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Osman R, Dema E, David A, Hughes G, Field N, Cole M, Didelot X, Saunders J. Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care. J Infect 2024; 88:106168. [PMID: 38670270 DOI: 10.1016/j.jinf.2024.106168] [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: 01/10/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVES The utility of whole genome sequencing (WGS) to inform sexually transmitted infection (STI) patient management is unclear. Timely WGS data might support clinical management of STIs by characterising epidemiological links and antimicrobial resistance profiles. We conducted a systematic review of clinical application of WGS to any human pathogen that may be transposable to gonorrhoea. METHODS We searched six databases for articles published between 01/01/2010-06/02/2023 that reported on real/near real-time human pathogen WGS to inform clinical intervention. All article types from all settings were included. Findings were analysed using narrative synthesis. RESULTS We identified 12,179 articles, of which eight reported applications to inform tuberculosis (n = 7) and gonorrhoea (n = 1) clinical patient management. WGS data were successfully used as an adjunct to clinical and epidemiological data to enhance contact-tracing (n = 2), inform antimicrobial therapy (n = 5) and identify cross-contamination (n = 1). WGS identified gonorrhoea transmission chains that were not established via partner notification. Future applications could include insights into pathogen exposure detected within sexual networks for targeted patient management. CONCLUSIONS While there was some evidence of WGS use to provide individualised tuberculosis and gonorrhoea treatment, the eight identified studies contained few participants. Future research should focus on testing WGS intervention effectiveness and examining ethical considerations of STI WGS use.
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Affiliation(s)
- Roeann Osman
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom.
| | - Emily Dema
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Alexandra David
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Gwenda Hughes
- Department of Infectious Disease Epidemiology and Dynamics, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Nigel Field
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom
| | - Michelle Cole
- UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry CV4 7AL, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Genomics and Enabling Data at Warwick University, United Kingdom
| | - John Saunders
- Institute for Global Health, University College London (UCL), Mortimer Market Centre, London WC1E 6JB, United Kingdom; National Institute for Health Research (NIHR) Health Protection Research Unit (HPRU) in Blood Borne and Sexually Transmitted Infections at University College London (UCL), London, United Kingdom; UK Health Security Agency (UK HSA), 61 Colindale Avenue, London NW9 5EQ, United Kingdom
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Byarugaba DK, Erima B, Wokorach G, Alafi S, Kibuuka H, Mworozi E, Musinguzi AK, Kiyengo J, Najjuka F, Wabwire-Mangen F. Resistome and virulome of high-risk pandemic clones of multidrug-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) isolated from tertiary healthcare settings in Uganda. PLoS One 2023; 18:e0294424. [PMID: 37992119 PMCID: PMC10664879 DOI: 10.1371/journal.pone.0294424] [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: 05/03/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023] Open
Abstract
Multi-drug resistant (MDR) globally disseminated extraintestinal pathogenic high-risk Escherichia coli (ExPEC) clones are threatening the gains in bacterial disease management. In this study, we evaluated the genomic structure including the resistome and virulome of the E. coli isolates from extraintestinal infections using whole genome sequencing (WGS). The results highlight that isolates were highly resistant (≥ 90.0%) to commonly used antibiotics (Ampicillin, Trimethoprim-Sulfamethoxazole, Nalidixic acid, and Piperacillin) and were less (<14%) resistant to last resort antibiotics; Imipenem (10.94%) and Meropenem (10.20%). A greater proportion of the E. coli isolates belonged to phylogroup B2 (30.52%) and phylogroup A (27.37%). The sequence types ST131 of phylogroup B2 (21.05%) and ST648 of phylogroup F (9.3%) were the dominant pandemic high-risk clones identified in addition to the ST1193, ST410, ST69, ST38, ST405, and ST10. Many of the isolates were MDR and most (64.58%) carried the blaCTX-M-15 gene for extended-spectrum β-lactamases. There was a high correlation between phylogroups and the occurrence of both antimicrobial resistance and virulence genes. The cephalosporin-resistance gene blaEC-5 was only found in phylogroup B2 while blaEC-8 and blaEC-19, were only found within phylogroup D and phylogroup F respectively. Aminoglycoside gene (aadA1) was only associated with phylogroups D and C. The isolates were armed with a broad range of virulence genes including adhesins, toxins, secreted proteases, iron uptake genes, and others. The yfcv, chuA, and kpsE genes preferentially occurred among isolates of phylogroup B2. The study underlines the predominance of MDR internationally disseminated high-risk ExPEC clones with a broad range of virulence genes known to be highly transmissible in healthcare and community settings.
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Affiliation(s)
- Denis K. Byarugaba
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala, Uganda
- Gulu University Multifunctional Research Laboratories, Gulu, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Edison Mworozi
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - James Kiyengo
- Uganda Peoples’ Defence Forces, Ministry of Defence, Kampala, Uganda
| | - Florence Najjuka
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala, Uganda
- College of Health Sciences, Makerere University, Kampala, Uganda
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3
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Shobo CO, Amoako DG, Allam M, Ismail A, Essack SY, Bester LA. A Genomic Snapshot of Antibiotic-Resistant Enterococcus faecalis within Public Hospital Environments in South Africa. Glob Health Epidemiol Genom 2023; 2023:6639983. [PMID: 37342729 PMCID: PMC10279497 DOI: 10.1155/2023/6639983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.
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Affiliation(s)
- Christiana O. Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- School of Laboratory Medicine and Medical Science, Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, UAE
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Linda A. Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
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4
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Colton H, Parker M, Stirrup O, Blackstone J, Loose M, McClure C, Roy S, Williams C, McLeod J, Smith D, Taha Y, Zhang P, Hsu S, Kele B, Harris K, Mapp F, Williams R, Flowers P, Breuer J, Partridge D, de Silva T. Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. J Hosp Infect 2023; 131:34-42. [PMID: 36228768 PMCID: PMC9550290 DOI: 10.1016/j.jhin.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. AIM To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. METHODS For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis. FINDINGS The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT. CONCLUSION Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.
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Affiliation(s)
- H. Colton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK,Directorate of Laboratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK,Corresponding author. Address: Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry & Health, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - M.D. Parker
- Sheffield Biomedical Research Centre, University of Sheffield, Sheffield, UK,Sheffield Bioinformatics Core, University of Sheffield, Sheffield, UK
| | - O. Stirrup
- Institute for Global Health, University College London, London, UK
| | - J. Blackstone
- The Comprehensive Clinical Trials Unit, University College London, London, UK
| | - M. Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - C.P. McClure
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - S. Roy
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - C. Williams
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - J. McLeod
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - D. Smith
- Department of Applied Biology, Cellular and Molecular Sciences/Microbiology Group, Northumbria University, Newcastle, UK
| | - Y. Taha
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Royal Victoria Infirmary, Newcastle Upon Tyne, UK
| | - P. Zhang
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - S.N. Hsu
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK,Sheffield Bioinformatics Core, University of Sheffield, Sheffield, UK
| | - B. Kele
- Virology Department, East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - K. Harris
- Virology Department, East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - F. Mapp
- Institute for Global Health, University College London, London, UK
| | - R. Williams
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | | | - P. Flowers
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - J. Breuer
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - D.G. Partridge
- Directorate of Laboratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - T.I. de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
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5
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Khan MAA, Ghosh P, Chowdhury R, Hossain F, Mahmud A, Faruque ASG, Ahmed T, Abd El Wahed A, Mondal D. Feasibility of MinION Nanopore Rapid Sequencing in the Detection of Common Diarrhea Pathogens in Fecal Specimen. Anal Chem 2022; 94:16658-16666. [DOI: 10.1021/acs.analchem.2c02771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Md Anik Ashfaq Khan
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, An den Tierkliniken 1, 04103Leipzig, Germany
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Araf Mahmud
- Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Abu S. G. Faruque
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Ahmed Abd El Wahed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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7
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Sundermann AJ, Babiker A, Marsh JW, Shutt KA, Mustapha MM, Pasculle AW, Ezeonwuka C, Saul MI, Pacey MP, Van Tyne D, Ayres AM, Cooper VS, Snyder GM, Harrison LH. Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole-genome Sequencing-based Surveillance. Clin Infect Dis 2021; 70:2336-2343. [PMID: 31312842 DOI: 10.1093/cid/ciz666] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/15/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Vancomycin-resistant enterococci (VRE) are a major cause of hospital-acquired infections. The risk of infection from interventional radiology (IR) procedures is not well documented. Whole-genome sequencing (WGS) surveillance of clinical bacterial isolates among hospitalized patients can identify previously unrecognized outbreaks. METHODS We analyzed WGS surveillance data from November 2016 to November 2017 for evidence of VRE transmission. A previously unrecognized cluster of 10 genetically related VRE (Enterococcus faecium) infections was discovered. Electronic health record review identified IR procedures as a potential source. An outbreak investigation was conducted. RESULTS Of the 10 outbreak patients, 9 had undergone an IR procedure with intravenous (IV) contrast ≤22 days before infection. In a matched case-control study, preceding IR procedure and IR procedure with contrast were associated with VRE infection (matched odds ratio [MOR], 16.72; 95% confidence interval [CI], 2.01 to 138.73; P = .009 and MOR, 39.35; 95% CI, 7.85 to infinity; P < .001, respectively). Investigation of IR practices and review of the manufacturer's training video revealed sterility breaches in contrast preparation. Our investigation also supported possible transmission from an IR technician. Infection prevention interventions were implemented, and no further IR-associated VRE transmissions have been observed. CONCLUSIONS A prolonged outbreak of VRE infections related to IR procedures with IV contrast resulted from nonsterile preparation of injectable contrast. The fact that our VRE outbreak was discovered through WGS surveillance and the manufacturer's training video that demonstrated nonsterile technique raise the possibility that infections following invasive IR procedures may be more common than previously recognized.
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Affiliation(s)
- Alexander J Sundermann
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Department of Infection Control and Hospital Epidemiology, University of Pittsburgh Medical Center, Pennsylvania
| | - Ahmed Babiker
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Jane W Marsh
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Kathleen A Shutt
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Mustapha M Mustapha
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | | | - Chinelo Ezeonwuka
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Melissa I Saul
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania
| | - Marissa P Pacey
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Ashley M Ayres
- Department of Infection Control and Hospital Epidemiology, University of Pittsburgh Medical Center, Pennsylvania
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pennsylvania
| | - Graham M Snyder
- Department of Infection Control and Hospital Epidemiology, University of Pittsburgh Medical Center, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
| | - Lee H Harrison
- Microbial Genomic Epidemiology Laboratory, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pennsylvania.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pennsylvania
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8
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Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY 2021; 1:e62. [PMID: 36168472 PMCID: PMC9495627 DOI: 10.1017/ash.2021.233] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/12/2022]
Abstract
Background: Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms. Objective: To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital. Design: Cost-effectiveness study. Setting: Intensive care unit and burn unit of large metropolitan hospital. Patients: Simulated intensive care unit and burn unit patients. Methods: We built a complex simulation model to estimate pathogen transmission, associated hospital costs, and quality-adjusted life years (QALYs) during a 32-month outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB). Model parameters were determined using microbiology surveillance data, genome sequencing results, hospital admission databases, and local clinical knowledge. The model was calibrated to the actual pathogen spread within the intensive care unit and burn unit (scenario 1) and compared with early use of WGS (scenario 2) and early use of WGS and metagenomics (scenario 3) to determine their respective cost-effectiveness. Sensitivity analyses were performed to address model uncertainty. Results: On average compared with scenario 1, scenario 2 resulted in 14 fewer patients with CRAB, 59 additional QALYs, and $75,099 cost savings. Scenario 3, compared with scenario 1, resulted in 18 fewer patients with CRAB, 74 additional QALYs, and $93,822 in hospital cost savings. The likelihoods that scenario 2 and scenario 3 were cost-effective were 57% and 60%, respectively. Conclusions: The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes.
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9
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Whole-genome sequencing for neonatal intensive care unit outbreak investigations: Insights and lessons learned. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY 2021; 1:e2. [PMID: 36168459 PMCID: PMC9495531 DOI: 10.1017/ash.2021.161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022]
Abstract
Abstract
Infectious diseases outbreaks are a cause of significant morbidity and mortality among hospitalized patients. Infants admitted to the neonatal intensive care unit (NICU) are particularly vulnerable to infectious complications during hospitalization. Thus, rapid recognition of and response to outbreaks in the NICU is essential. At Rush University Medical Center, whole-genome sequencing (WGS) has been utilized since early 2016 as an adjunctive method for outbreak investigations. The use of WGS and potential lessons learned are illustrated for 3 different NICU outbreak investigations involving methicillin-resistant Staphylococcus aureus (MRSA), group B Streptococcus (GBS), and Serratia marcescens. WGS has contributed to the understanding of the epidemiology of outbreaks in our NICU, and it has also provided further insight in settings of unusual diseases or when lower-resolution typing methods have been inadequate. WGS has emerged as the new gold standard for evaluating strain relatedness. As barriers to implementation are overcome, WGS has the potential to transform outbreak investigation in healthcare settings.
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11
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Loka TP, Tausch SH, Renard BY. Reliable variant calling during runtime of Illumina sequencing. Sci Rep 2019; 9:16502. [PMID: 31712740 PMCID: PMC6848508 DOI: 10.1038/s41598-019-52991-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 10/16/2019] [Indexed: 02/03/2023] Open
Abstract
The sequential paradigm of data acquisition and analysis in next-generation sequencing leads to high turnaround times for the generation of interpretable results. We combined a novel real-time read mapping algorithm with fast variant calling to obtain reliable variant calls still during the sequencing process. Thereby, our new algorithm allows for accurate read mapping results for intermediate cycles and supports large reference genomes such as the complete human reference. This enables the combination of real-time read mapping results with complex follow-up analysis. In this study, we showed the accuracy and scalability of our approach by applying real-time read mapping and variant calling to seven publicly available human whole exome sequencing datasets. Thereby, up to 89% of all detected SNPs were already identified after 40 sequencing cycles while showing similar precision as at the end of sequencing. Final results showed similar accuracy to those of conventional post-hoc analysis methods. When compared to standard routines, our live approach enables considerably faster interventions in clinical applications and infectious disease outbreaks. Besides variant calling, our approach can be adapted for a plethora of other mapping-based analyses.
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Affiliation(s)
- Tobias P Loka
- Bioinformatics Division (MF 1), Department for Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Simon H Tausch
- Bioinformatics Division (MF 1), Department for Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Centre for Biological Threats and Special Pathogens: Highly Pathogenic Viruses (ZBS 1), Robert Koch Institute, Berlin, Germany
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, Berlin, Germany
| | - Bernhard Y Renard
- Bioinformatics Division (MF 1), Department for Methodology and Research Infrastructure, Robert Koch Institute, Berlin, Germany.
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12
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Lee RS, Gonçalves da Silva A, Baines SL, Strachan J, Ballard S, Carter GP, Kwong JC, Schultz MB, Bulach DM, Seemann T, Stinear TP, Howden BP. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. J Antimicrob Chemother 2019; 73:3268-3278. [PMID: 30189014 DOI: 10.1093/jac/dky331] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/23/2018] [Indexed: 12/17/2022] Open
Abstract
Background Vancomycin-resistant Enterococcus faecium (VREfm) represent a major source of nosocomial infection worldwide. In Australia, there has been a recent concerning increase in bacteraemia associated with the vanA genotype, prompting investigation into the genomic epidemiology of VREfm. Methods A population-level study of VREfm (10 November-9 December 2015) was conducted. A total of 321 VREfm isolates (from 286 patients) across Victoria State were collected and sequenced with Illumina NextSeq. SNPs were used to assess relatedness. STs and genes associated with resistance and virulence were identified. The vanA-harbouring plasmid from an isolate from each ST was assembled using long-read data. Illumina reads from remaining isolates were then mapped to these assemblies to identify their probable vanA-harbouring plasmid. Results vanA-VREfm comprised 17.8% of isolates. ST203, ST80 and a pstS(-) clade, ST1421, predominated (30.5%, 30.5% and 37.2%, respectively). Most vanB-VREfm were ST796 (77.7%). vanA-VREfm were more closely related within hospitals versus between them [core SNPs 10 (IQR 1-357) versus 356 (179-416), respectively], suggesting discrete introductions of vanA-VREfm, with subsequent intra-hospital transmission. In contrast, vanB-VREfm had similar core SNP distributions within versus between hospitals, due to widespread dissemination of ST796. Different vanA-harbouring plasmids were found across STs. With the exception of ST78 and ST796, Tn1546 transposons also varied. Phylogenetic analysis revealed Australian strains were often interspersed with those from other countries, suggesting ongoing cross-continental transmission. Conclusions Emerging vanA-VREfm in Australia is polyclonal, indicating repeat introductions of vanA-VREfm into hospitals and subsequent dissemination. The close relationship to global strains reinforces the need for ongoing screening and control of VREfm in Australia and abroad.
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Affiliation(s)
- Robyn S Lee
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Level 5, Boston, MA, USA
| | - Anders Gonçalves da Silva
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Janet Strachan
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Susan Ballard
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Glen P Carter
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Jason C Kwong
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Mark B Schultz
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Dieter M Bulach
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics Group, Lab-14, 700 Swanston Street, Carlton, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Level 1, Melbourne, Victoria, Australia.,Infectious Diseases Department, Austin Health, Studley Rd, Heidelberg, Victoria, Australia
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13
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Snesrud E, McGann P, Walsh E, Ong A, Maybank R, Kwak Y, Campbell J, Jones A, Vore K, Hinkle M, Lesho E. Clinical and Genomic Features of the First Cases of Elizabethkingia anophelis Infection in New York, Including the First Case in a Healthy Infant Without Previous Nosocomial Exposure. J Pediatric Infect Dis Soc 2019; 8:269-271. [PMID: 30107596 DOI: 10.1093/jpids/piy071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/17/2018] [Indexed: 11/14/2022]
Abstract
Elizabethkingia spp are Gram-negative bacteria associated with neonatal meningitis. In 2015-2016, an outbreak of Elizabethkingia anophelis infection that involved 63 patients and 18 deaths occurred in Wisconsin. Despite a multistate investigation, as of September 2016 the source remained undetermined, and experts warned of reemergence. We describe here the first cases of E anophelis infection in New York, including the case of a healthy infant without previous healthcare contact.
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Affiliation(s)
- Erik Snesrud
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Patrick McGann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Edward Walsh
- Department of Medicine, University of Rochester School of Medicine, New York
| | - Ana Ong
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Yoon Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Jean Campbell
- Microbiology and Molecular Diagnostics, Rochester Regional Health, New York
| | - Anthony Jones
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Kelly Vore
- Infection Prevention, Rochester Regional Health, New York
| | - Mary Hinkle
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Emil Lesho
- Infectious Diseases Unit, Rochester Regional Health, New York
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14
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Franco-Duarte R, Černáková L, Kadam S, Kaushik KS, Salehi B, Bevilacqua A, Corbo MR, Antolak H, Dybka-Stępień K, Leszczewicz M, Relison Tintino S, Alexandrino de Souza VC, Sharifi-Rad J, Coutinho HDM, Martins N, Rodrigues CF. Advances in Chemical and Biological Methods to Identify Microorganisms-From Past to Present. Microorganisms 2019; 7:E130. [PMID: 31086084 PMCID: PMC6560418 DOI: 10.3390/microorganisms7050130] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations.
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Affiliation(s)
- Ricardo Franco-Duarte
- CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal.
- Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal.
| | - Lucia Černáková
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
| | - Snehal Kadam
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Karishma S Kaushik
- Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, India.
| | - Bahare Salehi
- Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran.
| | - Antonio Bevilacqua
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Maria Rosaria Corbo
- Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy.
| | - Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Katarzyna Dybka-Stępień
- Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland.
| | - Martyna Leszczewicz
- Laboratory of Industrial Biotechnology, Bionanopark Ltd, Dubois 114/116, 93-465 Lodz, Poland.
| | - Saulo Relison Tintino
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | | | - Javad Sharifi-Rad
- Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran.
| | - Henrique Douglas Melo Coutinho
- Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, 63105-000 Crato, Brazil.
| | - Natália Martins
- Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal.
| | - Célia F Rodrigues
- LEPABE⁻Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
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Muthuirulandi Sethuvel DP, Devanga Ragupathi NK, Bakthavatchalam YD, Vijayakumar S, Varghese R, Shankar C, Jacob JJ, Vasudevan K, Elangovan D, Balaji V. Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens. Indian J Med Microbiol 2019; 37:147-162. [PMID: 31745014 DOI: 10.4103/ijmm.ijmm_19_396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.
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Affiliation(s)
| | | | | | - Saranya Vijayakumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Divyaa Elangovan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Veeraraghavan Balaji
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H, Harris KA, Wang H, Eldholm V. From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends Microbiol 2018; 26:1035-1048. [PMID: 30193960 PMCID: PMC6249990 DOI: 10.1016/j.tim.2018.08.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.
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Affiliation(s)
- Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions.
| | - Ola Brønstad Brynildsrud
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway; These authors made equal contributions
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions
| | - Liam P Shaw
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Hongbin Chen
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Kathryn A Harris
- Great Ormond Street Hospital NHS Foundation Trust, Department of Microbiology, Virology & Infection Prevention & Control, London WC1N 3JH, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Vegard Eldholm
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway
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17
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Haddad N, Johnson N, Kathariou S, Métris A, Phister T, Pielaat A, Tassou C, Wells-Bennik MH, Zwietering MH. Next generation microbiological risk assessment—Potential of omics data for hazard characterisation. Int J Food Microbiol 2018; 287:28-39. [DOI: 10.1016/j.ijfoodmicro.2018.04.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 03/31/2018] [Accepted: 04/10/2018] [Indexed: 12/18/2022]
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18
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How to: molecular investigation of a hospital outbreak. Clin Microbiol Infect 2018; 25:688-695. [PMID: 30287413 DOI: 10.1016/j.cmi.2018.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 09/19/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Studying hospital outbreaks by using molecular tools, i.e. synthesizing the molecular epidemiology data to its appropriate clinical-epidemiologic context, is crucial in order to identify infection source, infer transmission dynamics, appropriately allocate prevention resources and implement control measures. Whole-genome sequencing (WGS) of pathogens has become the reference standard, as it is becoming more accessible and affordable. Consequently, sequencing of the full pathogen genome via WGS and major progress in fit-for-purpose genomic data analysis tools and interpretation is revolutionizing the field of outbreak investigations in hospitals. Metagenomics is an additional evolving field that might become commonly used in the future for outbreak investigations. Nevertheless, practitioners are frequently limited in terms of WGS or metagenomics, especially for local outbreak analyses, as a result of costs or logistical considerations, reduced or lack of locally available resources and/or expertise. As a result, traditional approaches, including pulsed-field gel electrophoresis, repetitive-element palindromic PCR and multilocus sequence typing, along with other typing methods, are still widely used. AIMS To provide practitioners with evidenced-based action plans for usage of the various typing techniques in order to investigate the molecular epidemiology of nosocomial outbreaks, of clinically significant pathogens in acute-care hospitals. SOURCES PubMed search with relevant keywords along with personal collection of relevant publications. CONTENT Representative case scenarios and critical review of the relevant scientific literature. IMPLICATIONS The review provides practical action plans to manage molecular epidemiologic investigations of outbreaks caused by clinically significant nosocomial pathogens, while prioritizing the use and timely integration of the various methodologies.
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20
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Kulsum U, Kapil A, Singh H, Kaur P. NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1052:39-49. [DOI: 10.1007/978-981-10-7572-8_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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21
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Importation, Mitigation, and Genomic Epidemiology of Candida auris at a Large Teaching Hospital. Infect Control Hosp Epidemiol 2017; 39:53-57. [PMID: 29208056 DOI: 10.1017/ice.2017.231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Candida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure. DESIGN Quasi-experimental observation. SETTING A 528-bed teaching hospital. PATIENTS The index case patient and 17 collocated ward mates. INTERVENTION Immediately after confirmation of CA in the bloodstream and urine of a patient admitted 6 days previously, active surveillance, enhanced transmission-based precautions, environmental cleaning with peracetic acid-hydrogen peroxide and ultraviolet light, and patient relocation were undertaken. Pre-existing agreements and foundational relationships among internal multidisciplinary teams and external partners were leveraged to bolster detection and mitigation efforts and to provide genomic epidemiology. RESULTS Candida auris was isolated from 3 of 132 surface samples on days 8, 9, and 15 of ward occupancy, and from no patient samples (0 of 48). Environmental and patient isolates were genetically identical (4-8 single-nucleotide polymorphisms [SNPs]) and most closely related to the 2013 India CA-6684 strain (~200 SNPs), supporting the epidemiological hypothesis that the source of environmental contamination was the index case patient, who probably acquired the South Asian strain from another New York hospital. All isolates contained a mutation associated with azole resistance (K163R) found in the India 2105 VPCI strain but not in CA-6684. The index patient remained colonized until death. No surfaces were CA-positive 1 month later. CONCLUSION Compared to previous descriptions, CA dissemination was minimal. Immediate access to rapid CA diagnostics facilitates early containment strategies and outbreak investigations. Infect Control Hosp Epidemiol 2018;39:53-57.
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22
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Motro Y, Moran-Gilad J. Next-generation sequencing applications in clinical bacteriology. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 14:1-6. [PMID: 29255684 PMCID: PMC5727008 DOI: 10.1016/j.bdq.2017.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 10/01/2017] [Accepted: 10/12/2017] [Indexed: 12/15/2022]
Abstract
With the rapid advances in next generation sequencing (NGS) technologies, clinical and public health microbiology laboratories are increasingly adopting NGS technology in their workflows into their existing diagnostic cycles. In this bacteriology focused review, we review aspects and considerations for applying NGS in the clinical microbiology settings, and highlight the impact of such implementation on the analytical and post-analytical stages of diagnosis
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Affiliation(s)
- Yair Motro
- Department of Health System Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jacob Moran-Gilad
- Department of Health System Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Public Health Services, Ministry of Health, Jerusalem, Israel
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
- Corresponding author at: Dept. of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev POB 653, Beer-Sheva, 8410501, Israel.
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23
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Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017; 30:1015-1063. [PMID: 28855266 PMCID: PMC5608882 DOI: 10.1128/cmr.00016-17] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.
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Affiliation(s)
- Scott Quainoo
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Jordy P M Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
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Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory. J Clin Microbiol 2017; 55:2502-2520. [PMID: 28592550 PMCID: PMC5527429 DOI: 10.1128/jcm.00361-17] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/26/2017] [Indexed: 11/24/2022] Open
Abstract
Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits.
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Jennison AV. Impact of whole genome sequencing in Public Health reference laboratories. MICROBIOLOGY AUSTRALIA 2017. [DOI: 10.1071/ma17060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Public Health Microbiology reference laboratories fulfil a critical role in providing overarching testing and surveillance for notifiable, emerging and important pathogens. These duties require the laboratory to possess an extensive repertoire of validated assays and the ability to rapidly respond to novel threats and outbreaks. For these, among other reasons, the ‘one stop shop' approach of whole genome sequencing (WGS) has been embraced by microbiology reference laboratories. The ability to replace multiple labour-intensive assays with a single technique of superior typeability and discrimination at an often competitive price, although not without its challenges, has already begun to change the workflow of Public Health reference laboratories.
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Acevedo-Rocha CG, Budisa N. Xenomicrobiology: a roadmap for genetic code engineering. Microb Biotechnol 2016; 9:666-76. [PMID: 27489097 PMCID: PMC4993186 DOI: 10.1111/1751-7915.12398] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 11/27/2022] Open
Abstract
Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high‐throughput and low‐cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non‐natural building blocks in living cells. In this context, genetic code engineering respectively enables the re‐design of genes/genomes and proteins/proteomes with non‐canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new‐to‐nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a ‘genetic firewall’ will also allow to study and understand the relation between code evolution and horizontal gene transfer.
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Affiliation(s)
- Carlos G Acevedo-Rocha
- Biosyntia ApS, 2970, Hørsholm, Denmark.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | - Nediljko Budisa
- Department of Chemistry, Technical University Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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Lesho EP, Clifford RJ. For Rapid Molecular Detection, Why Not a Whole Genome Approach? Clin Infect Dis 2016; 63:570-1. [PMID: 27225237 DOI: 10.1093/cid/ciw332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emil P Lesho
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Robert J Clifford
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland
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Lesho E, Clifford R, Onmus-Leone F, Appalla L, Snesrud E, Kwak Y, Ong A, Maybank R, Waterman P, Rohrbeck P, Julius M, Roth A, Martinez J, Nielsen L, Steele E, McGann P, Hinkle M. The Challenges of Implementing Next Generation Sequencing Across a Large Healthcare System, and the Molecular Epidemiology and Antibiotic Susceptibilities of Carbapenemase-Producing Bacteria in the Healthcare System of the U.S. Department of Defense. PLoS One 2016; 11:e0155770. [PMID: 27196272 PMCID: PMC4873006 DOI: 10.1371/journal.pone.0155770] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/03/2016] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE We sought to: 1) provide an overview of the genomic epidemiology of an extensive collection of carbapenemase-producing bacteria (CPB) collected in the U.S. Department of Defense health system; 2) increase awareness of the public availability of the sequences, isolates, and customized antimicrobial resistance database of that system; and 3) illustrate challenges and offer mitigations for implementing next generation sequencing (NGS) across large health systems. DESIGN Prospective surveillance and system-wide implementation of NGS. SETTING 288-hospital healthcare network. METHODS All phenotypically carbapenem resistant bacteria underwent CarbaNP® testing and PCR, followed by NGS. Commercial (Newbler and Geneious), on-line (ResFinder), and open-source software (Btrim, FLASh, Bowtie2, an Samtools) were used for assembly, SNP detection and clustering. Laboratory capacity, throughput, and response time were assessed. RESULTS From 2009 through 2015, 27,000 multidrug-resistant Gram-negative isolates were submitted. 225 contained carbapenemase-encoding genes (most commonly blaKPC, blaNDM, and blaOXA23). These were found in 15 species from 146 inpatients in 19 facilities. Genetically related CPB were found in more than one hospital. Other clusters or outbreaks were not clonal and involved genetically related plasmids, while some involved several unrelated plasmids. Relatedness depended on the clustering algorithm used. Transmission patterns of plasmids and other mobile genetic elements could not be determined without ultra-long read, single-molecule real-time sequencing. 80% of carbapenem-resistant phenotypes retained susceptibility to aminoglycosides, and 70% retained susceptibility to fluoroquinolones. However, among the CPB-confirmed genotypes, fewer than 25% retained susceptibility to aminoglycosides or fluoroquinolones. CONCLUSION Although NGS is increasingly acclaimed to revolutionize clinical practice, resource-constrained environments, large or geographically dispersed healthcare networks, and military or government-funded public health laboratories are likely to encounter constraints and challenges as they implement NGS across their health systems. These include lack of standardized definitions and quality control metrics, limitations of short-read sequencing, insufficient bandwidth, and the current limited availability of very expensive and scarcely available sequencing platforms. Possible solutions and mitigations are also proposed.
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Affiliation(s)
- Emil Lesho
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Robert Clifford
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Fatma Onmus-Leone
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Lakshmi Appalla
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Erik Snesrud
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Yoon Kwak
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Ana Ong
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Rosslyn Maybank
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Paige Waterman
- Global Emerging Infectious Disease Surveillance and Response Section, Armed Forces Health Surveillance Section, Silver Spring, MD, United States of America
| | - Patricia Rohrbeck
- Epidemiology and Analysis Section, Armed Forces Health Surveillance Center, Silver Spring, MD, United States of America
| | - Michael Julius
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Amanda Roth
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Joshua Martinez
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Lindsey Nielsen
- Department of Laboratory Medicine, San Antonio Military Medical Center, San Antonio, TX, United States of America
| | - Eric Steele
- Department of Laboratory Medicine, San Antonio Military Medical Center, San Antonio, TX, United States of America
| | - Patrick McGann
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Mary Hinkle
- Multidrug-resistant organism Repository and Surveillance Network (MRSN)-Antimicrobial Resistance Monitoring and Research (ARMoR) Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
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