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Xiang K, Zhang Z, Li N, Zhang P, Liu F, Li H, Duan H, Zhang C, Ge J. Whole-Genome Sequence and Pathogenicity Analysis of Providencia Heimbachae Causing Diarrhea in Weaned Piglets. Curr Microbiol 2023; 80:364. [PMID: 37812274 DOI: 10.1007/s00284-023-03478-8] [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: 05/06/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Providencia heimbachae was previously identified in piglets with post-weaned diarrhea and associated with hindlimb paralysis. However, the pathogenic mechanisms and virulence factors of P. heimbachae are not fully known. Whole-genome sequence analysis will be helpful to extend our understanding of the characterization of P. heimbachae at a genomic level. In this study, we sequenced the whole genome of P. heimbachae for the first time using PacBio RS II sequencers and assembled de novo through hierarchical genome assembly process (HGAP). Furthermore, we performed further genome annotation. The genome of P. heimbachae 99101 consists of a circular chromosome (4,262,828 bp) and a circular plasmid (231,957 bp) with G + C contents of 40.43 and 47.16%, respectively. Genome-wide sequence analysis yielded a total of 286 predicted virulence factors, 178 resistance genes, 17 chaperone protein manipulators of fimbriae, 47 genes involved in the encoding of flagellin, 12 cell membrane-associated virulence genes, 18 Enterobacteriaceae common antigens, etc. Based on genome analysis, we preliminarily confirmed through animal experiments that the capsule was the virulence factor of P. heimbachae causing hindlimb paralysis in animals. Our study provides a genetic basis for further elucidation of the characteristics and functional mechanisms of P. heimbachae as a conditionally pathogenic bacterium, as well as a direction for research into the mechanism of action of P. heimbachae infecting humans, extending knowledge of P. heimbachae as an important zoonotic pathogen.
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Affiliation(s)
- Kongrui Xiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Zhuo Zhang
- Shenyang Animal Disease Prevention and Control Center, Shenyang, 110031, China
| | - Nuowa Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ping Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Feng Liu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Hai Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Haoyuan Duan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Chuankun Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China.
- Heilongjiang Provincial Key Laboratory of Zoonosis, Harbin, 150030, China.
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Lumpe J, Gumbleton L, Gorzalski A, Libuit K, Varghese V, Lloyd T, Tadros F, Arsimendi T, Wagner E, Stephens C, Sevinsky J, Hess D, Pandori M. GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification. PLoS One 2023; 18:e0277575. [PMID: 36795668 PMCID: PMC9934365 DOI: 10.1371/journal.pone.0277575] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/29/2022] [Indexed: 02/17/2023] Open
Abstract
Whole genome sequencing (WGS) of clinical bacterial isolates has the potential to transform the fields of diagnostics and public health. To realize this potential, bioinformatic software that reports identification results needs to be developed that meets the quality standards of a diagnostic test. We developed GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) using k-mer based strategies for identification of bacteria based on WGS reads. GAMBIT incorporates this algorithm with a highly curated searchable database of 48,224 genomes. Herein, we describe validation of the scoring methodology, parameter robustness, establishment of confidence thresholds and the curation of the reference database. We assessed GAMBIT by way of validation studies when it was deployed as a laboratory-developed test in two public health laboratories. This method greatly reduces or eliminates false identifications which are often detrimental in a clinical setting.
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Affiliation(s)
- Jared Lumpe
- Independent Researcher, Meriden, Connecticut, United States of America
- * E-mail: (JL); (MP); (DH)
| | - Lynette Gumbleton
- Nevada State Public Health Laboratory, Reno, NV, United States of America
| | - Andrew Gorzalski
- Nevada State Public Health Laboratory, Reno, NV, United States of America
| | - Kevin Libuit
- Theiagen Consulting LLC, Highlands Ranch, CO, United States of America
| | - Vici Varghese
- Alameda County Department of Public Health, Oakland, CA, United States of America
| | - Tyler Lloyd
- Alameda County Department of Public Health, Oakland, CA, United States of America
| | - Farid Tadros
- Biology Department, Santa Clara University, Santa Clara, CA, United States of America
| | - Tyler Arsimendi
- Biology Department, Santa Clara University, Santa Clara, CA, United States of America
| | - Eileen Wagner
- Theiagen Consulting LLC, Highlands Ranch, CO, United States of America
| | - Craig Stephens
- Biology Department, Santa Clara University, Santa Clara, CA, United States of America
| | - Joel Sevinsky
- Theiagen Consulting LLC, Highlands Ranch, CO, United States of America
| | - David Hess
- Nevada State Public Health Laboratory, Reno, NV, United States of America
- Biology Department, Santa Clara University, Santa Clara, CA, United States of America
- Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United States of America
- * E-mail: (JL); (MP); (DH)
| | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, United States of America
- Alameda County Department of Public Health, Oakland, CA, United States of America
- Department of Pathology and Laboratory Medicine, University of Nevada, Reno School of Medicine, Reno, NV, United States of America
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, Reno, NV, United States of America
- * E-mail: (JL); (MP); (DH)
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Zhang S, Huang Y, Chen M, Yang G, Zhang J, Wu Q, Wang J, Ding Y, Ye Q, Lei T, Su Y, Pang R, Yang R, Zhang Y. Characterization of Escherichia coli O157:non-H7 isolated from retail food in China and first report of mcr-1/IncI2-carrying colistin-resistant E. coli O157:H26 and E. coli O157:H4. Int J Food Microbiol 2022; 378:109805. [DOI: 10.1016/j.ijfoodmicro.2022.109805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/23/2022] [Accepted: 06/12/2022] [Indexed: 10/18/2022]
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Aruhomukama D, Sserwadda I, Mboowa G. Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics. F1000Res 2019; 8:150. [PMID: 31354944 PMCID: PMC6635981 DOI: 10.12688/f1000research.18081.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Bacterial infections involving antibiotic-resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR), extensive-drug resistant (XDR) or pan-drug resistant (PDR) bacterial strains. Most recently, plasmid-mediated resistance to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR, XDR and PDR gram-negative bacteria has been reported. Plasmid-mediated colistin resistant gram-negative bacteria have been described to be PDR, implying a state devoid of alternative antibiotic therapeutic options. This review concisely describes the evolution of antibiotic resistance to plasmid-mediated colistin resistance and discusses the potential role of high-throughput sequencing technologies, genomics, and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antibiotic resistance as a whole.
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Affiliation(s)
- Dickson Aruhomukama
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
| | - Ivan Sserwadda
- Department of Immunology and Molecular Biology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
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Aruhomukama D, Sserwadda I, Mboowa G. Investigating colistin drug resistance: The role of high-throughput sequencing and bioinformatics. F1000Res 2019; 8:150. [PMID: 31354944 PMCID: PMC6635981 DOI: 10.12688/f1000research.18081.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/31/2019] [Indexed: 10/13/2023] Open
Abstract
Bacterial infections involving antibiotic resistant gram-negative bacteria continue to increase and represent a major global public health concern. Resistance to antibiotics in these bacteria is mediated by chromosomal and/or acquired resistance mechanisms, these give rise to multi-drug resistant (MDR) or extensive drug resistant (XDR) bacterial strains. Most recently, a novel acquired plasmid mediated resistance mechanism to colistin, an antibiotic that had been set apart as the last resort antibiotic in the treatment of infections involving MDR and XDR gram-negative bacteria, has been reported. Plasmid mediated colistin resistant gram-negative bacteria have been described to be pan-drug resistant, implying a state devoid of alternative antibiotic therapeutic options. This review describes the evolution of antibiotic resistance to plasmid mediated colistin resistance, and discusses the potential role of high-throughput sequencing technologies, genomics and bioinformatics towards improving antibiotic resistance surveillance, the search for novel drug targets and precision antibiotic therapy focused at combating colistin resistance, and antimicrobial resistance as a whole.
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Affiliation(s)
- Dickson Aruhomukama
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
| | - Ivan Sserwadda
- Department of Immunology and Molecular Biology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, School of Biomedical Sciences, Makerere University, Kampala, 7072, Uganda
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Gomes A, van Oosten M, Bijker KLB, Boiten KE, Salomon EN, Rosema S, Rossen JWA, Natour E, Douglas YL, Kampinga GA, van Assen S, Sinha B. Sonication of heart valves detects more bacteria in infective endocarditis. Sci Rep 2018; 8:12967. [PMID: 30154489 PMCID: PMC6113321 DOI: 10.1038/s41598-018-31029-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 08/10/2018] [Indexed: 11/09/2022] Open
Abstract
Optimal antimicrobial treatment of infective endocarditis requires identification and susceptibility patterns of pathogens. Sonication of explanted heart valves could increase the identification and culture of pathogens, as shown in prosthetic joint and pacemaker/ICD infections. We tested 26 explanted heart valves from 20 patients with active definite endocarditis for added diagnostic value of sonication to the standard microbiological workup in a prospective diagnostic proof of concept study. Two sonication protocols (broth enrichment vs. centrifugation) were compared in an additional 35 negative control valves for contamination rates. We selected sonication/centrifugation based on acceptable false positive rates (11.4%; 4/35). Sonication/enrichment yielded many false positive results in negative controls (28.6%; 10/35), mainly Propionibacterium acnes (next-generation sequencing excluded technical problems). Compared to direct culture only, adding sonication/centrifugation (including molecular testing) significantly increased the diagnostic yield from 6/26 to 17/26 valves (p = 0.003). Most importantly, culture positives almost doubled (from 6 to 10), providing unique quantitative information about antimicrobial susceptibility. Even if direct molecular testing was added to the standard workup, sonication/centrifugation provided additional diagnostic information in a significant number of valves (8/26; 31%; p = 0.013). We concluded that sonication/centrifugation added relevant diagnostic information in the workup of heart valves with infective endocarditis, with acceptable contamination rates.
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Affiliation(s)
- Anna Gomes
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Marleen van Oosten
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kasper L B Bijker
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kathleen E Boiten
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elisa N Salomon
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ehsan Natour
- Department of Thoracic Surgery, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Yvonne L Douglas
- Department of Cardio-Thoracic Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Greetje A Kampinga
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sander van Assen
- Department of Internal Medicine (Infectious Diseases), Treant Zorggroep, Hoogeveen, The Netherlands
| | - Bhanu Sinha
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Pietsch M, Irrgang A, Roschanski N, Brenner Michael G, Hamprecht A, Rieber H, Käsbohrer A, Schwarz S, Rösler U, Kreienbrock L, Pfeifer Y, Fuchs S, Werner G. Whole genome analyses of CMY-2-producing Escherichia coli isolates from humans, animals and food in Germany. BMC Genomics 2018; 19:601. [PMID: 30092762 PMCID: PMC6085623 DOI: 10.1186/s12864-018-4976-3] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/31/2018] [Indexed: 01/09/2023] Open
Abstract
Background Resistance to 3rd-generation cephalosporins in Escherichia coli is mostly mediated by extended-spectrum beta-lactamases (ESBLs) or AmpC beta-lactamases. Besides overexpression of the species-specific chromosomal ampC gene, acquisition of plasmid-encoded ampC genes, e.g. blaCMY-2, has been described worldwide in E. coli from humans and animals. To investigate a possible transmission of blaCMY-2 along the food production chain, we conducted a next-generation sequencing (NGS)-based analysis of 164 CMY-2-producing E. coli isolates from humans, livestock animals and foodstuff from Germany. Results The data of the 164 sequenced isolates revealed 59 different sequence types (STs); the most prevalent ones were ST38 (n = 19), ST131 (n = 16) and ST117 (n = 13). Two STs were present in all reservoirs: ST131 (human n = 8; food n = 2; animal n = 6) and ST38 (human n = 3; animal n = 9; food n = 7). All but one CMY-2-producing ST131 isolates belonged to the clade B (fimH22) that differed substantially from the worldwide dominant CTX-M-15-producing clonal lineage ST131-O25b clade C (fimH30). Plasmid replicon types IncI1 (n = 61) and IncK (n = 72) were identified for the majority of blaCMY-2-carrying plasmids. Plasmid sequence comparisons showed a remarkable sequence identity, especially for IncK plasmids. Associations of replicon types and distinct STs were shown for IncK and ST57, ST429 and ST38 as well as for IncI1 and ST58. Additional β-lactamase genes (blaTEM, blaCTX-M, blaOXA, blaSHV) were detected in 50% of the isolates, and twelve E. coli from chicken and retail chicken meat carried the colistin resistance gene mcr-1. Conclusion We found isolates of distinct E. coli clonal lineages (ST131 and ST38) in all three reservoirs. However, a direct clonal relationship of isolates from food animals and humans was only noticeable for a few cases. The CMY-2-producing E. coli-ST131 represents a clonal lineage different from the CTX-M-15-producing ST131-O25b cluster. Apart from the ST-driven spread, plasmid-mediated spread, especially via IncI1 and IncK plasmids, likely plays an important role for emergence and transmission of blaCMY-2 between animals and humans. Electronic supplementary material The online version of this article (10.1186/s12864-018-4976-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael Pietsch
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany
| | - Alexandra Irrgang
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Nicole Roschanski
- Freie Universität Berlin, Institute for Animal Hygiene and Environmental Health, Berlin, Germany
| | - Geovana Brenner Michael
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Axel Hamprecht
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Heime Rieber
- Medizinisches Versorgungszentrum Dr. Stein, Division of Microbiology, Mönchengladbach, Germany
| | - Annemarie Käsbohrer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany.,Veterinary University Vienna, Vienna, Austria
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Neustadt-Mariensee, Germany
| | - Uwe Rösler
- Freie Universität Berlin, Institute for Animal Hygiene and Environmental Health, Berlin, Germany
| | - Lothar Kreienbrock
- Institute for Biometrics, Epidemiology and Data Processing, University of Veterinary Medicine, Hanover, Germany
| | - Yvonne Pfeifer
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany
| | - Stephan Fuchs
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany
| | - Guido Werner
- Robert Koch-Institute, FG 13 Nosocomial Pathogens and Antibiotic Resistance, Burgstr, 37 38855, Wernigerode, Germany.
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Miskiewicz A, Kowalczyk P, Oraibi SM, Cybulska K, Misiewicz A. Bird feathers as potential sources of pathogenic microorganisms: a new look at old diseases. Antonie van Leeuwenhoek 2018; 111:1493-1507. [PMID: 29460207 PMCID: PMC6097735 DOI: 10.1007/s10482-018-1048-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/09/2018] [Indexed: 12/22/2022]
Abstract
This article describes methods of treatment for avian zoonoses, modern antibiotic therapy and drug resistance of selected pathogens, which pose a threat to the population’s health. A tabular form has been used to present the current data from the European Union from 2011 to 2017 regarding human morbidity and mortality and the costs incurred by national health systems for the treatment of zoonoses occurring in humans and animals. Moreover, the paper includes descriptions of selected diseases, which indirectly affect birds. Scientists can obtain information regarding the occurrence of particular diseases, their aetiology, epidemiology, incubation period and symptoms caused by dangerous microorganisms and parasites. This information should be of particular interest for people who have frequent contact with birds, such as ornithologists, as well as veterinarians, farm staff, owners of accompanying animals and zoological workers. This paper presents a review used for identification and genetic characterization of bacterial strains isolated from a variety of environmental sources, e.g., bird feathers along with their practical application. We describe the bacterial, viral and fungal serotypes present on avian feathers after the slaughter process. This review also enables us to effectively identify several of the early stages of infectious diseases from heterogeneous avian research material.
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Affiliation(s)
- Andrzej Miskiewicz
- Department of Periodontology and Oral Diseases, Medical University of Warsaw, 18 Miodowa St., 00-246, Warsaw, Poland
| | - Paweł Kowalczyk
- Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Jabłonna, Poland.
| | - Sanaa Mahdi Oraibi
- Department of Chemistry, Microbiology and Environmental Biotechnology, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology, Słowackiego 17 Str., 71-434, Szczecin, Poland
| | - Krystyna Cybulska
- Department of Chemistry, Microbiology and Environmental Biotechnology, Faculty of Environmental Management and Agriculture, West Pomeranian University of Technology, Słowackiego 17 Str., 71-434, Szczecin, Poland
| | - Anna Misiewicz
- Institute of Agricultural and Food Biotechnology, Rakowiecka 36, 02-532, Warsaw, Poland
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Rossen JWA, Friedrich AW, Moran-Gilad J. Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology. Clin Microbiol Infect 2017; 24:355-360. [PMID: 29117578 DOI: 10.1016/j.cmi.2017.11.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. AIM To review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories. SOURCES Review of the literature and expert opinion. CONTENT In this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories. IMPLICATIONS Further development is required to improve the workflow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic field.
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Affiliation(s)
- J W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands; European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland.
| | - A W Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, The Netherlands
| | - J Moran-Gilad
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland; Department of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Public Health Services, Ministry of Health, Jerusalem, Israel
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