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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a One Health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 PMCID: PMC11180571 DOI: 10.1016/j.anaerobe.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; National Center for Biotechnology Information, NIH, Bethesda, MD, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Chandramohan D, Beck EL, Ford D, Hopkins T, Dallas SD, Walter E, Cadena J. A Case of New Delhi Metallo-ß-Lactamase-Producing Enterobacter and a Review of Cases in the United States From January 2009 to September 2022. Cureus 2024; 16:e60200. [PMID: 38868241 PMCID: PMC11167570 DOI: 10.7759/cureus.60200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
Antimicrobial resistance is a growing problem. Novel resistance mechanisms continue to emerge, and the pipeline of antimicrobial development struggles to keep up. Antimicrobial stewardship and proper infection control are key in preventing the spread of these infections. A case of a carbapenem-resistant Enterobacter cloacae complex urinary isolate was identified in an 81-year-old male patient at the San Antonio Veterans Affairs hospital, Texas, USA. The patient was placed on isolation, and further testing of the isolate to other antibiotics requested. The purpose of this study is to analyze the details of reports of such cases and to review at-risk populations and appropriate treatment for resistant organisms.
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Affiliation(s)
- Divya Chandramohan
- Infectious Diseases, University of Texas Health Science Center at San Antonio, San Antonio, USA
| | - Erica L Beck
- Infection Prevention, South Texas Health System, San Antonio, USA
| | - Delvina Ford
- Infection Prevention, South Texas Health System, San Antonio, USA
| | - Teri Hopkins
- Pharmacy, South Texas Health System, San Antonio, USA
| | - Steven D Dallas
- Microbiology, University of Texas Health Science Center at San Antonio, San Antonio, USA
| | - Elizabeth Walter
- Infectious Diseases, South Texas Health System, San Antonio, USA
| | - Jose Cadena
- Infectious Diseases, South Texas Health System, San Antonio, USA
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3
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Cersosimo LM, Worley JN, Bry L. Approaching pathogenic Clostridia from a One Health perspective. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574718. [PMID: 38260382 PMCID: PMC10802438 DOI: 10.1101/2024.01.08.574718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M. Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
| | - Jay N. Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- National Center for Biotechnology Information, NIH, Bethesda, MD
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- Clinical Microbiology Laboratory, Dept. Pathology, Brigham & Women's Hospital, Boston, MA
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4
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Nosocomial Pluralibacter gergoviae Isolates Expressing NDM and KPC Carbapenemases Characterized Using Whole-Genome Sequencing. Antimicrob Agents Chemother 2022; 66:e0109322. [PMID: 36121219 PMCID: PMC9578427 DOI: 10.1128/aac.01093-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Farzana R, Jones LS, Rahman MA, Sands K, van Tonder AJ, Portal E, Criollo JM, Parkhill J, Guest MF, Watkins WJ, Pervin M, Boostrom I, Hassan B, Mathias J, Kalam MA, Walsh TR. Genomic Insights Into the Mechanism of Carbapenem Resistance Dissemination in Enterobacterales From a Tertiary Public Heath Setting in South Asia. Clin Infect Dis 2022; 76:119-133. [PMID: 35412593 PMCID: PMC9825829 DOI: 10.1093/cid/ciac287] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 01/12/2023] Open
Abstract
SUMMARY 10.6% patients were CRE positive. Only 27% patients were prescribed at least 1 antibiotic to which infecting pathogen was susceptible. Burn and ICU admission and antibiotics exposures facilitate CRE acquisition. Escherichia coli ST167 was the dominant CRE clone. BACKGROUND Given the high prevalence of multidrug resistance (MDR) across South Asian (SA) hospitals, we documented the epidemiology of carbapenem-resistant Enterobacterales (CRE) infections at Dhaka Medical College Hospital between October 2016 and September 2017. METHODS We enrolled patients and collected epidemiology and outcome data. All Enterobacterales were characterized phenotypically and by whole-genome sequencing. Risk assessment for the patients with CRE was performed compared with patients with carbapenem-susceptible Enterobacterales (CSE). RESULTS 10.6% of all 1831 patients with a clinical specimen collected had CRE. In-hospital 30-day mortality was significantly higher with CRE [50/180 (27.8%)] than CSE [42/312 (13.5%)] (P = .001); however, for bloodstream infections, this was nonsignificant. Of 643 Enterobacterales isolated, 210 were CRE; blaNDM was present in 180 isolates, blaOXA-232 in 26, blaOXA-181 in 24, and blaKPC-2 in 5. Despite this, ceftriaxone was the most commonly prescribed empirical antibiotic and only 27% of patients were prescribed at least 1 antibiotic to which their infecting pathogen was susceptible. Significant risk factors for CRE isolation included burns unit and intensive care unit admission, and prior exposure to levofloxacin, amikacin, clindamycin, and meropenem. Escherichia coli ST167 was the dominant CRE clone. Clustering suggested clonal transmission of Klebsiella pneumoniae ST15 and the MDR hypervirulent clone, ST23. The major trajectories involved in horizontal gene transfer were IncFII and IncX3, IS26, and Tn3. CONCLUSIONS This is the largest study from an SA public hospital combining outcome, microbiology, and genomics. The findings indicate the urgent implementation of targeted diagnostics, appropriate antibiotic use, and infection-control interventions in SA public institutions.
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Affiliation(s)
- Refath Farzana
- Correspondence: R. Farzana, Department of Zoology, University of Oxford, Oxford, United Kingdom; Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, UK ()
| | - Lim S Jones
- Public Health Wales Microbiology, University Hospital of Wales, Cardiff, United Kingdom
| | | | - Kirsty Sands
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Andries J van Tonder
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jose Munoz Criollo
- Advanced Research Computing @Cardiff (ARCCA), Cardiff University, Cardiff, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Martyn F Guest
- Advanced Research Computing @Cardiff (ARCCA), Cardiff University, Cardiff, United Kingdom
| | - W John Watkins
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Monira Pervin
- Department of Virology, Dhaka Medical College, Dhaka, Bangladesh
| | - Ian Boostrom
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Brekhna Hassan
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jordan Mathias
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Md Abul Kalam
- Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, Bangladesh
| | - Timothy R Walsh
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Liu C, Xu M, Li X, Dong H, Ming L. Trends in antimicrobial resistance in bloodstream infections at a large tertiary-care hospital in China: a 10-year retrospective study (2010-2019). J Glob Antimicrob Resist 2021; 29:413-419. [PMID: 34800707 DOI: 10.1016/j.jgar.2021.09.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/13/2021] [Accepted: 09/27/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Bloodstream infections (BSIs) are considered as a major cause of morbidity and mortality all over the world. The purpose of this study was to explore the distribution and antimicrobial resistance trends of pathogens causing BSIs at a large tertiary-care hospital in Henan province, east-central China. METHODS In this surveillance study, blood culture specimens were routinely taken from patients with fever or suspicion of sepsis from 2010 to 2019 at the First Affiliated Hospital of Zhengzhou University. Identification of organisms was carried out using the VITEK 2 Compact system and/or the VITEK MS system. Antimicrobial susceptibility tests were carried out by the minimum inhibitory concentration (MIC) method and/or the disk diffusion according to Clinical & Laboratory Standards Institute guidelines. RESULTS A total of 18180 strains were isolated from blood culture specimens, the most common pathogen was E. coli (21.6%), followed by CoNS (coagulase negative staphylococci, 18.8%), K. pneumoniae (13.0%), S. aureus (6.6%), E. faecium (5.0%), A. baumannii (4.4%), and P. aeruginosa (3.8%). The resistance rates of E. coli to ceftazidime, cefotaxime, cefepime and aztreonam showed a significant declined trend, and the frequency of carbapenem-resistant E. coli was below 6.0% over time. It is noteworthy that the proportion of carbapenem-resistant K. pneumoniae exhibited sharp upward trend during the ten years (from 6.7% to 56.7%). The prevalence of carbapenem-resistant A.baumannii has remained at a high level (>75%). In contrast, the resistance rates for P. aeruginosa against all tested agents were lower than 25%, and the resistance rates to aminoglycosides and fluoroquinolones showed a significant downward trend. The frequency of methicillin-resistant CoNS maintained a high level over the past decade (>70%), however, the isolation rate of MRSA ranged from 58.0% to 34.9%, showed a significant decline. CONCLUSIONS It was particularly noteworthy that the dramatic and consistent increase in carbapenem-resistance in K. pneumoniae during the 10-year surveillance period and effective infection control measures and stewardship efforts should be taken to prevent the spread. Our results indicate the the importance of active surveillance for bacterial etiology and their antibiotic resistance causing BSIs.
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Affiliation(s)
- Cailin Liu
- Department of clinical laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China; Henan province Key Laboratory of Medicine, Zhengzhou 450052, Henan, China
| | - Min Xu
- Department of clinical laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China; Henan province Key Laboratory of Medicine, Zhengzhou 450052, Henan, China
| | - Xiaogai Li
- Department of clinical laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China; Henan province Key Laboratory of Medicine, Zhengzhou 450052, Henan, China
| | - Huiyue Dong
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Liang Ming
- Department of clinical laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China; Henan province Key Laboratory of Medicine, Zhengzhou 450052, Henan, China.
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Earle W, Bonegio RGB, Smith DB, Branch-Elliman W. Plazomicin for the treatment of multidrug-resistant Klebsiella bacteraemia in a patient with underlying chronic kidney disease and acute renal failure requiring renal replacement therapy. BMJ Case Rep 2021; 14:e243609. [PMID: 34413038 PMCID: PMC8378394 DOI: 10.1136/bcr-2021-243609] [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] [Accepted: 08/02/2021] [Indexed: 11/04/2022] Open
Abstract
A 75-year-old man presented with shortness of breath and somnolence and was found to have urosepsis. Blood and urine cultures subsequently grew multidrug-resistant (MDR) Klebsiella pneumoniae (Kp) with the New Delhi metallo-β-lactamase gene. The patient was treated successfully with plazomicin and meropenem/vaborbactam combination therapy. The course was complicated by acute kidney injury temporarily requiring haemodialysis, gastrointestinal bleed requiring multiple transfusions and hospital readmission with blood cultures again positive with MDR Kp. Plazomicin drug levels were persistently high during treatment, suggesting that therapeutic drug monitoring may be needed to safely use this drug in patients with severe renal dysfunction. This case marks the first use of plazomicin for bacteraemia in the literature outside of a clinical trial and demonstrates its safe and effective use in a patient with advanced renal disease, and provides important insights about dosing and therapeutic drug monitoring considerations in this patient population.
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Affiliation(s)
- William Earle
- Department of Medicine, VA Boston Healthcare System, West Roxbury, Massachusetts, USA
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Ramón G B Bonegio
- Department of Medicine, VA Boston Healthcare System, West Roxbury, Massachusetts, USA
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Donald B Smith
- Department of Pharmacy, VA Boston Healthcare System, West Roxbury, Massachusetts, USA
| | - Westyn Branch-Elliman
- Department of Medicine, Section of Infectious Diseases, VA Boston Healthcare System, West Roxbury, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Genomic Drivers of Multidrug-Resistant Shigella Affecting Vulnerable Patient Populations in the United States and Abroad. mBio 2021; 12:mBio.03188-20. [PMID: 33500335 PMCID: PMC7858064 DOI: 10.1128/mbio.03188-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant Shigella isolates with resistance to macrolides are an emerging public health threat. We define a plasmid/pathogen complex behind infections seen in the United States and globally in vulnerable patient populations and identify multiple outbreaks in the United States and evidence of intercontinental transmission. Multidrug-resistant (MDR) Shigella infections have been identified globally among men who have sex with men (MSM). The highly drug-resistant phenotype often confounds initial antimicrobial therapy, placing patients at risk for adverse outcomes, the development of more drug-resistant strains, and additional treatment failures. New macrolide-resistant Shigella strains complicate treatment further as azithromycin is a next-in-line antibiotic for MDR strains, and an antibiotic-strain combination confounded by gaps in validated clinical breakpoints for clinical laboratories to interpret macrolide resistance in Shigella. We present the first high-resolution genomic analyses of 2,097 U.S. Shigella isolates, including those from MDR outbreaks. A sentinel shigellosis case in an MSM patient revealed a strain carrying 12 plasmids, of which two carried known resistance genes, the pKSR100-related plasmid pMHMC-004 and spA-related plasmid pMHMC-012. Genomic-epidemiologic analyses of isolates revealed high carriage rates of pMHMC-004 predominantly in U.S. isolates from men and not in other demographic groups. Isolates genetically related to the sentinel case further harbored elevated numbers of unique replicons, showing the receptivity of this Shigella lineage to plasmid acquisition. Findings from integrated genomic-epidemiologic analyses were leveraged to direct targeted clinical actions to improve rapid diagnosis and patient care and for public health efforts to further reduce spread.
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Ooi N, Lee VE, Chalam-Judge N, Newman R, Wilkinson AJ, Cooper IR, Orr D, Lee S, Savage VJ. Restoring carbapenem efficacy: a novel carbapenem companion targeting metallo-β-lactamases in carbapenem-resistant Enterobacterales. J Antimicrob Chemother 2021; 76:460-466. [PMID: 33152764 PMCID: PMC8600017 DOI: 10.1093/jac/dkaa455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The dissemination of MBLs compromises effective use of many β-lactams in the treatment of patients with life-threatening bacterial infections. Predicted global increases in the prevalence of MBL-producing carbapenem-resistant Enterobacterales (CRE) are being realized, yielding infections that are untreatable with existing therapies including newly approved β-lactam/β-lactamase inhibitor combinations. Developing MBL inhibitors (MBLIs) now is essential to address the growing threat that MBL-producing CRE pose to patients. METHODS A novel MBLI series was assessed by susceptibility testing and time-kill assays. Target activity and selectivity was evaluated using bacterial NDM, VIM and IMP enzyme assays and human matrix metallopeptidase enzyme assays, respectively, and cytotoxicity was assessed in HepG2 cells. In vivo efficacy of meropenem/MBLI combinations was evaluated in a mouse thigh infection model using an NDM-1-producing Escherichia coli strain. RESULTS Combination of MBLIs with carbapenems reduced MICs for NDM/IMP/VIM-producing Enterobacterales by up to 128-fold compared with the carbapenems alone. Supplementation of meropenem with the promising compound 272 reduced the MIC90 from 128 to 0.25 mg/L in a panel of MBL-producing CRE clinical isolates (n = 115). Compound 272 restored the bactericidal activity of meropenem and was non-cytotoxic, potentiating the antimicrobial action of meropenem through specific inhibition of NDM, IMP and VIM. In vivo efficacy was achieved in a mouse thigh infection model with meropenem/272 dosed subcutaneously. CONCLUSIONS We have developed a series of rationally designed MBLIs that restore activity of carbapenems against NDM/IMP/VIM-producing Enterobacterales. This series warrants further development towards a novel combination therapy that combats antibiotic-resistant organisms, which pose a critical threat to human health.
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Affiliation(s)
- Nicola Ooi
- Infex Therapeutics Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | - Victoria E Lee
- Infex Therapeutics Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | | | - Rebecca Newman
- Infex Therapeutics Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | | | - Ian R Cooper
- Infex Therapeutics Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | - David Orr
- Infex Therapeutics Ltd, Alderley Park, Macclesfield, Cheshire, UK
| | - Sally Lee
- Infex Therapeutics Ltd, Alderley Park, Macclesfield, Cheshire, UK
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Piza-Buitrago A, Rincón V, Donato J, Saavedra SY, Duarte C, Morero J, Falquet L, Reguero MT, Barreto-Hernández E. Genome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases. BMC Microbiol 2020; 20:345. [PMID: 33183231 PMCID: PMC7664025 DOI: 10.1186/s12866-020-02030-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 11/02/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá - Colombia, 2015. RESULTS Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six β-lactamase genes in both isolates: blaNDM-1, blaVIM-2, blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1. Additionally, various resistance genes associated with antibiotic target alteration (arnA, PmrE, PmrF, LpxA, LpxC, gyrB, folP, murA, rpoB, rpsL, tet34) were found and four efflux pumps (RosAB, EmrD, mdtH and cmlA). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates. The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015. CONCLUSIONS We report the coexistence of the carbapenemase genes blaNDM-1, and blaVIM-2, together with the β-lactamase genes blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1, in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further.
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Affiliation(s)
- Adriana Piza-Buitrago
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Verónica Rincón
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - John Donato
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Jaime Morero
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Laurent Falquet
- Biochemistry/Bioinformatics Unit, Université de Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - María Teresa Reguero
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Emiliano Barreto-Hernández
- Bioinformatics Group, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia.
- Molecular Epidemiology Laboratory, Biotechnology Institute, Universidad Nacional de Colombia, Bogotá, Colombia.
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Timme RE, Wolfgang WJ, Balkey M, Venkata SLG, Randolph R, Allard M, Strain E. Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. ONE HEALTH OUTLOOK 2020; 2:20. [PMID: 33103064 PMCID: PMC7568946 DOI: 10.1186/s42522-020-00026-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
The holistic approach of One Health, which sees human, animal, plant, and environmental health as a unit, rather than discrete parts, requires not only interdisciplinary cooperation, but standardized methods for communicating and archiving data, enabling participants to easily share what they have learned and allow others to build upon their findings. Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and universities. Here we describe how microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow. First, we describe the open pathogen surveillance framework, hosted on the NCBI platform. We cover the current community standards for WGS quality, provide an SOP for assessing your own sequence quality and recommend QC thresholds for all submitters to follow. We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database. These Best Practices can be models for other open data projects, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.
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Affiliation(s)
- Ruth E. Timme
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740 USA
| | | | - Maria Balkey
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740 USA
| | | | - Robyn Randolph
- Association of Public Health Laboratories, Silver Spring, MD USA
| | - Marc Allard
- U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, 5001 Campus Drive, College Park, MD 20740 USA
| | - Errol Strain
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD USA
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Taggar G, Attiq Rheman M, Boerlin P, Diarra MS. Molecular Epidemiology of Carbapenemases in Enterobacteriales from Humans, Animals, Food and the Environment. Antibiotics (Basel) 2020; 9:antibiotics9100693. [PMID: 33066205 PMCID: PMC7602032 DOI: 10.3390/antibiotics9100693] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
The Enterobacteriales order consists of seven families including Enterobacteriaceae, Erwiniaceae, Pectobacteriaceae, Yersiniaceae, Hafniaceae, Morganellaceae, and Budviciaceae and 60 genera encompassing over 250 species. The Enterobacteriaceae is currently considered as the most taxonomically diverse among all seven recognized families. The emergence of carbapenem resistance (CR) in Enterobacteriaceae caused by hydrolytic enzymes called carbapenemases has become a major concern worldwide. Carbapenem-resistant Enterobacteriaceae (CRE) isolates have been reported not only in nosocomial and community-acquired pathogens but also in food-producing animals, companion animals, and the environment. The reported carbapenemases in Enterobacteriaceae from different sources belong to the Ambler class A (blaKPC), class B (blaIMP, blaVIM, blaNDM), and class D (blaOXA-48) β-lactamases. The carbapenem encoding genes are often located on plasmids or associated with various mobile genetic elements (MGEs) like transposons and integrons, which contribute significantly to their spread. These genes are most of the time associated with other antimicrobial resistance genes such as other β-lactamases, as well as aminoglycosides and fluoroquinolones resistance genes leading to multidrug resistance phenotypes. Control strategies to prevent infections due to CRE and their dissemination in human, animal and food have become necessary. Several factors involved in the emergence of CRE have been described. This review mainly focuses on the molecular epidemiology of carbapenemases in members of Enterobacteriaceae family from humans, animals, food and the environment.
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Affiliation(s)
- Gurleen Taggar
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Muhammad Attiq Rheman
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Moussa Sory Diarra
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), 93, Stone Road West, Guelph, ON N1G 5C6, Canada; (G.T.); (M.A.R.)
- Correspondence:
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Tian X, Huang C, Ye X, Jiang H, Zhang R, Hu X, Xu D. Carbapenem-Resistant Enterobacter cloacae Causing Nosocomial Infections in Southwestern China: Molecular Epidemiology, Risk Factors, and Predictors of Mortality. Infect Drug Resist 2020; 13:129-137. [PMID: 32021327 PMCID: PMC6959490 DOI: 10.2147/idr.s234678] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/13/2019] [Indexed: 11/23/2022] Open
Abstract
Background The emergence and spread of carbapenem-resistant Enterobacter cloacae (CR-ECL) have posed a serious threat to clinical management. This retrospective study assessed the epidemiological characteristics of CR-ECL to explore the risk factors and predictors of mortality in patients with CR-ECL infection. Methods We performed a retrospective 1:2 case-control study of hospitalized patients from January 2014 to December 2017. A total of 85 consecutive unique CR-ECL strains comprised the case group, and 170 matched patients with carbapenem-susceptible Enterobacter cloacae (CS-ECL) infection at the same period as the control group. Isolates were screened for potential resistance genes by polymerase chain reaction (PCR) and molecular typing was performed by multilocus sequence typing (MLST). Results The results of drug resistance gene detection showed that blaNDM-1 was the most common carbapenem resistance gene. The MLST results showed that ST51 was the predominant epidemic type, followed by ST88. ICU admission (P<0.001), drainage tube (P=0.002), central venous catheter (P=0.005), and carbapenem exposure (P=0.003) were independent risk factors for CR-ECL infection. Significant predictors for 28-day mortality included solid tumours (P=0.005), septic shock (P=0.019), and mechanical ventilation (P=0.027). Conclusion Our study indicated that ST51 and ST88, which are closely related, were the predominant epidemic types of CR-ECL producing blaNDM-1 in southwestern China. Strengthening the surveillance of patients with solid tumours, septic shock and mechanical ventilation is an urgent need.
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Affiliation(s)
- Xiaolang Tian
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Changwu Huang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Xiaoli Ye
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Hongyan Jiang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Rufang Zhang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Xiaofang Hu
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
| | - Dongshuang Xu
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital (Fifth People's Hospital of Chongqing), Chongqing, People's Republic of China
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14
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Conlan S, Lau AF, Deming C, Spalding CD, Lee-Lin S, Thomas PJ, Park M, Dekker JP, Frank KM, Palmore TN, Segre JA. Plasmid Dissemination and Selection of a Multidrug-Resistant Klebsiella pneumoniae Strain during Transplant-Associated Antibiotic Therapy. mBio 2019; 10:e00652-19. [PMID: 31594809 PMCID: PMC6786864 DOI: 10.1128/mbio.00652-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Antibiotics, which are used both to prevent and to treat infections, are a mainstay therapy for lifesaving procedures such as transplantation. For this reason, and many others, increased antibiotic resistance among human-associated pathogens, such as the carbapenem-resistant Enterobacteriaceae species, is of grave concern. In this study, we report on a hematopoietic stem cell transplant recipient in whom cultures detected the emergence of carbapenem resistance and spread across five strains of bacteria that persisted for over a year. Carbapenem resistance in Citrobacter freundii, Enterobacter cloacae, Klebsiella aerogenes, and Klebsiella pneumoniae was linked to a pair of plasmids, each carrying the Klebsiella pneumoniae carbapenemase gene (blaKPC). Surveillance cultures identified a carbapenem-susceptible strain of Citrobacter freundii that may have become resistant through horizontal gene transfer of these plasmids. Selection of a multidrug-resistant Klebsiella pneumoniae strain was also detected following combination antibiotic therapy. Here we report a plasmid carrying the blaKPC gene with broad host range that poses the additional threat of spreading to endogenous members of the human gut microbiome.IMPORTANCE Antibiotic-resistant bacteria are a serious threat to medically fragile patient populations. The spread of antibiotic resistance through plasmid-mediated mechanisms is of grave concern as it can lead to the conversion of endogenous patient-associated strains to difficult-to-treat pathogens.
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Affiliation(s)
- Sean Conlan
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Anna F Lau
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Clay Deming
- National Human Genome Research Institute, Bethesda, Maryland, USA
| | | | | | - Pamela J Thomas
- National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA
| | - Morgan Park
- National Institutes of Health Intramural Sequencing Center (NISC), Rockville, Maryland, USA
| | - John P Dekker
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Karen M Frank
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Tara N Palmore
- National Institutes of Health Clinical Center, Bethesda, Maryland, USA
| | - Julia A Segre
- National Human Genome Research Institute, Bethesda, Maryland, USA
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