-genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking. Here, we used both simulated datasets and a large set of real E. coli WGS data (n=1818 isolates) to systematically investigate genotyping methods in greater detail. Simulated constructs and real sequences were processed using four different bioinformatic programs (ABRicate, ARIBA, KmerResistance and SRST2, run with the ResFinder database) and their outputs compared. For simulation tests where 3079 AMR gene variants were inserted into random sequence constructs, KmerResistance was correct for 3076 (99.9 %) simulations, ABRicate for 3054 (99.2 %), ARIBA for 2783 (90.4 %) and SRST2 for 2108 (68.5 %). For simulation tests where two closely related gene variants were inserted into random sequence constructs, KmerResistance identified the correct alleles in 35 338/46 318 (76.3 %) simulations, ABRicate identified them in 11 842/46 318 (25.6 %) simulations, ARIBA identified them in 1679/46 318 (3.6 %) simulations and SRST2 identified them in 2000/46 318 (4.3 %) simulations. In real data, across all methods, 1392/1818 (76 %) isolates had discrepant allele calls for at least 1 gene. In addition to highlighting areas for improvement in challenging scenarios, (e.g. identification of AMR genes at <10× coverage, identifying multiple closely related AMR genes present in the same sample), our evaluations identified some more systematic errors that could be readily soluble, such as repeated misclassification (i.e. naming) of genes as shorter variants of the same gene present within the reference resistance gene database. Such naming errors accounted for at least 2530/4321 (59 %) of the discrepancies seen in real data. Moreover, many of the remaining discrepancies were likely 'artefactual', with reporting of cut-off differences accounting for at least 1430/4321 (33 %) discrepants. Whilst we found that comparing outputs generated by running multiple algorithms on the same dataset could identify and resolve these algorithmic artefacts, the results of our evaluations emphasize the need for developing new and more robust genotyping algorithms to further improve accuracy and performance.
Collapse
Affiliation(s)
- Timothy J. Davies
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Hayleigh Pickford
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Samuel Lipworth
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Manal AbuOun
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J. Ellington
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | | | - Susan Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Division, UK Health Security Agency, London, UK
| | - Katie L. Hopkins
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- HCAI, Fungal, AMR, AMU and Sepsis Division, UK Health Security Agency, London, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy E. A. Peto
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Muna F. Anjum
- Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, Oxford University, Oxford, UK
- National Institute for Health Research (NIHR) Health Protection Research Unit on Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| |
Collapse
|
27
|
Ghielmetti G, Loubser J, Kerr TJ, Stuber T, Thacker T, Martin LC, O'Hare MA, Mhlophe SK, Okunola A, Loxton AG, Warren RM, Moseley MH, Miller MA, Goosen WJ. Advancing animal tuberculosis surveillance using culture-independent long-read whole-genome sequencing. Front Microbiol 2023; 14:1307440. [PMID: 38075895 PMCID: PMC10699144 DOI: 10.3389/fmicb.2023.1307440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 02/12/2024] Open
Abstract
Animal tuberculosis is a significant infectious disease affecting both livestock and wildlife populations worldwide. Effective disease surveillance and characterization of Mycobacterium bovis (M. bovis) strains are essential for understanding transmission dynamics and implementing control measures. Currently, sequencing of genomic information has relied on culture-based methods, which are time-consuming, resource-demanding, and concerning in terms of biosafety. This study explores the use of culture-independent long-read whole-genome sequencing (WGS) for a better understanding of M. bovis epidemiology in African buffaloes (Syncerus caffer). By comparing two sequencing approaches, we evaluated the efficacy of Illumina WGS performed on culture extracts and culture-independent Oxford Nanopore adaptive sampling (NAS). Our objective was to assess the potential of NAS to detect genomic variants without sample culture. In addition, culture-independent amplicon sequencing, targeting mycobacterial-specific housekeeping and full-length 16S rRNA genes, was applied to investigate the presence of microorganisms, including nontuberculous mycobacteria. The sequencing quality obtained from DNA extracted directly from tissues using NAS is comparable to the sequencing quality of reads generated from culture-derived DNA using both NAS and Illumina technologies. We present a new approach that provides complete and accurate genome sequence reconstruction, culture independently, and using an economically affordable technique.
Collapse
Affiliation(s)
- Giovanni Ghielmetti
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Johannes Loubser
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tanya J. Kerr
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Tyler Thacker
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, United States
| | - Lauren C. Martin
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michaela A. O'Hare
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Sinegugu K. Mhlophe
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Abisola Okunola
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre G. Loxton
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mark H. Moseley
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Michele A. Miller
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wynand J. Goosen
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
28
|
Bianconi I, Aschbacher R, Pagani E. Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology. Antibiotics (Basel) 2023; 12:1580. [PMID: 37998782 PMCID: PMC10668849 DOI: 10.3390/antibiotics12111580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023] Open
Abstract
Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.
Collapse
Affiliation(s)
- Irene Bianconi
- Laboratory of Microbiology and Virology, Provincial Hospital of Bolzano (SABES-ASDAA), Lehrkrankenhaus der Paracelsus Medizinischen Privatuniversitätvia Amba Alagi 5, 39100 Bolzano, Italy; (R.A.); (E.P.)
| | | | | |
Collapse
|
29
|
Bessa LJ, Shaaban M, Aminov R. Editorial: Insights in antimicrobials, resistance & chemotherapy: 2022. Front Microbiol 2023; 14:1310156. [PMID: 37928656 PMCID: PMC10622649 DOI: 10.3389/fmicb.2023.1310156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Affiliation(s)
- Lucinda J. Bessa
- Egas Moniz Center for Interdisciplinary Research (CiiEM), Egas Moniz School of Health and Science, Almada, Portugal
| | - Mona Shaaban
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Rustam Aminov
- The School of Medicine, Medical Sciences, and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| |
Collapse
|
30
|
Eladawy M, Thomas JC, Hoyles L. Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital. Microb Genom 2023; 9:001125. [PMID: 37902186 PMCID: PMC10634444 DOI: 10.1099/mgen.0.001125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, and Pseudomonas aeruginosa is a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31 P. aeruginosa isolates recovered from CAUTIs in an Egyptian hospital over a 3 month period. Genomes of isolates were of good quality and were confirmed to be P. aeruginosa by comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which ST357 and ST773 are considered to be high-risk clones. Antimicrobial resistance (AMR) testing according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines showed that the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)] and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422 938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms and were predicted to encode virulence genes associated with adherence, antimicrobial activity, anti-phagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles of P. aeruginosa contributing to CAUTIs in Egypt.
Collapse
Affiliation(s)
- Mohamed Eladawy
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Jonathan C. Thomas
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| |
Collapse
|
31
|
Uhland FC, Li XZ, Mulvey MR, Reid-Smith R, Sherk LM, Ziraldo H, Jin G, Young KM, Reist M, Carson CA. Extended Spectrum β-Lactamase-Producing Enterobacterales of Shrimp and Salmon Available for Purchase by Consumers in Canada-A Risk Profile Using the Codex Framework. Antibiotics (Basel) 2023; 12:1412. [PMID: 37760708 PMCID: PMC10525137 DOI: 10.3390/antibiotics12091412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
The extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-EB) encompass several important human pathogens and are found on the World Health Organization (WHO) priority pathogens list of antibiotic-resistant bacteria. They are a group of organisms which demonstrate resistance to third-generation cephalosporins (3GC) and their presence has been documented worldwide, including in aquaculture and the aquatic environment. This risk profile was developed following the Codex Guidelines for Risk Analysis of Foodborne Antimicrobial Resistance with the objectives of describing the current state of knowledge of ESBL-EB in relation to retail shrimp and salmon available to consumers in Canada, the primary aquacultured species consumed in Canada. The risk profile found that Enterobacterales and ESBL-EB have been found in multiple aquatic environments, as well as multiple host species and production levels. Although the information available did not permit the conclusion as to whether there is a human health risk related to ESBLs in Enterobacterales in salmon and shrimp available for consumption by Canadians, ESBL-EB in imported seafood available at the retail level in Canada have been found. Surveillance activities to detect ESBL-EB in seafood are needed; salmon and shrimp could be used in initial surveillance activities, representing domestic and imported products.
Collapse
Affiliation(s)
- F. Carl Uhland
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Xian-Zhi Li
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Michael R. Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Richard Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Lauren M. Sherk
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Hilary Ziraldo
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Grace Jin
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| | - Kaitlin M. Young
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Mark Reist
- Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Carolee A. Carson
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON N1H 7M7, Canada
| |
Collapse
|
32
|
Mentasti M, David S, Turton J, Morgan M, Turner L, Westlake J, Jenkins J, Williams C, Rey S, Watkins J, Daniel V, Mitchell S, Forbes G, Wootton M, Jones L. Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK. Microb Genom 2023; 9:001104. [PMID: 37668148 PMCID: PMC10569728 DOI: 10.1099/mgen.0.001104] [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: 05/20/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023] Open
Abstract
A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla SHV-232, bla TEM-1, bla CTX-M-15 and bla OXA-1 were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla OXA-48 carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists.
Collapse
Affiliation(s)
- Massimo Mentasti
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, OX3 7LF, UK
| | - Jane Turton
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, NW9 5HT, UK
| | - Mari Morgan
- Healthcare Associated Infection, Antimicrobial Resistance Prescribing Programme, Public Health Wales Health Protection, Cardiff, CF10 4BZ, UK
| | - Luke Turner
- Bacteriology Department, Public Health Wales Microbiology, Swansea, SA2 8QA, UK
| | - Joseph Westlake
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Jonathan Jenkins
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Catie Williams
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Sara Rey
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Joanne Watkins
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Victoria Daniel
- Bacteriology Department, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Shanine Mitchell
- Bacteriology Department, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Gavin Forbes
- Bacteriology Department, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Lim Jones
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| |
Collapse
|
33
|
Chung HC, Foxx CL, Hicks JA, Stuber TP, Friedberg I, Dorman KS, Harris B. An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species. PLoS One 2023; 18:e0290473. [PMID: 37616210 PMCID: PMC10449230 DOI: 10.1371/journal.pone.0290473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.
Collapse
Affiliation(s)
- Henri C. Chung
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
| | - Christine L. Foxx
- Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States of America
| | - Jessica A. Hicks
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
| | - Tod P. Stuber
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States of America
| | - Karin S. Dorman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States of America
- Department of Statistics, Iowa State University, Ames, IA, United States of America
| | - Beth Harris
- National Animal Health Laboratory Network, National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA, United States of America
| |
Collapse
|
34
|
Zavišić G, Popović M, Stojkov S, Medić D, Gusman V, Jovanović Lješković N, Jovanović Galović A. Antibiotic Resistance and Probiotics: Knowledge Gaps, Market Overview and Preliminary Screening. Antibiotics (Basel) 2023; 12:1281. [PMID: 37627701 PMCID: PMC10451169 DOI: 10.3390/antibiotics12081281] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
Probiotics are among those products, the use of which is increasing, and they are available primarily as food/dietary supplements, as well as in the form of medicines. This study aims to assess the attitudes and practices of health professionals and students of health sciences, give a short overview of the probiotics currently on the market, and conduct a screening of five food supplements and one drug with respect to antibiotic resistance. Nearly half of the respondents in our survey state that probiotics have no side effects, while only 6.3% believe that the use of probiotics can lead to antibiotic resistance. In addition, more than 40% of the participants throw unused probiotics into municipal waste. The market analysis results indicate that probiotic products on the Serbian market have highly variable CFU counts, while the declared health claims cover numerous beneficial health effects, and they are sometimes even registered as medicines. Lactobacilli are frequently present in probiotic supplements, and are sold in pharmacies and online. The experimental results showed that antibiotic resistance is present in different types of lactobacilli in probiotic products. The risk of using probiotics, regardless of their beneficial health effects, should be taken into account in the future. An update to the regulations governing probiotics, including a stipulation for antimicrobial resistance (AMR) testing, should be established, and guidelines for their proper use and disposal put into place.
Collapse
Affiliation(s)
- Gordana Zavišić
- Faculty of Pharmacy Novi Sad, University Business Academy, Trg Mladenaca 5, 21000 Novi Sad, Serbia; (G.Z.); (S.S.); (N.J.L.)
| | - Milka Popović
- Department of Hygiene, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia;
- Center for Hygiene and Human Ecology, Institute of Public Health of Vojvodina, Futoška 121, 21000 Novi Sad, Serbia;
| | - Svetlana Stojkov
- Faculty of Pharmacy Novi Sad, University Business Academy, Trg Mladenaca 5, 21000 Novi Sad, Serbia; (G.Z.); (S.S.); (N.J.L.)
- College of Vocational Studies for the Education of Preschool Teachers and Sports Trainers in Subotica, Banijska 67, 24000 Subotica, Serbia
| | - Deana Medić
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia;
- Center for Microbiology, Institute of Public Health of Vojvodina, Futoška 121, 21000 Novi Sad, Serbia
| | - Vera Gusman
- Center for Hygiene and Human Ecology, Institute of Public Health of Vojvodina, Futoška 121, 21000 Novi Sad, Serbia;
- Department of Microbiology, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21000 Novi Sad, Serbia;
| | - Nataša Jovanović Lješković
- Faculty of Pharmacy Novi Sad, University Business Academy, Trg Mladenaca 5, 21000 Novi Sad, Serbia; (G.Z.); (S.S.); (N.J.L.)
| | - Aleksandra Jovanović Galović
- Faculty of Pharmacy Novi Sad, University Business Academy, Trg Mladenaca 5, 21000 Novi Sad, Serbia; (G.Z.); (S.S.); (N.J.L.)
| |
Collapse
|
35
|
Kristensen T, Sørensen LH, Pedersen SK, Jensen JD, Mordhorst H, Lacy-Roberts N, Lukjancenko O, Luo Y, Hoffmann M, Hendriksen RS. Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities. Microb Genom 2023; 9:mgen001076. [PMID: 37526643 PMCID: PMC10483428 DOI: 10.1099/mgen.0.001076] [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: 03/22/2023] [Accepted: 07/05/2023] [Indexed: 08/02/2023] Open
Abstract
The global surveillance and outbreak investigation of antimicrobial resistance (AMR) is amidst a paradigm shift from traditional biology to bioinformatics. This is due to developments in whole-genome-sequencing (WGS) technologies, bioinformatics tools, and reduced costs. The increased use of WGS is accompanied by challenges such as standardization, quality control (QC), and data sharing. Thus, there is global need for inter-laboratory WGS proficiency test (PT) schemes to evaluate laboratories' capacity to produce reliable genomic data. Here, we present the results of the first iteration of the Genomic PT (GPT) organized by the Global Capacity Building Group at the Technical University of Denmark in 2020. Participating laboratories sequenced two isolates and corresponding DNA of Salmonella enterica, Escherichia coli and Campylobacter coli, using WGS methodologies routinely employed at their laboratories. The participants' ability to obtain consistently good-quality WGS data was assessed based on several QC WGS metrics. A total of 21 laboratories from 21 European countries submitted WGS and meta-data. Most delivered high-quality sequence data with only two laboratories identified as overall underperforming. The QC metrics, N50 and number of contigs, were identified as good indicators for high-sequencing quality. We propose QC thresholds for N50 greater than 20 000 and 25 000 for Campylobacter coli and Escherichia coli, respectively, and number of contigs >200 bp greater than 225, 265 and 100 for Salmonella enterica, Escherichia coli and Campylobacter coli, respectively. The GPT2020 results confirm the importance of systematic QC procedures, ensuring the submission of reliable WGS data for surveillance and outbreak investigation to meet the requirements of the paradigm shift in methodology.
Collapse
Affiliation(s)
- Thea Kristensen
- National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Plant and Environmental Sciences, Section for Organismal Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Lauge Holm Sørensen
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Susanne Karlsmose Pedersen
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jacob Dyring Jensen
- National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hanne Mordhorst
- National Food Institute, Research Group of Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Niamh Lacy-Roberts
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Yan Luo
- Center for Food and Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Maria Hoffmann
- Center for Food and Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Rene S. Hendriksen
- National Food Institute, Research Group of Global Capacity Building, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
36
|
Ortega-Sanz I, Barbero-Aparicio JA, Canepa-Oneto A, Rovira J, Melero B. CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter. BMC Bioinformatics 2023; 24:291. [PMID: 37474912 PMCID: PMC10357626 DOI: 10.1186/s12859-023-05414-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge. RESULTS To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation. CONCLUSIONS The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .
Collapse
Affiliation(s)
- Irene Ortega-Sanz
- Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain
| | | | | | - Jordi Rovira
- Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain
| | - Beatriz Melero
- Department of Biotechnology and Food Science, University of Burgos, 09006, Burgos, Spain.
| |
Collapse
|
37
|
Maganga R, Sindiyo E, Musyoki VM, Shirima G, Mmbaga BT. Comparative analysis of clinical breakpoints, normalized resistance interpretation and epidemiological cut-offs in interpreting antimicrobial resistance of Escherichia coli isolates originating from poultry in different farm types in Tanzania. Access Microbiol 2023; 5:acmi000540.v4. [PMID: 37601443 PMCID: PMC10436012 DOI: 10.1099/acmi.0.000540.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 06/13/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance (AMR) data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is a need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation. Gap statement There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs (ECOFFs) and normalized resistance interpretation (NRI) breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries. Aim The aim of this study was to compare antimicrobial resistance in Escherichia coli isolates using ECOFFs, CLSI and NRI breakpoints. Methodology A total of 59 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA PCR. Kirby Bauer disc diffusion was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI and NRI bespoke breakpoints were used for resistance interpretation. Results According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8 -69.5 %), than those for ciprofloxacin (CIPRO) (18.6 -32.2 %), imipenem (IMI) (3.4 -35 %) and ceftazidime (CEF) (1.7 -45.8 %). Prevalence estimates of AMR using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7 % CB and 1.7 % COWT), IMI (3.4 % CB and 4.0 % COWT) and TET (67.8 % CB and 69.5 % COWT). However, with ECOFFs, AMR estimates for CEF, IMI and CIP were significantly higher (45.8, 35.6 and 64.4 %, respectively; P<0.05). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2 % CB, 64.4 % ECOFFs and 18.6 % COWT, P<0.05). Conclusion AMR interpretation is influenced by the breakpoint used, necessitating further standardization, especially for microbiological breakpoints, in order to harmonize outputs. The AMR ECOFF estimates in the present study were significantly higher compared to CLSI and NRI.
Collapse
Affiliation(s)
- Ruth Maganga
- University of Birmingham, Birmingham, B15 2TT, UK
- University of Glasgow, Glasgow, G12 8QQ, UK
- Kilimanjaro Christian Medical Center/Kilimanjaro Clinical Research Institute, PO Box 2236, Moshi, Tanzania
| | - Emmanuel Sindiyo
- The Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - Victor Moses Musyoki
- Department of Medical Microbiology, University of Nairobi, PO Box 19676-00202, Nairobi, Kenya
| | - Gabriel Shirima
- The Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Christian Medical Center/Kilimanjaro Clinical Research Institute, PO Box 2236, Moshi, Tanzania
| |
Collapse
|
38
|
Abraham R, Allison HS, Lee T, Pavic A, Chia R, Hewson K, Lee ZZ, Hampson DJ, Jordan D, Abraham S. A national study confirms that Escherichia coli from Australian commercial layer hens remain susceptible to critically important antimicrobials. PLoS One 2023; 18:e0281848. [PMID: 37418382 PMCID: PMC10328298 DOI: 10.1371/journal.pone.0281848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Controlling the use of the most critically important antimicrobials (CIAs) in food animals has been identified as one of the key measures required to curb the transmission of antimicrobial resistant bacteria from animals to humans. Expanding the evidence demonstrating the effectiveness of restricting CIA usage for preventing the emergence of resistance to key drugs amongst commensal organisms in animal production would do much to strengthen international efforts to control antimicrobial resistance (AMR). As Australia has strict controls on antimicrobial use in layer hens, and internationally comparatively low levels of poultry disease due to strict national biosecurity measures, we investigated whether these circumstances have resulted in curtailing development of critical forms of AMR. The work comprised a cross-sectional national survey of 62 commercial layer farms with each assessed for AMR in Escherichia coli isolates recovered from faeces. Minimum inhibitory concentration analysis using a panel of 13 antimicrobials was performed on 296 isolates, with those exhibiting phenotypic resistance to fluoroquinolones (a CIA) or multi-class drug resistance (MCR) subjected to whole genome sequencing. Overall, 53.0% of isolates were susceptible to all antimicrobials tested, and all isolates were susceptible to cefoxitin, ceftiofur, ceftriaxone, chloramphenicol and colistin. Resistance was observed for amoxicillin-clavulanate (9.1%), ampicillin (16.2%), ciprofloxacin (2.7%), florfenicol (2.4%), gentamicin (1.0%), streptomycin (4.7%), tetracycline (37.8%) and trimethoprim/sulfamethoxazole (9.5%). MCR was observed in 21 isolates (7.0%), with two isolates exhibiting resistance to four antimicrobial classes. Whole genome sequencing revealed that ciprofloxacin-resistant (fluoroquinolone) isolates were devoid of both known chromosomal mutations in the quinolone resistance determinant regions and plasmid-mediated quinolone resistance genes (qnr)-other than in one isolate (ST155) which carried the qnrS gene. Two MCR E. coli isolates with ciprofloxacin-resistance were found to be carrying known resistance genes including aadA1, dfrA1, strA, strB, sul1, sul2, tet(A), blaTEM-1B, qnrS1 and tet(A). Overall, this study found that E. coli from layer hens in Australia have low rates of AMR, likely due to strict control on antimicrobial usage achieved by the sum of regulation and voluntary measures.
Collapse
Affiliation(s)
- Rebecca Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Hui San Allison
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Terence Lee
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Anthony Pavic
- Birling Avian Laboratories, Bringelly, New South Wales, Australia
| | - Raymond Chia
- Australian Eggs, North Sydney, New South Wales, Australia
| | - Kylie Hewson
- Sativus Pty Ltd, Beenleigh, Queensland, Australia
| | - Zheng Zhou Lee
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - David J Hampson
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - David Jordan
- New South Wales Department of Primary industries, Wollongbar, New South Wales, Australia
| | - Sam Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| |
Collapse
|
39
|
Doganay MT, Chelliah CJ, Tozluyurt A, Hujer AM, Obaro SK, Gurkan U, Patel R, Bonomo RA, Draz M. 3D Printed Materials for Combating Antimicrobial Resistance. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2023; 67:371-398. [PMID: 37790286 PMCID: PMC10545363 DOI: 10.1016/j.mattod.2023.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Three-dimensional (3D) printing is a rapidly growing technology with a significant capacity for translational applications in both biology and medicine. 3D-printed living and non-living materials are being widely tested as a potential replacement for conventional solutions for testing and combating antimicrobial resistance (AMR). The precise control of cells and their microenvironment, while simulating the complexity and dynamics of an in vivo environment, provides an excellent opportunity to advance the modeling and treatment of challenging infections and other health conditions. 3D-printing models the complicated niches of microbes and host-pathogen interactions, and most importantly, how microbes develop resistance to antibiotics. In addition, 3D-printed materials can be applied to testing and delivering antibiotics. Here, we provide an overview of 3D printed materials and biosystems and their biomedical applications, focusing on ever increasing AMR. Recent applications of 3D printing to alleviate the impact of AMR, including developed bioprinted systems, targeted bacterial infections, and tested antibiotics are presented.
Collapse
Affiliation(s)
- Mert Tunca Doganay
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cyril John Chelliah
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Abdullah Tozluyurt
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | | | - Umut Gurkan
- Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology and Division of Public Health, Infectious Diseases, and Occupational medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA
| | - Mohamed Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH 44106, USA
| |
Collapse
|
40
|
Brouwer MSM, Zandbergen Van Essen A, Kant A, Rapallini M, Harders F, Bossers A, Wullings B, Wit B, Veldman KT. Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat. J Antimicrob Chemother 2023:7185845. [PMID: 37248737 DOI: 10.1093/jac/dkad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted from WGS data. WGS has added value in the wealth of additional information that is present in the data. OBJECTIVES In this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli. METHODS Susceptibility testing was performed with broth microdilution of selectively isolated E. coli. Short-read WGS was performed in parallel and phenotypes predicted based on the sequence data, which was also used to determine the phylogeny of the isolates. RESULTS The phenotypically determined resistance and the predicted resistance correlated 90%-100% for the different antimicrobial classes. Furthermore, clonal relationships were detected amongst ESBL-producing E. coli within livestock sectors and the meat produced by this sector. CONCLUSIONS Further implementation of WGS analysis of ESBL/AmpC-producing E. coli within the AMR monitoring programme of EU member states and global surveillance programmes will contribute to determining the attribution of livestock in the prevalence of ESBL/AmpC-encoding E. coli in humans.
Collapse
Affiliation(s)
- Michael S M Brouwer
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Alieda Zandbergen Van Essen
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Arie Kant
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Michel Rapallini
- Department of Bacteriology, Molecular Biology and AMR, Wageningen Food Safety Research part of Wageningen University and Research, Akkermaalsbos 2, Wageningen, The Netherlands
| | - Frank Harders
- Department of Bioinformatics, Epidemiology and Animal Models, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Alex Bossers
- Department of Bioinformatics, Epidemiology and Animal Models, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Bart Wullings
- Department of Bacteriology, Molecular Biology and AMR, Wageningen Food Safety Research part of Wageningen University and Research, Akkermaalsbos 2, Wageningen, The Netherlands
| | - Ben Wit
- Department of Food Safety, Netherlands Food and Consumer Product Safety Authority (NVWA), Catharijnesingel 59, Utrecht, The Netherlands
| | - Kees T Veldman
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| |
Collapse
|
41
|
Fauzia KA, Alfaray RI, Yamaoka Y. Advantages of Whole Genome Sequencing in Mitigating the Helicobacter pylori Antimicrobial Resistance Problem. Microorganisms 2023; 11:1239. [PMID: 37317213 DOI: 10.3390/microorganisms11051239] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Helicobacter pylori antimicrobial resistance is a critical public health issue. Typically, antimicrobial resistance epidemiology reports include only the antimicrobial susceptibility test results for H. pylori. However, this phenotypic approach is less capable of answering queries related to resistance mechanisms and specific mutations found in particular global regions. Whole genome sequencing can help address these two questions while still offering quality control and is routinely validated against AST standards. A comprehensive understanding of the mechanisms of resistance should improve H. pylori eradication efforts and prevent gastric cancer.
Collapse
Affiliation(s)
- Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya 60115, Indonesia
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu 879-5593, Japan
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya 60115, Indonesia
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030, USA
- Borneo Medical and Health Research Centre, University Malaysia Sabah, Kota Kinabalu, Sabah 88400, Malaysia
- Research Center for Global and Local Infectious Diseases, Oita University, Yufu 879-5593, Japan
| |
Collapse
|
42
|
Kahlmeter G, Turnidge J. The determination of epidemiological cut-off values requires a systematic and joint approach based on quality controlled, non-truncated minimum inhibitory concentration series. Eur Respir J 2023; 61:61/5/2202259. [PMID: 37147008 DOI: 10.1183/13993003.02259-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/26/2023] [Indexed: 05/07/2023]
Affiliation(s)
- Gunnar Kahlmeter
- Department of Clinical Microbiology, Central Hospital, and EUCAST Development Laboratory, Växjö, Sweden
| | - John Turnidge
- School of Biological Sciences and Adelaide Medical School, University of Adelaide, Adelaide, Australia
| |
Collapse
|
43
|
Edalatmand A, McArthur AG. CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database. Database (Oxford) 2023; 2023:7133783. [PMID: 37079891 PMCID: PMC10118295 DOI: 10.1093/database/baad023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/01/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
Scientific literature is published at a rate that makes manual data extraction a highly time-consuming task. The Comprehensive Antibiotic Resistance Database (CARD) utilizes literature to curate information on antimicrobial resistance genes and to enable time-efficient triage of publications we have developed a classification algorithm for identifying publications describing first reports of new resistance genes. Trained on publications contained in the CARD, CARD*Shark downloads, processes and identifies publications recently added to PubMed that should be reviewed by biocurators. With CARD*Shark, we can minimize the monthly scope of articles a biocurator reviews from hundreds of articles to a few dozen, drastically improving the speed of curation while ensuring no relevant publications are overlooked. Database URL http://card.mcmaster.ca.
Collapse
Affiliation(s)
- Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| |
Collapse
|
44
|
Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
| |
Collapse
|
45
|
Casaux ML, D'Alessandro B, Vignoli R, Fraga M. Phenotypic and genotypic survey of antibiotic resistance in Salmonella enterica isolates from dairy farms in Uruguay. Front Vet Sci 2023; 10:1055432. [PMID: 36968467 PMCID: PMC10033963 DOI: 10.3389/fvets.2023.1055432] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella enterica is an important zoonotic pathogen that is frequently identified in dairy farming systems. An increase in antibiotic resistance has led to inadequate results of treatments, with impacts on animal and human health. Here, the phenotypic and genotypic susceptibility patterns of Salmonella isolates from dairy cattle and dairy farm environments were evaluated and compared. A collection of 75 S. enterica isolates were evaluated, and their phenotypic susceptibility was determined. For genotypic characterization, the whole genomes of the isolates were sequenced, and geno-serotypes, sequence types (STs) and core-genome-sequence types were determined using the EnteroBase pipeline. To characterize antibiotic resistance genes and gene mutations, tools from the Center for Genomic Epidemiology were used. Salmonella Dublin (SDu), S. Typhimurium (STy), S. Anatum (SAn), S. Newport (SNe), S. Agona (Sag), S. Montevideo (SMo) and IIIb 61:i:z53 were included in the collection. A single sequence type was detected per serovar. Phenotypic non-susceptibility to streptomycin and tetracycline was very frequent in the collection, and high non-susceptibility to ciprofloxacin was also observed. Multidrug resistance (MDR) was observed in 42 isolates (56.0%), with SAn and STy presenting higher MDR than the other serovars, showing non-susceptibility to up to 6 groups of antibiotics. Genomic analysis revealed the presence of 21 genes associated with antimicrobial resistance (AMR) in Salmonella isolates. More than 60% of the isolates carried some gene associated with resistance to aminoglycosides and tetracyclines. Only one gene associated with beta-lactam resistance was found, in seven isolates. Two different mutations were identified, parC_T57S and acrB_R717Q, which confer resistance to quinolones and azithromycin, respectively. The accuracy of predicting antimicrobial resistance phenotypes based on AMR genotypes was 83.7%. The genomic approach does not replace the phenotypic assay but offers valuable information for the survey of circulating antimicrobial resistance. This work represents one of the first studies evaluating phenotypic and genotypic AMR in Salmonella from dairy cattle in South America.
Collapse
Affiliation(s)
- María Laura Casaux
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- *Correspondence: María Laura Casaux
| | - Bruno D'Alessandro
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Martín Fraga
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- Martín Fraga
| |
Collapse
|
46
|
Peykov S, Strateva T. Whole-Genome Sequencing-Based Resistome Analysis of Nosocomial Multidrug-Resistant Non-Fermenting Gram-Negative Pathogens from the Balkans. Microorganisms 2023; 11:microorganisms11030651. [PMID: 36985224 PMCID: PMC10051916 DOI: 10.3390/microorganisms11030651] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Non-fermenting Gram-negative bacilli (NFGNB), such as Pseudomonas aeruginosa and Acinetobacter baumannii, are among the major opportunistic pathogens involved in the global antibiotic resistance epidemic. They are designated as urgent/serious threats by the Centers for Disease Control and Prevention and are part of the World Health Organization’s list of critical priority pathogens. Also, Stenotrophomonas maltophilia is increasingly recognized as an emerging cause for healthcare-associated infections in intensive care units, life-threatening diseases in immunocompromised patients, and severe pulmonary infections in cystic fibrosis and COVID-19 individuals. The last annual report of the ECDC showed drastic differences in the proportions of NFGNB with resistance towards key antibiotics in different European Union/European Economic Area countries. The data for the Balkans are of particular concern, indicating more than 80% and 30% of invasive Acinetobacter spp. and P. aeruginosa isolates, respectively, to be carbapenem-resistant. Moreover, multidrug-resistant and extensively drug-resistant S. maltophilia from the region have been recently reported. The current situation in the Balkans includes a migrant crisis and reshaping of the Schengen Area border. This results in collision of diverse human populations subjected to different protocols for antimicrobial stewardship and infection control. The present review article summarizes the findings of whole-genome sequencing-based resistome analyses of nosocomial multidrug-resistant NFGNBs in the Balkan countries.
Collapse
Affiliation(s)
- Slavil Peykov
- Department of Genetics, Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8, Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2, Zdrave Str., 1431 Sofia, Bulgaria
- BioInfoTech Laboratory, Sofia Tech Park, 111, Tsarigradsko Shosse Blvd., 1784 Sofia, Bulgaria
- Correspondence: (S.P.); (T.S.); Tel.: +359-87-6454492 (S.P.); +359-2-9172750 (T.S.)
| | - Tanya Strateva
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, 2, Zdrave Str., 1431 Sofia, Bulgaria
- Correspondence: (S.P.); (T.S.); Tel.: +359-87-6454492 (S.P.); +359-2-9172750 (T.S.)
| |
Collapse
|
47
|
Panda L, Pradhan A, EnketeswaraSubudhi, Nanda B. Facile fabrication of plasmonic Ag modified CaTiO3: for boosting photocatalytic reduction of Cr6+ and antimicrobial study. INORG CHEM COMMUN 2023. [DOI: 10.1016/j.inoche.2023.110486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
|
48
|
Sharma T, Kumar R, Kalra JS, Singh S, Bhalla GS, Bhardwaj A. Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes. Front Microbiol 2023; 13:1041847. [PMID: 36817105 PMCID: PMC9933921 DOI: 10.3389/fmicb.2022.1041847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 12/21/2022] [Indexed: 01/28/2023] Open
Abstract
Introduction Antimicrobial susceptibility testing (AST) is used to determine the susceptibility of an organism to antibiotics. The determination of susceptibility is based on MIC breakpoints and is provided by EUCAST and CLSI. Likewise, phenotypic classification criteria developed by CDC/ECDC are used for the classification of pathogens into susceptible, multidrug-resistant, extremely drug-resistant, or totally drug-resistant categories. Whole-genome sequencing (WGS)-based diagnosis is now supplementing existing gold-standard microbiology methods for rapid and more precise AST, and therefore, EUCAST recommended quality criteria to assess whole-genome sequence for reporting the same. In this study, these three global standards, MIC breakpoints, phenotypic classification, and genome quality, are applied to the largest publicly available data for Acinetobacter baumannii (AB), the most critical priority pathogen identified by WHO. Materials and Methods The drug sensitivity profile and genomes for isolates of AB were obtained from PATRIC and evaluated with respect to AST standards (CLSI and EUCAST). Whole genome quality assessment and antimicrobial resistance mapping is performed with QUAST and ABRicate, respectively. Four in-house methods are developed for mapping standards and are integrated into a Galaxy workflow based system, Galaxy-ASIST. Analysis of the extent of agreement between CLSI 2022 and EUCAST 2022 for antibiotics was carried out using Cohen's kappa statistics. Results and Discussion An automated pipeline, Galaxy-ASIST, is designed and developed for the characterization of clinical isolates based on these standards. Evaluation of over 6,500 AB strains using Galaxy-ASIST indicated that only 10% of the publicly available datasets have metadata to implement these standards. Furthermore, given that CLSI and EUCAST have different MIC breakpoints, discrepancies are observed in the classification of resistant and susceptible isolates following these standards. It is, therefore, imperative that platforms are developed that allow the evaluation of ever increasing phenotypic and genome sequence datasets for AST. Galaxy-ASIST offers a centralized repository and a structured metadata architecture to provide a single globally acceptable framework for AST profiling of clinical isolates based on global standards. The platform also offers subsequent fine mapping of antimicrobial-resistant determinants. Galaxy-ASIST is freely available at https://ab-openlab.csir.res.in/asist.
Collapse
Affiliation(s)
- Tina Sharma
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rakesh Kumar
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Shreya Singh
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Anshu Bhardwaj
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Anshu Bhardwaj, ✉
| |
Collapse
|
49
|
Shemirani MI, Tilevik D, Tilevik A, Jurcevic S, Arnellos D, Enroth H, Pernestig AK. Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis. BMC Infect Dis 2023; 23:39. [PMID: 36670352 PMCID: PMC9863170 DOI: 10.1186/s12879-022-07977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/28/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic susceptibility and virulence genes simultaneously. To accomplish the aforementioned points, the commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well as to reference methods in the clinical laboratory. METHODS Whole-genome sequencing data retrieved from 264 Staphylococcus aureus isolates using the Illumina HiSeq X next-generation sequencing technology was used. The S. aureus isolates were collected during a prospective observational study of community-onset severe sepsis and septic shock in adults at Skaraborg Hospital, in the western region of Sweden. The collected isolates were characterized according to accredited laboratory methods i.e., species identification by MALDI-TOF MS analysis and phenotypic antibiotic susceptibility testing (AST) by following the EUCAST guidelines. Concordance between laboratory methods and bioinformatic tools, as well as concordance between the bioinformatic tools was assessed by calculating the percent of agreement. RESULTS There was an overall high agreement between predicted genotypic AST and phenotypic AST results, 98.0% (989/1006, 95% CI 97.3-99.0). Nevertheless, the 1928 platform delivered predicted genotypic AST results with lower very major error rates but somewhat higher major error rates compared to the in-house pipeline. There were differences in processing times i.e., minutes versus hours, where the 1928 platform delivered the results faster. Furthermore, the bioinformatic workflows showed overall 99.4% (1267/1275, 95% CI 98.7-99.7) agreement in genetic prediction of the virulence gene characteristics and overall 97.9% (231/236, 95% CI 95.0-99.2%) agreement in predicting the sequence types (ST) of the S. aureus isolates. CONCLUSIONS Altogether, the benchmarking disclosed that both bioinformatic workflows are able to deliver results with high accuracy aiding diagnostics of severe infections caused by S. aureus. It also illustrates the need of international agreement on quality control and metrics to facilitate standardization of analytical approaches for whole-genome sequencing based predictions.
Collapse
Affiliation(s)
- Mahnaz Irani Shemirani
- grid.8761.80000 0000 9919 9582Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Diana Tilevik
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
| | - Andreas Tilevik
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
| | - Sanja Jurcevic
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
| | | | - Helena Enroth
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden ,Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skövde, Sweden
| | - Anna-Karin Pernestig
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
| |
Collapse
|
50
|
Perikleous EP, Gkentzi D, Bertzouanis A, Paraskakis E, Sovtic A, Fouzas S. Antibiotic Resistance in Patients with Cystic Fibrosis: Past, Present, and Future. Antibiotics (Basel) 2023; 12:antibiotics12020217. [PMID: 36830128 PMCID: PMC9951886 DOI: 10.3390/antibiotics12020217] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/15/2023] [Accepted: 01/19/2023] [Indexed: 01/22/2023] Open
Abstract
Patients with cystic fibrosis (CF) are repeatedly exposed to antibiotics, especially during the pulmonary exacerbations of the disease. However, the available therapeutic strategies are frequently inadequate to eradicate the involved pathogens and most importantly, facilitate the development of antimicrobial resistance (AMR). The evaluation of AMR is demanding; conventional culture-based susceptibility-testing techniques cannot account for the lung microenvironment and/or the adaptive mechanisms developed by the pathogens, such as biofilm formation. Moreover, features linked to modified pharmaco-kinetics and pulmonary parenchyma penetration make the dosing of antibiotics even more challenging. In this review, we present the existing knowledge regarding AMR in CF, we shortly review the existing therapeutic strategies, and we discuss the future directions of antimicrobial stewardship. Due to the increasing difficulty in eradicating strains that develop AMR, the appropriate management should rely on targeting the underlying resistance mechanisms; thus, the interest in novel, molecular-based diagnostic tools, such as metagenomic sequencing and next-generation transcriptomics, has increased exponentially. Moreover, since the development of new antibiotics has a slow pace, the design of effective treatment strategies to eradicate persistent infections represents an urgency that requires consorted work. In this regard, both the management and monitoring of antibiotics usage are obligatory and more relevant than ever.
Collapse
Affiliation(s)
| | - Despoina Gkentzi
- Department of Pediatrics, University of Patras Medical School, 26504 Patras, Greece
| | - Aris Bertzouanis
- Department of Pediatrics, University of Patras Medical School, 26504 Patras, Greece
- Pediatric Respiratory Unit, University Hospital of Patras, 26504 Patras, Greece
| | - Emmanouil Paraskakis
- Pediatric Respiratory Unit, Department of Pediatrics, University of Crete, 71500 Heraklion, Greece
| | - Aleksandar Sovtic
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Department of Pulmonology, Mother and Child Health Institute of Serbia, 11070 Belgrade, Serbia
| | - Sotirios Fouzas
- Department of Pediatrics, University of Patras Medical School, 26504 Patras, Greece
- Pediatric Respiratory Unit, University Hospital of Patras, 26504 Patras, Greece
- Correspondence: ; Tel.: +30-2610-999980
| |
Collapse
|