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Khoshbayan A, Narimisa N, Elahi Z, Bostanghadiri N, Razavi S, Shariati A. Global prevalence of mutation in the mgrB gene among clinical isolates of colistin-resistant Klebsiella pneumoniae: a systematic review and meta-analysis. Front Microbiol 2024; 15:1386478. [PMID: 38912352 PMCID: PMC11190090 DOI: 10.3389/fmicb.2024.1386478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background Colistin is used as a last resort for managing infections caused by multidrug-resistant bacteria. However, the high emergence of colistin-resistant strains has restricted the clinical use of this antibiotic in the clinical setting. In the present study, we evaluated the global prevalence of the mutation in the mgrB gene, one of the most important mechanisms of colistin resistance in Klebsiella pneumoniae. Methods Several databases, including Scopus, Medline (via PubMed), and Web of Science, were searched (until August 2023) to identify those studies that address the mgrB mutation in clinical isolates of K. pneumoniae. Using Stata software, the pooled prevalence of mgrB mutation and subgroup analyses for the year of publication, country, continent, mgrB mutation types, and detection methods of mgrB mutation were analyzed. Results Out of the 115 studies included in the analysis, the prevalence of mgrB mutations in colistin-resistant K. pneumoniae isolates was estimated at 65% of isolates, and mgrB variations with insertional inactivation had the highest prevalence among the five investigated mutations with 69%. The year subgroup analysis indicated an increase in mutated mgrB from 46% in 2014 to 61% in 2022. Europe had the highest prevalence of mutated mgrB at 73%, while Africa had the lowest at 54%. Conclusion Mutations in the mgrB gene are reported as one of the most common mechanisms of colistin resistance in K. pneumoniae, and the results of the present study showed that 65% of the reported colistin-resistant K. pneumoniae had a mutation in this gene.
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Affiliation(s)
- Amin Khoshbayan
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Negar Narimisa
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Vice Chancellery of Education and Research, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Narjess Bostanghadiri
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aref Shariati
- Molecular and Medicine research center, Khomein University of Medical Sciences, Khomein, Iran
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
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Talat A, Khan F, Khan AU. Genome analyses of colistin-resistant high-risk bla NDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings. BMC Microbiol 2024; 24:174. [PMID: 38769479 PMCID: PMC11103832 DOI: 10.1186/s12866-024-03306-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT). RESULTS This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32-128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357). CONCLUSION The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.
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Affiliation(s)
- Absar Talat
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Fatima Khan
- Microbiology Department, JNMC and Hospital, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Doğan E, Sydow K, Heiden SE, Eger E, Wassilew G, Proctor RA, Bohnert JA, Idelevich EA, Schaufler K, Becker K. Klebsiella pneumoniae exhibiting a phenotypic hyper-splitting phenomenon including the formation of small colony variants. Front Cell Infect Microbiol 2024; 14:1372704. [PMID: 38601740 PMCID: PMC11004228 DOI: 10.3389/fcimb.2024.1372704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
In this study, we characterized a Klebsiella pneumoniae strain in a patient with shrapnel hip injury, which resulted in multiple phenotypic changes, including the formation of a small colony variant (SCV) phenotype. Although already described since the 1960s, there is little knowledge about SCV phenotypes in Enterobacteriaceae. The formation of SCVs has been recognized as a bacterial strategy to evade host immune responses and compromise the efficacy of antimicrobial therapies, leading to persistent and recurrent courses of infections. In this case, 14 isolates with different resisto- and morpho-types were distinguished from the patient's urine and tissue samples. Whole genome sequencing revealed that all isolates were clonally identical belonging to the K. pneumoniae high-risk sequence type 147. Subculturing the SCV colonies consistently resulted in the reappearance of the initial SCV phenotype and three stable normal-sized phenotypes with distinct morphological characteristics. Additionally, an increase in resistance was observed over time in isolates that shared the same colony appearance. Our findings highlight the complexity of bacterial behavior by revealing a case of phenotypic "hyper-splitting" in a K. pneumoniae SCV and its potential clinical significance.
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Affiliation(s)
- Eyüp Doğan
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Katharina Sydow
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
| | - Stefan E. Heiden
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
| | - Elias Eger
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
| | - Georgi Wassilew
- Center for Orthopedics, Trauma Surgery and Rehabilitation Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Richard A. Proctor
- Departments of Medical Microbiology/Immunology and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jürgen A. Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Evgeny A. Idelevich
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Katharina Schaufler
- Department of Epidemiology and Ecology of Antimicrobial Resistance, Helmholtz Institute for One Health, Helmholtz Centre for Infection Research Helmholtz Center for Infection Research (HZI), Greifswald, Germany
- University Medicine Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
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Wang X, Qin J, Xiang G, Wang C, Wang Q, Qin J, Wang H, Shen Z. Nosocomial dissemination of blaIMP-4 among Klebsiella pneumoniae by horizontal gene transfer and clonal spread: the epidemic IncN plasmids and the emerging high-risk IMP-4-producing ST101 clone. J Antimicrob Chemother 2023; 78:2890-2894. [PMID: 37875024 DOI: 10.1093/jac/dkad326] [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: 06/06/2023] [Accepted: 09/29/2023] [Indexed: 10/26/2023] Open
Abstract
OBJECTIVES To determine the genomic features of IMP-4-producing Klebsiella pneumoniae isolates recovered from paediatric patients and the transmission dynamics of blaIMP-4. METHODS IMP-producing K. pneumoniae isolates were collected from paediatric patients in Shanghai Children's Medical Center from 2013 to 2020. WGS was performed for all isolates, and the complete genomes of three IMP-4-producing isolates were generated. The distribution of blaIMP-4-harbouring plasmids was determined, and a conjugation assay was employed to investigate the horizontal transfer of blaIMP-4-harbouring plasmids. RESULTS We collected 21 blaIMP-carrying K. pneumoniae isolates, with IMP-4 (16/21, 76.2%) as the predominant subtype, followed by IMP-8 (n = 3) and IMP-26 (n = 2). IMP-4-producing isolates displayed a diverse population structure and all blaIMP-4 genes were located on plasmids, including IncN (n = 9), IncHI5 (n = 5), IncFII(K) (n = 1) and IncFII(pKP91) (n = 1), although only IncN plasmids were conjugative. Clonal transmission of ST101 strains carrying IncHI5 blaIMP-4-harbouring plasmids was observed, and the acquisition of blaIMP-4 by the international high-risk ST101 clone constituted a novel combination of ST101 clone and carbapenemase genes. Plasmid analysis demonstrated that the conjugal transfer of the IncHI5 blaIMP-4-harbouring plasmid might be blocked by the ST101 bacterial host. CONCLUSIONS The horizontal transfer of IncN plasmids and clonal spread of the international high-risk ST101 clone facilitated the nosocomial dissemination of blaIMP-4 among K. pneumoniae. The emerging IMP-4-producing ST101 clone displays diverse combinations of carbapenemase genes, and this clone could be a continually evolving threat and warrants prospective monitoring.
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Affiliation(s)
- Xing Wang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Qin
- Department of Clinical Laboratory, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Clinical Microbiology Laboratory, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoxiu Xiang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qichen Wang
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Juanxiu Qin
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haiying Wang
- Department of Clinical Laboratory, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhen Shen
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Kedišaletše M, Phumuzile D, Angela D, Andrew W, Mae NF. Epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Enterobacterales in Africa: A systematic review. J Glob Antimicrob Resist 2023; 35:297-306. [PMID: 37879456 DOI: 10.1016/j.jgar.2023.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVES Carbapenem-resistant Enterobacterales (CRE) commonly cause hospital-acquired infections and hospital outbreaks worldwide, with an alarming increase in Africa, necessitating review of regional CRE epidemiological trends. METHODS A systematic review was conducted using PRISMA guidelines, searching PubMed, Scopus and Web of Science databases for studies describing CRE distribution, risk factors for CRE acquisition and clinical outcome of CRE infections in Africa. RESULTS One-hundred and sixty-nine studies were included, with the majority from North Africa (92/169, 54.4%). Most studies (136/169; 80.4%) focused only on infection, with a total of 15666 CRE isolates (97.4% clinical infection, 2.6% colonisation). The leading bacterial species included Klebsiella (72.2%), Escherichia coli (13.5%), and Enterobacter (8.3%). The most frequently detected carbapenemases were NDM (43.1%) and OXA-48-like (42.9%). Sequence types were reported in 44 studies, with ST101 and ST147 most commonly reported in K. pneumoniae, and ST410, ST167 and ST38 in E. coli. Previous antibiotic use, prior hospitalisation, surgical procedures, indwelling devices, intensive care unit admission and prolonged hospital stay, were the most frequent factors associated with CRE infection/colonisation. Crude mortality for CRE infection was 37%. CONCLUSION Although K. pneumoniae and E. coli remain the most frequent CRE in Africa, observed sequence types are not the commonly reported global 'high-risk' clones. The distribution of species and carbapenemases differs across African regions, while risk factors for CRE colonisation/infection, and patient outcomes are similar to those reported globally. There are limited data on CREs from parts of Africa, highlighting the need to strengthen epidemiologic surveillance programmes in the region.
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Affiliation(s)
- Moloto Kedišaletše
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Dube Phumuzile
- Synthetic Biology Center, NextGeneration Health, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Dramowski Angela
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Whitelaw Andrew
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Newton-Foot Mae
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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Arıcı N, Tanrıverdi ES, Çalık Ş, Kansak N, Adaleti R, Otlu B, Aksaray S. Carbapenem-resistant Klebsiella pneumoniae outbreak with monoclonal spread: Evaluation of resistance genes and ceftazidime-avibactam susceptibility. Indian J Med Microbiol 2023; 46:100431. [PMID: 37945124 DOI: 10.1016/j.ijmmb.2023.100431] [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: 03/14/2023] [Revised: 06/23/2023] [Accepted: 07/17/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE The aim of this study was to investigate ceftazidime-avibactam (CAZ-AVI) susceptibility, carbapenemase genes, and clonal relationship in carbapenem-resistant Klebsiella pneumoniae (CrKp) isolates. METHODS A total of 28 non-repetitive CrKp isolates with positive carbapenemase production determined by the modified carbapenem inactivation method (mCIM), were included in the study. Identification of the isolates was performed with MALDI-TOF MS (VITEK-MS, bioMerieux, France). The automated system (VITEK-2, bioMerieux) and gradient diffusion test (Etest, bioMerieux) were used to determine antibiotic susceptibility. The mCIM was performed according to CLSI (2021) recommendations. CAZ-AVI susceptibility was carried out using the standard disc diffusion method. Results were evaluated according to EUCAST 2022 criteria. The blaOXA-48, blaNDM, blaKPC, blaIMP and blaVIM genes were investigated by multiplex PCR. The clonal relationship between isolates was determined by both AP-PCR and PFGE methods. RESULTS Of the total 28 isolates, 89.3% were susceptible to CAZ-AVI. blaOXA-48 gene was found in 85.7% of the isolates, blaOXA-48+blaNDM gene in 10.7%, and blaNDM gene in 3.6%. blaKPC, blaIMP and blaVIM genes were not detected. Three clusters with three different genotypes were determined by the PFGE method. The largest cluster was Genotype A (n:24), followed by Genotype B (n:3), and Genotype C (n:1). AP-PCR was highly compatible with PFGE. The isolates of Genotype A, mostly from the intensive care unit (ICU), were evaluated as outbreak strains with monoclonal dissemination. CONCLUSIONS OXA-48 remains the most frequently detected enzyme in CrKp strains in our country. The ceftazidime-avibactam susceptibility rate of 89.3% indicates that this antibiotic is still effective against CrKp isolates. The unnoticed outbreak detected in our study revealed the severity of intra-hospital cross-contamination affecting different wards, including the ICU. Therefore, in order to limit the spread of CrKp isolates, it is of great importance to implement strict infection control measures, and molecular surveillance programs, especially in the ICU.
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Affiliation(s)
- Neslihan Arıcı
- University of Health Sciences, Haydarpasa Numune Research and Training Hospital, Medical Microbiology, Istanbul, Turkey.
| | - Elif Seren Tanrıverdi
- Inonu University, Medical Faculty, Department of Medical Microbiology, Malatya, Turkey.
| | - Şeyma Çalık
- University of Health Sciences, Haydarpasa Numune Research and Training Hospital, Medical Microbiology, Istanbul, Turkey.
| | - Nilgün Kansak
- University of Health Sciences, Haydarpasa Numune Research and Training Hospital, Medical Microbiology, Istanbul, Turkey.
| | - Rıza Adaleti
- University of Health Sciences, Haydarpasa Numune Research and Training Hospital, Medical Microbiology, Istanbul, Turkey.
| | - Barış Otlu
- Inonu University, Medical Faculty, Department of Medical Microbiology, Malatya, Turkey.
| | - Sebahat Aksaray
- University of Health Sciences, Hamidiye Medical Faculty, Department of Medical Microbiology, Istanbul, Turkey.
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Sivasankar S, Premnath MA, Boppe A, Grobusch MP, Jeyaraj S. Screening of MMV pandemic response and pathogen box compounds against pan-drug-resistant Klebsiella pneumoniae to identify potent inhibitory compounds. New Microbes New Infect 2023; 55:101193. [PMID: 38046897 PMCID: PMC10690571 DOI: 10.1016/j.nmni.2023.101193] [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: 09/15/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023] Open
Abstract
Background The recent emergence of pan-drug-resistant (PDR) K. pneumoniae strains hinders the success rate of treatment procedures for patients. High mortality, extended duration of hospitalization with high costs is associated with such infections. Discovery and identification of new drugs are inevitable to combat PDR clinical pathogens. We aim to identify and evaluate new compounds in vitro against a PDR clinical K. pneumoniae isolate using compounds of Pathogen Box and Pandemic Response Box from Medicines for Malaria Venture (MMV). Methods The PDR strain was initially screened with the 601 compounds from both Boxes at 10 μM concentration. Formation of dormant cells against the drug activity was assessed using persister assay. MIC was determined for the drugs inhibiting PDR K. pneumoniae during initial screening. Results Five compounds were identified to inhibit the test strain. MMV1580854 (94.60 %), MMV1579788 (94.65 %), MMV1578574 (eravacycline; 93.13 %), MMV1578566 (epetraborole; 95.29 %) and MMV1578564 (96.32 %) were able to exhibit a higher percentage of growth inhibition. Persisters were found to be growing in a range from 104 to 107 CFU/ml. Minimum inhibitory concentrations (MIC) of all compounds were ≥ 2 μM except for MMV1579788, which had a MIC of ≥ 5 μM. Conclusion Five novel compounds were identified against the highly evolved pan-drug-resistant K. pneumoniae. Among the five, epetraborole andMMV1578564 were identified as highly potent based on the persister frequency and MICs. The pan-drug resistant clinical isolate used in this study was found to be acting differently from the reference or wild type strains against the test compounds in a previous study.
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Affiliation(s)
- Seshan Sivasankar
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
- PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, India
| | - Mari Abinaya Premnath
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
- PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, India
| | - Appalaraju Boppe
- Department of Microbiology, PSG Institute of Medical Sciences and Research, Coimbatore, India
| | - Martin Peter Grobusch
- Centre de Recherches Médicales de Lambaréné CERMEL, Hospital Albert Schweitzer, BP 242, Lambaréné, Gabon
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection and Immunity, Amsterdam Public Health, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands
- Institut für Tropenmedizin, Eberhard Karls Universität Tübingen and German Center for Infection Research (DZIF), Tubingen, Germany
- Masanga Medical Research Unit, Masanga, Sierra Leone
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Sankarganesh Jeyaraj
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, India
- PSG Center for Genetics and Molecular Biology, Off Avinashi Road, Coimbatore, India
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8
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Zahedi Bialvaei A, Eslami P, Ganji L, Dolatyar Dehkharghani A, Asgari F, Koupahi H, Barzegarian Pashacolaei HR, Rahbar M. Prevalence and epidemiological investigation of mgrB-dependent colistin resistance in extensively drug resistant Klebsiella pneumoniae in Iran. Sci Rep 2023; 13:10680. [PMID: 37393362 PMCID: PMC10314893 DOI: 10.1038/s41598-023-37845-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Carbapenemases-producing K. pneumoniae are challenging antimicrobial therapy of hospitalised patients, which is further complicated by colistin resistance. The aim of this study was to investigate the molecular epidemiological insights into carbapenemases-producing and colistin-resistant clinical K. pneumoniaeA total of 162 colistin resistant clinical strains of K. pneumoniae were collected during 2017-2019. Antimicrobial susceptibility and the colistin minimum inhibitory concentration were determined. Using PCR assay, the prevalence of resistance-associated genes including blaKPC, blaIMP, blaVIM, blaOXA-48, blaNDM-1 and mcr-1 to -9 was examined. Additionally, a PCR assay was used to examine the mgrB gene in colistin-resistant bacteria. 94.4% of the tested strains were resistant to imipenem and 96.3% were resistant to meropenem. Colistin resistance (MIC > 4 µg/L) was observed in 161 isolates (99.4%) by Colistin Broth Disk Elution method. The KPC enzyme was the most common carbapenemase and was identified in 95 strains (58.6%), followed by the IMP, VIM and OXA-48 detected in 47 (29%), 23 (14.2%) and 12 (7.4%) isolates, respectively. However, no NDM-1 gene was detected. Additionally, none of the studied isolates harbored mcr variants, while mgrB gene was observed in 152 (92.6%) isolates. Colistin resistance of K. pneumoniae isolates may be associated with mgrB gene mutation. To stop the spread of resistant K. pneumoniae, surveillance must be improved, infection prevention protocols must be followed, and antibiotic stewardship must be practised.
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Affiliation(s)
- Abed Zahedi Bialvaei
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Parisa Eslami
- Department of Microbiology, Milad Hospital, Tehran, Iran
| | - Leila Ganji
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran
| | - Alireza Dolatyar Dehkharghani
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran
| | - Farhad Asgari
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran
| | - Hossein Koupahi
- Department of Microbiology, Islamic Azad University, Varamin-Pishva Branch, Varamin, Iran
| | | | - Mohammad Rahbar
- Department of Microbiology, Ministry of Health & Medical Education, Iranian Reference Health Laboratories Research Center, Tehran, Iran.
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Arcari G, Carattoli A. Global spread and evolutionary convergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae high-risk clones. Pathog Glob Health 2023; 117:328-341. [PMID: 36089853 PMCID: PMC10177687 DOI: 10.1080/20477724.2022.2121362] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
For people living in developed countries life span is growing at a faster pace than ever. One of the main reasons for such success is attributable to the introduction and extensive use in the clinical practice of antibiotics over the course of the last seven decades. In hospital settings, Klebsiella pneumoniae represents a well-known and commonly described opportunistic pathogen, typically characterized by resistance to several antibiotic classes. On the other hand, the broad wedge of population living in Low and/or Middle Income Countries is increasing rapidly, allowing the spread of several commensal bacteria which are transmitted via human contact. Community transmission has been the original milieu of K. pneumoniae isolates characterized by an outstanding virulence (hypervirulent). These two characteristics, also defined as "pathotypes", originally emerged as different pathways in the evolutionary history of K. pneumoniae. For a long time, the Sequence Type (ST), which is defined by the combination of alleles of the 7 housekeeping genes of the Multi-Locus Sequence Typing, has been a reliable marker of the pathotype: multidrug-resistant clones (e.g. ST258, ST147, ST101) in the Western world and hypervirulent clones (e.g. ST23, ST65, ST86) in the Eastern. Currently, the boundaries separating the two pathotypes are fading away due to several factors, and we are witnessing a worrisome convergence in certain high-risk clones. Here we review the evidence available on confluence of multidrug-resistance and hypervirulence in specific K. pneumoniae clones.
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Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Gomes MZR, de Lima EM, Martins Aires CA, Pereira PS, Yim J, Silva FH, Rodrigues CAS, Oliveira TRTE, da Silva PP, Eller CM, de Souza CMR, Rybak MJ, Albano RM, de Miranda AB, Machado E, Catanho M. Outbreak report of polymyxin-carbapenem-resistant Klebsiella pneumoniae causing untreatable infections evidenced by synergy tests and bacterial genomes. Sci Rep 2023; 13:6238. [PMID: 37069157 PMCID: PMC10110528 DOI: 10.1038/s41598-023-31901-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023] Open
Abstract
Polymyxin-carbapenem-resistant Klebsiella pneumoniae (PCR-Kp) with pan (PDR)- or extensively drug-resistant phenotypes has been increasingly described worldwide. Here, we report a PCR-Kp outbreak causing untreatable infections descriptively correlated with bacterial genomes. Hospital-wide surveillance of PCR-Kp was initiated in December-2014, after the first detection of a K. pneumoniae phenotype initially classified as PDR, recovered from close spatiotemporal cases of a sentinel hospital in Rio de Janeiro. Whole-genome sequencing of clinical PCR-Kp was performed to investigate similarities and dissimilarities in phylogeny, resistance and virulence genes, plasmid structures and genetic polymorphisms. A target phenotypic profile was detected in 10% (12/117) of the tested K. pneumoniae complex bacteria recovered from patients (8.5%, 8/94) who had epidemiological links and were involved in intractable infections and death, with combined therapeutic drugs failing to meet synergy. Two resistant bacterial clades belong to the same transmission cluster (ST437) or might have different sources (ST11). The severity of infection was likely related to patients' comorbidities, lack of antimicrobial therapy and predicted bacterial genes related to high resistance, survival, and proliferation. This report contributes to the actual knowledge about the natural history of PCR-Kp infection, while reporting from a time when there were no licensed drugs in the world to treat some of these infections. More studies comparing clinical findings with bacterial genetic markers during clonal spread are needed.
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Affiliation(s)
- Marisa Zenaide Ribeiro Gomes
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
- Hospital Federal Servidores do Estado, Ministry of Health, Rio de Janeiro, Brazil.
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
- Hospital Infection Control Committee, Hospital Universitário Pedro Ernesto, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.
| | | | - Caio Augusto Martins Aires
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
- Departamento de Ciência da Saúde, Universidade Federal Rural do Semi-Árido (UFERSA), Mossoró, Rio Grande do Norte, Brazil
| | - Polyana Silva Pereira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Juwon Yim
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Fernando Henrique Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | | | - Priscila Pinho da Silva
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Cristiane Monteiro Eller
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Claudio Marcos Rocha de Souza
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Michael J Rybak
- Anti-Infective Research Laboratory, Eugene Applebaum College of Pharmacy and Health Sciences, Department of Medicine, Division of Infectious Diseases, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Rodolpho Mattos Albano
- Departamento de Bioquímica, IBRAG, Universidade do Estado do Rio de Janeiro,, Rio de Janeiro, Brazil
| | - Antonio Basílio de Miranda
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Edson Machado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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Prevalence of Mutated Colistin-Resistant Klebsiella pneumoniae: A Systematic Review and Meta-Analysis. Trop Med Infect Dis 2022; 7:tropicalmed7120414. [PMID: 36548669 PMCID: PMC9782491 DOI: 10.3390/tropicalmed7120414] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
The emergence of genetic mutations in chromosomal genes and the transmissible plasmid-mediated colistin resistance gene may have helped in the spread of colistin resistance among various Klebsiella pneumoniae (K. pneumoniae) isolates and other different bacteria. In this study, the prevalence of mutated colistin-resistant K. pneumoniae isolates was studied globally using a systematic review and meta-analysis approach. A systematic search was conducted in databases including PubMed, ScienceDirect, Scopus and Google Scholar. The pooled prevalence of mutated colistin resistance in K. pneumoniae isolates was analyzed using Comprehensive Meta-Analysis Software (CMA). A total of 50 articles were included in this study. The pooled prevalence of mutated colistin resistance in K. pneumoniae was estimated at 75.4% (95% CI = 67.2−82.1) at high heterogeneity (I2 = 81.742%, p-value < 0.001). Meanwhile, the results of the subgroup analysis demonstrated the highest prevalence in Saudi Arabia with 97.9% (95% CI = 74.1−99.9%) and Egypt, with 4.5% (95% CI = 0.6−26.1%), had the lowest. The majority of mutations could be observed in the mgrB gene (88%), pmrB gene (54%) and phoQ gene (44%). The current study showed a high prevalence of the mutation of colistin resistance genes in K. pneumoniae. Therefore, it is recommended that regular monitoring be performed to control the spread of colistin resistance.
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Exploring the Antibiotic Resistance Profile of Clinical Klebsiella pneumoniae Isolates in Portugal. Antibiotics (Basel) 2022; 11:antibiotics11111613. [PMID: 36421258 PMCID: PMC9686965 DOI: 10.3390/antibiotics11111613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
While antibiotic resistance is rising to dangerously high levels, resistance mechanisms are spreading globally among diverse bacterial species. The emergence of antibiotic-resistant Klebsiella pneumoniae, mainly due to the production of antibiotic-inactivating enzymes, is currently responsible for most treatment failures, threatening the effectiveness of classes of antibiotics used for decades. This study assessed the presence of genetic determinants of β-lactam resistance in 102 multi-drug resistant (MDR) K. pneumoniae isolates from patients admitted to two central hospitals in northern Portugal from 2010 to 2020. Antimicrobial susceptibility testing revealed a high rate (>90%) of resistance to most β-lactam antibiotics, except for carbapenems and cephamycins, which showed antimicrobial susceptibility rates in the range of 23.5−34.3% and 40.2−68.6%, respectively. A diverse pool of β-lactam resistance genetic determinants, including carbapenemases- (i.e., blaKPC-like and blaOXA-48-like), extended-spectrum β-lactamases (ESBL; i.e., blaTEM-like, blaCTX-M-like and blaSHV-like), and AmpC β-lactamases-coding genes (i.e., blaCMY-2-like and blaDHA-like) were found in most K. pneumoniae isolates. blaKPC-like (72.5%) and ESBL genes (37.3−74.5%) were the most detected, with approximately 80% of K. pneumoniae isolates presenting two or more resistance genes. As the optimal treatment of β-lactamase-producing K. pneumoniae infections remains problematic, the high co-occurrence of multiple β-lactam resistance genes must be seen as a serious warning of the problem of antimicrobial resistance.
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13
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De Koster S, Rodriguez Ruiz JP, Rajakani SG, Lammens C, Glupczynski Y, Goossens H, Xavier BB. Diversity in the Characteristics of Klebsiella pneumoniae ST101 of Human, Environmental, and Animal Origin. Front Microbiol 2022; 13:838207. [PMID: 35222344 PMCID: PMC8866942 DOI: 10.3389/fmicb.2022.838207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Background Klebsiella pneumoniae ST101 is an emerging high-risk clone which exhibits extensive drug resistance. Bacterial strains residing in multiple hosts show unique signatures related to host adaptation. In this study, we assess the genetic relationship of K. pneumoniae ST101 isolated from hospital samples, the environment, community, and livestock using whole genome sequencing (WGS). Materials and Methods We selected ten K. pneumoniae ST101 strains from hospitalized patients in Italy (n = 3) (2014) and Spain (n = 5) (2015–2016) as well as Belgian livestock animals (n = 2) (2017–2018). WGS was performed with 2 × 250 bp paired-end sequencing (Nextera XT) sample preparation kit and MiSeq (Illumina Inc.). Long-read sequencing (Pacbio Sequel I) was used to sequence the two livestock strains and three Italian hospital-associated strains. Furthermore, a public ST101 sequence collection of 586 strains (566 hospital-associated strains, 12 environmental strains, six strains from healthy individuals, one food-associated strain and one pig strain) was obtained. BacPipe and Kleborate were used to conduct genome analysis. ISFinder was used to find IS elements, and PHASTER was utilized to identify prophages. A phylogenetic tree was constructed to illustrate genetic relatedness. Results Hospital-associated K. pneumoniae ST101 showed higher resistance scores than non-clinical isolates from healthy individuals, the environment, food and livestock (1.85 ± 0.72 in hospital-associated isolates vs. 1.14 ± 1.13 in non-clinical isolates, p < 0.01). Importantly, the lack of integrative conjugative elements ICEKp bearing iron-scavenging yersiniabactin siderophores (ybt) in livestock-associated strains suggests a lower pathogenicity potential than hospital-associated strains. Mobile genetic elements (MGE) appear to be an important source of diversity in K. pneumoniae ST101 strains from different origins, with a highly stable genome and few recombination events outside the prophage-containing regions. Core genome MLST based analysis revealed a distinct genetic clustering between human and livestock-associated isolates. Conclusion The study of K. pneumoniae ST101 hospital-associated and strains from healthy individuals and animals revealed a genetic diversity between these two groups, allowing us to identify the presence of yersiniabactin siderophores in hospital-associated isolates. Resistance and virulence levels in livestock-associated strains were considerably lower than hospital-associated strains, implying that the public health risk remains low. The introduction of an ICEKp into animal strains, on the other hand, might pose a public threat over time.
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Polyclonal Endemicity of Carbapenemase-Producing Klebsiella pneumoniae in ICUs of a Greek Tertiary Care Hospital. Antibiotics (Basel) 2022; 11:antibiotics11020149. [PMID: 35203752 PMCID: PMC8868164 DOI: 10.3390/antibiotics11020149] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/04/2022] Open
Abstract
Carbapenemase-producing Klebsiella pneumoniae (CPKP) emerged in Greece in 2002 and became endemic thereafter. Driven by a notable variability in the phenotypic testing results for carbapenemase production in K. pneumoniae isolates from the intensive care units (ICUs) of our hospital, we performed a study to assess the molecular epidemiology of CPKP isolated between 2016 and 2019 using pulse-field gel electrophoresis (PFGE) including isolates recovered from 165 single patients. We investigated the molecular relatedness among strains recovered from rectal surveillance cultures and from respective subsequent infections due to CPKP in the same individual (48/165 cases). For the optimal interpretation of our findings, we carried out a systematic review regarding the clonality of CPKP isolated from clinical samples in ICUs in Europe. In our study, we identified 128 distinguishable pulsotypes and 17 clusters that indicated extended dissemination of CPKP within the hospital ICU setting throughout the study period. Among the clinical isolates, 122 harbored KPC genes (74%), 2 harbored KPC+NDM (1.2%), 38 harbored NDM (23%), 1 harbored NDM+OXA-48 (0.6%), 1 harbored NDM+VIM (0.6%) and 1 harbored the VIM (0.6%) gene. Multiple CPKP strains in our hospital have achieved sustained transmission. The polyclonal endemicity of CPKP presents a further threat for the selection of pathogens resistant to last-resort antimicrobial agents.
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Šuto S, Bedenić B, Likić S, Kibel S, Anušić M, Tičić V, Zarfel G, Grisold A, Barišić I, Vraneš J. Diffusion of OXA-48 carbapenemase among urinary isolates of Klebsiella pneumoniae in non-hospitalized elderly patients. BMC Microbiol 2022; 22:30. [PMID: 35045829 PMCID: PMC8767700 DOI: 10.1186/s12866-022-02443-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background Recently, a dramatic increase of Klebsiella pneumoniae positive for OXA-48 β-lactamases was observed first in the hospital setting and later in the long-term care facilities (LTCFs) and community in the Zagreb County, particularly, in urinary isolates. The aim of the study was to analyse the epidemiology and the mechanisms of antibiotic resistance of OXA-48 carbapenemase producing K. pneumoniae strains isolated from urine of non-hospitalized elderly patients. Results The isolates were classified into two groups: one originated from the LTCFs and the other from the community. Extended-spectrum β-lactamases (ESBLs) were detected by double disk-synergy (DDST) and combined disk tests in 55% of the isolates (51/92). The ESBL-positive isolates exhibited resistance to expanded-spectrum cephalosporins (ESC) and in majority of cases to gentamicin. LTCFs isolates showed a significantly lower rate of additional ESBLs and consequential resistance to ESC and a lower gentamicin resistance rate compared to the community isolates, similarly to hospital isolates in Zagreb, pointing out to the possible transmission from hospitals.ESBL production was associated with group 1 of CTX-M or SHV-12 β-lactamases. Ertapenem resistance was transferable from only 12 isolates. blaOXA-48 genes were carried by IncL plasmid in 42 isolates. In addition IncFII and IncFIB were identified in 18 and 2 isolates, respectively. Two new sequence types were reported: ST4870 and ST4781. Conclusions This study showed eruptive and extensive diffusion of OXA-48 carbapenemase to LTCFs and community population in Zagreb County, particularly affecting patients with UTIs and urinary catheters. On the basis of susceptibility testing, β-lactamase production, conjugation experiments, MLST and plasmid characterization it can be concluded that there was horizontal gene transfer between unrelated isolates, responsible for epidemic spread of OXA-48 carbapenemase in the LTCFs and the community The rapid spread of OXA-48 producing K. pneumoniae points out to the shortcomings in the infection control measures.
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16
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Rodrigues C, Desai S, Passet V, Gajjar D, Brisse S. Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147. Microb Genom 2022; 8. [PMID: 35019836 PMCID: PMC8914359 DOI: 10.1099/mgen.0.000737] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The rapid emergence of multidrug-resistant Klebsiella pneumoniae is being driven largely by the spread of specific clonal groups (CGs). Of these, CG147 includes 7-gene multilocus sequence typing (MLST) sequence types (STs) ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147. Antimicrobial-susceptibility testing following European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines and genome sequencing (Illumina and Oxford Nanopore Technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes [National Center for Biotechnology Information (NCBI), May 2019]. CG147 evolution was inferred within a temporal phylogenetic framework (beast) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, phaster, ICEfinder and CRISPRCasFinder). Strain DJ had a pandrug-resistance phenotype. Its genome comprised the chromosome, seven plasmids and one linear phage-plasmid. Four carbapenemase genes were detected: blaNDM-5 and two copies of blaOXA-181 in the chromosome, and a second copy of blaNDM-5 on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63 % carried a carbapenemase gene and 83 % harboured blaCTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype I-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74 %, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20 %, emerged in 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Furthermore, subclades within ST147-KL64 differed at the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system. K. pneumoniae CG147 comprises pandrug-resistant or extensively resistant isolates, and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomal blaNDM-5. Its emergence is being driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo–spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.
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Affiliation(s)
- Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
| | - Siddhi Desai
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
| | - Devarshi Gajjar
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université de Paris, Paris, France
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17
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Epidemiology and in vitro activity of ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, eravacycline, plazomicin, and comparators against Greek carbapenemase-producing Klebsiella pneumoniae isolates. Infection 2021; 50:467-474. [PMID: 34854060 DOI: 10.1007/s15010-021-01735-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/20/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND The increase in carbapenem-resistant Klebsiella pneumoniae (CRKP) infections is of great concern because of limited treatment options. New antimicrobials were recently approved for clinical therapy. This study evaluated the epidemiology of carbapenemase-producing K. pneumoniae isolates collected at a Greek university hospital during 2017-2020, and their susceptibilities to ceftazidime-avibactam (CAZ/AVI), meropenem-vaborbactam (M/V), imipenem-relebactam (I/R), eravacycline, plazomicin, and comparators. METHODS Minimum inhibitory concentrations (MICs) were evaluated by Etest. Only colistin MICs were determined by the broth microdilution method. Carbapenemase genes were detected by PCR. Selected isolates were typed by multilocus sequence typing (MLST). RESULTS A total of 266 carbapenemase-producing K. pneumoniae strains were isolated during the 4-year study period. Among them, KPC was the most prevalent (75.6%), followed by NDM (11.7%), VIM (5.6%), and OXA-48 (4.1%). KPC-producing isolates belonged mainly to ST258 and NDM producers belonged to ST11, whereas OXA-48- and VIM producers were polyclonal. Susceptibility to tigecycline, fosfomycin, and colistin was 80.5%, 83.8%, and 65.8%, respectively. Of the novel agents tested, plazomicin was the most active inhibiting 94% of the isolates at ≤ 1.5 μg/ml. CAZ/AVI and M/V inhibited all KPC producers and I/R 98.5% of them. All OXA-48 producers were susceptible to CAZ/AVI and plazomicin. The novel β-lactam/β-lactamase inhibitors (BLBLIs) tested were inactive against MBL-positive isolates, while eravacycline inhibited 61.3% and 66.7% of the NDM and VIM producers, respectively. CONCLUSIONS KPC remains the predominant carbapenemase among K. pneumoniae, followed by NDM. Novel BLBLIs, eravacycline, and plazomicin are promising agents for combating infections by carbapenemase-producing K. pneumoniae. However, the emergence of resistance to these agents highlights the need for continuous surveillance and application of enhanced antimicrobial stewardship.
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18
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Arca-Suárez J, Rodiño-Janeiro BK, Pérez A, Guijarro-Sánchez P, Vázquez-Ucha JC, Cruz F, Gómez-Garrido J, Alioto TS, Álvarez-Tejado M, Gut M, Gut I, Oviaño M, Beceiro A, Bou G. Emergence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacterales in Spain studied by whole-genome sequencing. Int J Antimicrob Agents 2021; 59:106456. [PMID: 34688835 DOI: 10.1016/j.ijantimicag.2021.106456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 11/27/2022]
Abstract
The emergence of 16S rRNA methyltransferases (RMTs) in Gram-negative pathogens bearing other clinically relevant resistance mechanisms, such as carbapenemase-producing Enterobacterales (CPE), is becoming an alarming concern. We investigated the prevalence, antimicrobial susceptibility, resistance mechanisms, molecular epidemiology and genetic support of RMTs in CPE isolates from Spain. This study included a collection of 468 CPE isolates recovered during 2018 from 32 participating Spanish hospitals. MICs were determined using the broth microdilution method, the agar dilution method (fosfomycin) or MIC gradient strips (plazomicin). All isolates were subjected to hybrid whole-genome sequencing (WGS). Sequence types (STs), core genome phylogenetic relatedness, horizontally acquired resistance mechanisms, plasmid analysis and the genetic environment of RMTs were determined in silico from WGS data in all RMT-positive isolates. Among the 468 CPE isolates evaluated, 24 isolates (5.1%) recovered from nine different hospitals spanning five Spanish regions showed resistance to all aminoglycosides and were positive for an RMT (21 RmtF, 2 ArmA and 1 RmtC). All RMT-producers showed high-level resistance to all aminoglycosides, including plazomicin, and in most cases exhibited an extensively drug-resistant susceptibility profile. The RMT-positive isolates showed low genetic diversity and were global clones of Klebsiella pneumoniae (ST147, ST101, ST395) and Enterobacter cloacae (ST93) bearing blaOXA-48, blaNDM-1 or blaVIM-1 carbapenemase genes. RMTs were harboured in five different multidrug resistance plasmids and linked to efficient mobile genetic elements. Our findings highlight that RMTs are emerging among clinical CPE isolates from Spain and their spread should be monitored to preserve the future clinical utility of aminoglycosides and plazomicin.
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Affiliation(s)
- Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Bruno K Rodiño-Janeiro
- Prof. Martin Polz Laboratory, University of Vienna, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Vienna, Austria
| | - Astrid Pérez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Juan C Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Tyler S Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universistat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universistat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universistat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marina Oviaño
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain.
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- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
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Binsker U, Käsbohrer A, Hammerl JA. Global colistin use: A review of the emergence of resistant Enterobacterales and the impact on their genetic basis. FEMS Microbiol Rev 2021; 46:6382128. [PMID: 34612488 PMCID: PMC8829026 DOI: 10.1093/femsre/fuab049] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
The dramatic global rise of MDR and XDR Enterobacterales in human medicine forced clinicians to the reintroduction of colistin as last-resort drug. Meanwhile, colistin is used in the veterinary medicine since its discovery, leading to a steadily increasing prevalence of resistant isolates in the livestock and meat-based food sector. Consequently, transmission of resistant isolates from animals to humans, acquisition via food and exposure to colistin in the clinic are reasons for the increased prevalence of colistin-resistant Enterobacterales in humans in the last decades. Initially, resistance mechanisms were caused by mutations in chromosomal genes. However, since the discovery in 2015, the focus has shifted exclusively to mobile colistin resistances (mcr). This review will advance the understanding of chromosomal-mediated resistance mechanisms in Enterobacterales. We provide an overview about genes involved in colistin resistance and the current global situation of colistin-resistant Enterobacterales. A comparison of the global colistin use in veterinary and human medicine highlights the effort to reduce colistin sales in veterinary medicine under the One Health approach. In contrast, it uncovers the alarming rise in colistin consumption in human medicine due to the emergence of MDR Enterobacterales, which might be an important driver for the increasing emergence of chromosome-mediated colistin resistance.
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Affiliation(s)
- Ulrike Binsker
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Annemarie Käsbohrer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Department for Farm Animals and Veterinary Public Health, Institute of Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jens A Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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20
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Gatti M, Viaggi B, Rossolini GM, Pea F, Viale P. An evidence-based multidisciplinary approach focused at creating algorithms for targeted therapy of infection-related ventilator associated complications (IVACs) caused by Enterobacterales in critically ill adult patients. Expert Rev Anti Infect Ther 2021; 20:331-352. [PMID: 34488527 DOI: 10.1080/14787210.2021.1976145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Prompt implementation of appropriate targeted antibiotic therapy representsa valuable approach in improving clinical and ecological outcome in critically septic patients. Thismultidisciplinary opinion article aims to develop evidence-based algorithms for targeted antibiotictherapy of infection-related ventilator associated complications (IVACs) caused by Enterobacterales,which are among the most common pathogens associated with these conditions. AREAS COVERED A multidisciplinary team of four experts had several rounds of assessment for developingalgorithms devoted to targeted antimicrobial therapy of IVACs caused by Enterobacterales.A literature search was performed on PubMed-MEDLINE (until March 2021) to provide evidence forsupporting therapeutic choices. Quality and strength of evidence was established according toa hierarchical scale of the study design. Six different algorithms with associated recommendations concerning therapeutic choice and dosing optimization were suggested according to the susceptibilitypattern of Enterobacterales: multi-susceptible, extended-spectrum beta-lactamase (ESBL)-producing,AmpC beta-lactamase-producing, Klebsiella pneumoniae carbapenemase (KPC)-producing, OXA-48-producing, and metallo-beta-lactamase (MBL)-producing Enterobacterales. EXPERT OPINION The implementation of algorithms focused on prompt revision of antibiotic regimensguided by results of conventional and rapid diagnostic methodologies, appropriate place in therapy ofnovel beta-lactams, implementation of strategies for sparing the broadest-spectrum antibiotics, and PK/PD optimization of antibiotic dosing regimens is strongly suggested.
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Affiliation(s)
- Milo Gatti
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Ssd Clinical Pharmacology, Irccs Azienda Ospedaliero Universitaria Di Bologna, Bologna, Italy
| | - Bruno Viaggi
- Neurointensive Care Unit, Department of Anesthesiology, Careggi, University Hospital, Florence, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Federico Pea
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Ssd Clinical Pharmacology, Irccs Azienda Ospedaliero Universitaria Di Bologna, Bologna, Italy
| | - Pierluigi Viale
- Department of Medical and Surgical Sciences, Alma Mater Studiorum, University of Bologna, Bologna, Italy.,Infectious Diseases Unit, Irccs Azienda Ospedaliero Universitaria Di Bologna, Bologna, Italy
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21
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Virulence Determinants of Colistin-Resistant K. pneumoniae High-Risk Clones. BIOLOGY 2021; 10:biology10050436. [PMID: 34068937 PMCID: PMC8155863 DOI: 10.3390/biology10050436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 11/17/2022]
Abstract
We proposed the hypothesis that high-risk clones of colistin-resistant K. pneumoniae (ColR-Kp) possesses a high number of virulence factors and has enhanced survival capacity against the neutrophil activity. We studied virulence genes of ColR-Kp isolates and neutrophil response in 142 patients with invasive ColR-Kp infections. The ST101 and ST395 ColR-Kp infections had higher 30-day mortality (58%, p = 0.005 and 75%, p = 0.003). The presence of yersiniabactin biosynthesis gene (ybtS) and ferric uptake operon associated gene (kfu) were significantly higher in ST101 (99%, p ≤ 0.001) and ST395 (94%, p < 0.012). Being in ICU (OR: 7.9; CI: 1.43-55.98; p = 0.024), kfu (OR:27.0; CI: 5.67-179.65; p < 0.001) and ST101 (OR: 17.2; CI: 2.45-350.40; p = 0.01) were found to be predictors of 30-day mortality. Even the neutrophil uptake of kfu+-ybtS+ ColR-Kp was significantly higher than kfu--ybtS- ColR-Kp (phagocytosis rate: 78% vs. 65%, p < 0.001), and the kfu+-ybtS+ ColR-Kp survived more than kfu--ybtS- ColR-Kp (median survival index: 7.90 vs. 4.22; p = 0.001). The kfu+-ybtS+ ColR-Kp stimulated excessive NET formation. Iron uptake systems in high-risk clones of colistin-resistant K. pneumoniae enhance the success of survival against the neutrophil phagocytic defense and stimulate excessive NET formation. The drugs targeted to iron uptake systems would be a promising approach for the treatment of colistin-resistant high-risk clones of K. pneumoniae infections.
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22
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Arato V, Raso MM, Gasperini G, Berlanda Scorza F, Micoli F. Prophylaxis and Treatment against Klebsiella pneumoniae: Current Insights on This Emerging Anti-Microbial Resistant Global Threat. Int J Mol Sci 2021; 22:4042. [PMID: 33919847 PMCID: PMC8070759 DOI: 10.3390/ijms22084042] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/06/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023] Open
Abstract
Klebsiella pneumoniae (Kp) is an opportunistic pathogen and the leading cause of healthcare-associated infections, mostly affecting subjects with compromised immune systems or suffering from concurrent bacterial infections. However, the dramatic increase in hypervirulent strains and the emergence of new multidrug-resistant clones resulted in Kp occurrence among previously healthy people and in increased morbidity and mortality, including neonatal sepsis and death across low- and middle-income countries. As a consequence, carbapenem-resistant and extended spectrum β-lactamase-producing Kp have been prioritized as a critical anti-microbial resistance threat by the World Health Organization and this has renewed the interest of the scientific community in developing a vaccine as well as treatments alternative to the now ineffective antibiotics. Capsule polysaccharide is the most important virulence factor of Kp and plays major roles in the pathogenesis but its high variability (more than 100 different types have been reported) makes the identification of a universal treatment or prevention strategy very challenging. However, less variable virulence factors such as the O-Antigen, outer membrane proteins as fimbriae and siderophores might also be key players in the fight against Kp infections. Here, we review elements of the current status of the epidemiology and the molecular pathogenesis of Kp and explore specific bacterial antigens as potential targets for both prophylactic and therapeutic solutions.
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Affiliation(s)
| | | | | | | | - Francesca Micoli
- GSK Vaccines Institute for Global Health (GVGH) S.r.l., via Fiorentina 1, 53100 Siena, Italy; (V.A.); (M.M.R.); (G.G.); (F.B.S.)
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23
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Özad Düzgün A. From Turkey: First Report of KPC-3- and CTX-M-27-Producing Multidrug-Resistant Klebsiella pneumoniae ST147 Clone Carrying OmpK36 and Ompk37 Porin Mutations. Microb Drug Resist 2021; 27:1265-1270. [PMID: 33794115 DOI: 10.1089/mdr.2020.0274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aim: The aim of this study was to identify antimicrobial resistance genes, virulence factor genes, and porin loss or mutations exhibited by the multidrug-resistant Klebsiella pneumoniae strain. Materials and Methods: Whole-genome sequencing was done via the Illumina NovaSeq 6000 platform. Strain identification and antibiotic susceptibility testing of strains were performed by the Vitek 2 automated system. Multilocus sequence typing analysis was carried out using seven conserved housekeeping genes. Results: The strain was resistant to penicillins, cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, fosfomycin, and trimethoprim/sulfamethoxazole. The isolate was found to carry KPC-3, CTX-M-27, SHV-11, SHV-67, and TEM-1 β-lactamases. The clonal subtype of the isolate was ST147, and it possessed wzi64 and wzc38 alleles. Fifteen different point mutations (N49S, L59V, R146H, V178P, G189T, F198Y, V202L, F207Y, A217S, T222L, D223G, H235N, A280V, N304E, and S346N) were detected in the OmpK36 porin. A frame shift was observed in OmpK35 and two different point mutations (I70M and I128M) were found in the OmpK37 porin, in addition to seven mutations observed on the AcrR. Conclusions: This study demonstrated for the first time that the ST147 clone produced CTX-M-27 as well as KPC-3. In addition, new mutations were detected in the outer membrane proteins. These mutations together with the production of extended-spectrum β-lactamase and carbapenemase were found to contribute to the resistance of the ST147 clone to carbapenem and other antibiotics.
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Affiliation(s)
- Azer Özad Düzgün
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, Gumushane University, Gümüşhane, Turkey
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24
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Phenotypic and genotypic characterization of antibiotic resistance in military hospital-associated bacteria from war injuries in the Eastern Ukraine conflict between 2014 and 2020. J Hosp Infect 2021; 112:69-76. [PMID: 33789157 DOI: 10.1016/j.jhin.2021.03.020] [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: 12/13/2020] [Revised: 03/18/2021] [Accepted: 03/21/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Infections from the recent conflict in Ukraine have been poorly investigated. AIM To describe the phenotypic and genotypic mechanisms of antibiotic resistance in pathogens associated with war injuries in the Ukraine conflict. METHODS This report describes a retrospective multi-centre microbiological survey conducted in four Ukrainian military hospitals between 2014 and 2020. The phenotypes of 813 organisms obtained from 1061 tests of 162 patients were analysed. Fifty-two isolates underwent whole-genome sequencing. FINDINGS Resistance was highest in Acinetobacter baumannii, with 92.5% ((48/52) 95% confidence interval (CI) 81.8-97.9) resistant to fluoroquinolones, 83.0% ((43/52) 95% CI 70.2-91.9) resistant to aminoglycosides, and 67.9% ((37/52) 95% CI 53.7-80.1) resistant to carbapenems. In contrast, resistance to carbapenems was 55.6% ((30/52) 95% CI 41.4-69.1) in Pseudomonas aeruginosa, 42.9% in Escherichia coli ((12/28) 95% CI 24.5-62.8), and 32.8% in Klebsiella pneumoniae ((20/34) 95% CI 21.3-46.0). Multi-drug-resistant strains harboured an abundance of antibiotic resistance genes. K. pneumoniae co-produced class A and D β-lactamases, in one case with blaNDM-1 and rmtC 16S rRNA methyltransferase. A. baumannii carried class A and D β-lactamases but not metallo-β-lactamases; in four isolates, carbapenemases were present with the RmtASE gene armA. P. aeruginosa harboured a wide range of class A and D β-lactamases along with metallo-β-lactamases, as well as the RmtB4 RmtASE gene. Gram-positive cocci were generally sensitive to the tested antibiotics. CONCLUSION The incidence of resistance among the studied pathogens was higher than that in Ukrainian civilian hospitals and European countries. The discovery of P. aeruginosa, A. baumannii, and K. pneumoniae co-producing carbapenemases and RmtASEs is of particular importance, and hospitals should be vigilant for their emergence.
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25
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Santiago Rodríguez M, Bravata Alcántara JC, Martínez Briseño JC, Díaz Escamilla E, Cortes Ortiz IA, Martínez Benitez MB, Lopez-Canovas L. Rapid Protocol for Characterizing Klebsiella pneumoniae Isolates by Pulsed Field Gel Electrophoresis (PFGE) in Contour Clamped Homogeneous Electric Field (CHEF) Minigels. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1776310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Sherif M, Palmieri M, Mirande C, El-Mahallawy H, Rashed HG, Abd-El-Reheem F, El-Manakhly AR, Abdel-Latif RAR, Aboulela AG, Saeed LY, Abdel-Rahman S, Elsayed E, van Belkum A, El-Kholy A. Whole-genome sequencing of Egyptian multidrug-resistant Klebsiella pneumoniae isolates: a multi-center pilot study. Eur J Clin Microbiol Infect Dis 2021; 40:1451-1460. [PMID: 33559021 DOI: 10.1007/s10096-021-04177-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/25/2021] [Indexed: 10/22/2022]
Abstract
Multidrug-resistant (MDR) Klebsiella pneumoniae is a common infectious pathogen. We performed whole-genome sequencing (WGS) of 39 randomly selected, geographically diverse MDR K. pneumoniae from nine Egyptian hospitals. Clinical sources, phenotypic antibiotic resistance, and hyper-mucoviscosity were documented. WGS data were epidemiologically interpreted and tested for the presence of antibiotic resistance and virulence genes. Based on WGS data, we identified 18 classical multi-locus sequence types (MLST), the most common type being ST101 (23.1%) followed by ST147 (17.9%). Phylogenetic analyses identified small numbers of closely related isolates in a few of the centers, so we mostly documented independent nosocomial acquisition or import from public sources. The most common acquired resistance gene found was blaCTX-M-15, detected in 27 isolates (69.2%). Carbapenemase genes encountered were blaNDM-1 (n = 13), blaNDM-5 (n = 1), blaOXA-48 (n = 12), blaOXA-181 (n = 2), and blaKPC2 (n = 1). Seven strains (18%) contained more than a single carbapenemase gene. While searching for virulence-associated genes, sixteen wzi alleles were identified with wzi137, wzi64, and wzi50 most commonly found in ST101, ST147, and ST16, respectively. Yersiniabactin was the most common virulence factor (69.2%). Hyper-mucoviscosity was documented for 6 out of 39 isolates.This is the first genomic study of MDR K. pneumoniae from Egypt. The study revealed a clear spread of well-known international clones and their associated antimicrobial resistance and (hyper)virulence traits. The clinical situation in Egypt seems to reflect the scenario documented in many other countries and requires close attention.
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Affiliation(s)
- May Sherif
- Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mattia Palmieri
- bioMérieux, Open Innovation and Partnerships, 3 route de Port Michaud 38390, Les Grottes, La Balme, France
| | - Caroline Mirande
- bioMérieux, Open Innovation and Partnerships, 3 route de Port Michaud 38390, Les Grottes, La Balme, France
| | - Hadir El-Mahallawy
- Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Hebatallah G Rashed
- Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Fadwa Abd-El-Reheem
- Department of Clinical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Arwa Ramadan El-Manakhly
- Department of Microbiology and Infection Control, Dar-Al-Fouad Hospital, 6th of October City, Egypt.,Department of Microbiology and Immunology, Faculty of Pharmacy, Russian University in Cairo, Cairo, Egypt
| | | | | | - Laila Yosef Saeed
- Department of Clinical Pathology, Faculty of Medicine, Sohag University, Sohag, Egypt
| | - Soheir Abdel-Rahman
- Department of Clinical Pathology, Faculty of Medicine, Banha University, Banha, Egypt
| | - Eman Elsayed
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, 3 route de Port Michaud 38390, Les Grottes, La Balme, France
| | - Amani El-Kholy
- Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt.
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27
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Klebsiella pneumoniae carbapenemase (KPC) in urinary infection isolates. Arch Microbiol 2021; 203:1825-1831. [PMID: 33507339 DOI: 10.1007/s00203-020-02161-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/25/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
Recently, emergence of carbapenem-resistance, in particular due to Klebsiella pneumoniae carbapenemase (KPC), was observed among K. pneumoniae causing urinary tract infections in Croatia. The aim of the study was to characterize, antimicrobial susceptibility, carbapenem resistance, virulence traits and plasmid types of the urinary KPC positive isolates of K. pneumoniae. The antimicrobial susceptibility to a wide range of antibiotics was determined by broth microdilution method. The transferability of meropenem resistance was determined by conjugation (broth mating method) employing Escherichia coli J63 strain resistant to sodium azide. Genes encoding broad and extended-spectrum β-lactamases, plasmid-mediated AmpC β-lactamases, group A and B carbapenemases, and carbapenem hydrolyzing oxacillinases (blaOXA-48like), respectively, were determined by Polymerase chain reaction (PCR). In total 30 KPC-positive K. pneumoniae urinary isolates collected from different regions of Croatia were analysed. The isolates were uniformly resistant to all tested antibiotics except for variable susceptibility to gentamicin, sulphamethoxazole/trimethoprim, and colistin, respectively. Four isolates were resistant to colistin with MICs values ranging from 4 to 16 mg/L. All tested isolates were susceptible to ceftazidime/avibactam. Sixteen isolates transferred meropenem resistance to E. coli recipient strain by conjugation. Other resistance markers were not co-transferred. PCR was positive for blaKPC and blaSHV genes in all isolates whereas 13 isolates tested positive also for blaTEM genes. PCR based replicon typing (PBRT) revealed the presence of FIIs in 13 and FIA plasmid in two strains. The study showed dissemination of KPC-producing K. pneumoniae in urinary isolates, posing a new epidemiological and treatment challenge. Sulphamethoxazole/trimethoprim, colistin, and ceftazidime/avibactam remain so far, as the therapeutic options.
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28
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Tavoschi L, Forni S, Porretta A, Righi L, Pieralli F, Menichetti F, Falcone M, Gemignani G, Sani S, Vivani P, Bellandi T, Tacconi D, Turini L, Toccafondi G, Privitera G, Lopalco P, Baggiani A, Gemmi F, Luchini G, Petrillo M, Roti L, Pezzotti P, Pantosti A, Iannazzo S, Mechi MT, Rossolini GM, On Behalf Of The Tuscan Clinical Microbiology Laboratory Network. Prolonged outbreak of New Delhi metallo-beta-lactamase-producing carbapenem-resistant Enterobacterales (NDM-CRE), Tuscany, Italy, 2018 to 2019. ACTA ACUST UNITED AC 2021; 25. [PMID: 32070467 PMCID: PMC7029447 DOI: 10.2807/1560-7917.es.2020.25.6.2000085] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In Tuscany, Italy, New Delhi metallo-beta-lactamase-producing carbapenem-resistant Enterobacterales (NDM-CRE) have increased since November 2018. Between November 2018 and October 2019, 1,645 samples were NDM-CRE-positive: 1,270 (77.2%) cases of intestinal carriage, 129 (7.8%) bloodstream infections and 246 (14.9%) infections/colonisations at other sites. Klebsiella pneumoniae were prevalent (1,495; 90.9%), with ST147/NDM-1 the dominant clone. Delayed outbreak identification and response resulted in sustained NDM-CRE transmission in the North-West area of Tuscany, but successfully contained spread within the region.
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Affiliation(s)
- Lara Tavoschi
- Department of Translational Research and New technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Silvia Forni
- Regional Health Agency of Tuscany, Florence, Italy
| | - Andrea Porretta
- University Hospital of Pisa, Pisa, Italy.,Department of Translational Research and New technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Lorenzo Righi
- Quality of care and Clinical networks, Tuscany Region, Florence, Italy
| | | | | | | | | | - Spartaco Sani
- Livorno Hospital, Toscana North-West Health Authority, Livorno, Italy
| | - Paola Vivani
- Massa Carrara Hospital, Toscana North-West Health Authority, Massa Carrara, Italy
| | | | - Danilo Tacconi
- Arezzo Hospital, Toscana South-East Health Authority, Arezzo, Italy
| | - Lucia Turini
- Toscana North-West Health Authority, Pisa, Italy
| | - Giulio Toccafondi
- Quality of care and Clinical networks, Tuscany Region, Florence, Italy
| | - Gaetano Privitera
- University Hospital of Pisa, Pisa, Italy.,Department of Translational Research and New technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Pierluigi Lopalco
- University Hospital of Pisa, Pisa, Italy.,Department of Translational Research and New technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Angelo Baggiani
- University Hospital of Pisa, Pisa, Italy.,Department of Translational Research and New technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | | | | | - Lorenzo Roti
- Toscana North-West Health Authority, Pisa, Italy
| | | | | | | | | | - Gian Maria Rossolini
- Department of Experimental Medicine, University of Florence, Florence, Italy.,Florence Careggi University Hospital, Florence, Italy
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Antibiotic Resistance and Mobile Genetic Elements in Extensively Drug-Resistant Klebsiella pneumoniae Sequence Type 147 Recovered from Germany. Antibiotics (Basel) 2020; 9:antibiotics9100675. [PMID: 33028048 PMCID: PMC7600919 DOI: 10.3390/antibiotics9100675] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/30/2022] Open
Abstract
Mobile genetic elements (MGEs), especially multidrug-resistance plasmids, are major vehicles for the dissemination of antimicrobial resistance determinants. Herein, we analyse the MGEs in three extensively drug-resistant (XDR) Klebsiella pneumoniae isolates from Germany. Whole genome sequencing (WGS) is performed using Illumina and MinION platforms followed by core-genome multi-locus sequence typing (MLST). The plasmid content is analysed by conjugation, S1-pulsed-field gel electrophoresis (S1-PFGE) and Southern blot experiments. The K. pneumoniae isolates belong to the international high-risk clone ST147 and form a cluster of closely related isolates. They harbour the blaOXA-181 carbapenemase on a ColKP3 plasmid, and 12 antibiotic resistance determinants on an multidrug-resistant (MDR) IncR plasmid with a recombinogenic nature and encoding a large number of insertion elements. The IncR plasmids within the three isolates share a high degree of homology, but present also genetic variations, such as inversion or deletion of genetic regions in close proximity to MGEs. In addition, six plasmids not harbouring any antibiotic resistance determinants are present in each isolate. Our study indicates that genetic variations can be observed within a cluster of closely related isolates, due to the dynamic nature of MGEs. The mobilome of the K. pneumoniae isolates combined with the emergence of the XDR ST147 high-risk clone have the potential to become a major challenge for global healthcare.
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30
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Emerging Antimicrobial-Resistant High-Risk Klebsiella pneumoniae Clones ST307 and ST147. Antimicrob Agents Chemother 2020; 64:AAC.01148-20. [PMID: 32747358 DOI: 10.1128/aac.01148-20] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
There is an enormous global public health burden due to antimicrobial-resistant (AMR) Klebsiella pneumoniae high-risk clones. K. pneumoniae ST307 and ST147 are recent additions to the family of successful clones in the species. Both clones likely emerged in Europe during the early to mid-1990s and, in a relatively short time, became prominent global pathogens, spreading to all continents (with the exception of Antarctica). ST307 and ST147 consist of multiple clades/clusters and are associated with various carbapenemases (i.e., KPCs, NDMs, OXA-48-like, and VIMs). ST307 is endemic in Italy, Colombia, the United States (Texas), and South Africa, while ST147 is endemic in India, Italy, Greece, and certain North African countries. Both clones have been introduced into regions of nonendemicity, leading to worldwide nosocomial outbreaks. Genomic studies showed ST307 and ST147 contain identical gyrA and parC mutations and likely obtained plasmids with bla CTX-M-15 during the early to mid-2000s, which aided in their global distribution. ST307 and ST147 then acquired plasmids with various carbapenemases during the late 2000s, establishing themselves as important AMR pathogens in certain regions. Both clones are likely underreported due to restricted detection methodologies. ST307 and ST147 have the ability to become major threats to public health due to their worldwide distribution, ability to cause serious infections, and association with AMR, including panresistance. The medical community at large, especially those concerned with antimicrobial resistance, should be aware of the looming threat posed by emerging AMR high-risk clones such as K. pneumoniae ST307 and ST147.
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31
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Brolund A, Lagerqvist N, Byfors S, Struelens MJ, Monnet DL, Albiger B, Kohlenberg A. Worsening epidemiological situation of carbapenemase-producing Enterobacteriaceae in Europe, assessment by national experts from 37 countries, July 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 30862330 PMCID: PMC6402177 DOI: 10.2807/1560-7917.es.2019.24.9.1900123] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A survey on the epidemiological situation, surveillance and containment activities for carbapenemase-producing Enterobacteriaceae (CPE) was conducted in European countries in 2018. All 37 participating countries reported CPE cases. Since 2015, the epidemiological stage of CPE expansion has increased in 11 countries. Reference laboratory capability, dedicated surveillance and a specific national containment plan are in existence in 33, 27 and 14 countries, respectively. Enhanced control efforts are needed for CPE containment in Europe.
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Affiliation(s)
- Alma Brolund
- These authors contributed equally to this work.,Public Health Agency of Sweden, Solna, Sweden
| | - Nina Lagerqvist
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden.,These authors contributed equally to this work.,Public Health Agency of Sweden, Solna, Sweden
| | - Sara Byfors
- Public Health Agency of Sweden, Solna, Sweden
| | - Marc J Struelens
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | | | - Barbara Albiger
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Anke Kohlenberg
- European Centre for Disease Prevention and Control, Stockholm, Sweden
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32
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Fuster B, Salvador C, Tormo N, García-González N, Gimeno C, González-Candelas F. Molecular epidemiology and drug-resistance mechanisms in carbapenem-resistant Klebsiella pneumoniae isolated in patients from a tertiary hospital in Valencia, Spain. J Glob Antimicrob Resist 2020; 22:718-725. [PMID: 32446938 DOI: 10.1016/j.jgar.2020.05.002] [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: 10/15/2019] [Revised: 03/16/2020] [Accepted: 05/06/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVES The aim of this study has been to characterize carbapenem-resistant Klebsiella pneumoniae isolates and to determine the resistance mechanisms involved, the clonal relationship between strains and clinical and demographical data of the infected patients. METHODS Clinical and demographical data from patients were collected and statistically analysed. Antimicrobial susceptibility testing was performed and resistance genes were detected both phenotypically and genotypically. Conjugation assays were performed to show horizontal transferability of resistance genes. Clonal relationship was also studied. Next-generation sequencing (NGS) was performed to obtain information regarding resistance genes, sequence types, virulence factors and plasmid types. RESULTS Statistical significance was shown by the presence of an infection if there had been a previous hospital stay; urinary catheter carriage and chronic renal disease also indicated higher probabilities of being infected. More than 95% of the isolates were non-susceptible to third-generation cephalosporins, and more than 90% were non-susceptible to quinolones. Phenotypic and genotypic methods for resistance detection were concordant and later confirmed by NGS. This is the first detection of OXA-48, NDM-1 and CTX-M-15 co-production in the area. No plasmid-mediated colistin resistance was found. Tetracycline, sulfonamides and aminoglycoside resistance genes were found in almost all the isolates studied. No virulence factors were detected. Multilocus sequence typing showed more than 15 different sequence types, with ST101, ST307 and ST11 being the most prevalent. CONCLUSIONS This study is the first to report such a large group of OXA-48 carbapenemases with clonal dissemination among carbapenem-resistant K. pneumoniae in Valencia. This is also the first detection of OXA-48, NDM-1 and CTX-M-15 co-production in the area.
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Affiliation(s)
- Begoña Fuster
- Microbiology Department, Valencia General University Hospital, Valencia, Spain.
| | - Carme Salvador
- Microbiology Department, Valencia General University Hospital, Valencia, Spain
| | - Nuria Tormo
- Microbiology Department, Valencia General University Hospital, Valencia, Spain
| | - Neris García-González
- Joint Research Unit (Infection and Public Health), FISABIO, University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Concepción Gimeno
- Microbiology Department, Valencia General University Hospital, Valencia, Spain; Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit (Infection and Public Health), FISABIO, University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain; CIBER Epidemiology and Public Health, Valencia, Spain
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Hassoun-Kheir N, Snitser O, Hussein K, Rabino G, Eluk O, Warman S, Aboalhega W, Geffen Y, Mendelson S, Kishony R, Paul M. Concordance between epidemiological evaluation of probability of transmission and whole genome sequence relatedness among hospitalized patients acquiring Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae. Clin Microbiol Infect 2020; 27:468.e1-468.e7. [PMID: 32360206 DOI: 10.1016/j.cmi.2020.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/28/2020] [Accepted: 04/16/2020] [Indexed: 12/23/2022]
Abstract
OBJECTIVES We aimed to evaluate the concordance between epidemiologically determined transmission and genetic linkage of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp). METHODS We included consecutive KPC-Kp carriers between December 2016 and April 2017 in a hospital endemic for KPC-Kp. We assessed epidemiological relatedness between patients by prospective investigations by the infection control team. The probability of epidemiological relatedness was classified into four groups: no suspected transmission, low, moderate and high probability of transmission. Whole-genome sequencing of isolates was performed. Genetic linkage between KPC-Kp isolates was expressed by distance between isolates in single nucleotide polymorphisms (SNPs). We established an SNP cut-off defining a different strain based on the reconstructed phylogenetic tree. We compared the epidemiological and genetic linkage of all isolates from all patients. RESULTS The study included 25 KPC-Kp carriers with 49 isolates. SNP variance was available for 1129 crossed patient-isolate pairs. Genomic linkage, based on a cut-off of 80 SNPs to define related isolates, was found in 115/708 (16.2%) of isolates with no transmission suspected epidemiologically, 27/319 (8.5%) of low, 11/26 (42.3%) of moderate and 64/76 (84.2%) of high epidemiological transmission risk determination (p < 0.001 for trend). Similar results and significant trends were shown on sensitivity analyses using a lower SNP cut-off (six SNPs) and patient-isolate unique pairs, analysing the first isolate from each patient. CONCLUSIONS While significant concordance between epidemiological and genomic transmission patterns was found, epidemiological investigations of transmission are limited by the possibility of unidentified transmissions or over-estimation of associations. Genetic linkage analysis is an important aid to epidemiological transmission assessment.
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Affiliation(s)
- N Hassoun-Kheir
- Infectious Diseases and Infection-Control Unit, Rambam Health Care Campus, Haifa, Israel; Technion - Israel Institute of Technology, Haifa, Israel.
| | - O Snitser
- Technion - Israel Institute of Technology, Haifa, Israel
| | - K Hussein
- Infectious Diseases and Infection-Control Unit, Rambam Health Care Campus, Haifa, Israel; Technion - Israel Institute of Technology, Haifa, Israel
| | - G Rabino
- Infectious Diseases and Infection-Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - O Eluk
- Infectious Diseases and Infection-Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - S Warman
- Infectious Diseases and Infection-Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - W Aboalhega
- Infectious Diseases and Infection-Control Unit, Rambam Health Care Campus, Haifa, Israel
| | - Y Geffen
- Technion - Israel Institute of Technology, Haifa, Israel; Clinical Microbiology Laboratory, Rambam Health Care Campus, Haifa, Israel
| | - S Mendelson
- Clinical Microbiology Laboratory, Rambam Health Care Campus, Haifa, Israel
| | - R Kishony
- Technion - Israel Institute of Technology, Haifa, Israel
| | - M Paul
- Infectious Diseases and Infection-Control Unit, Rambam Health Care Campus, Haifa, Israel; Technion - Israel Institute of Technology, Haifa, Israel
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Xu J, Zhao Z, Ge Y, He F. Rapid Emergence of a Pandrug-Resistant Klebsiella pneumoniae ST11 Isolate in an Inpatient in a Teaching Hospital in China After Treatment with Multiple Broad-Spectrum Antibiotics. Infect Drug Resist 2020; 13:799-804. [PMID: 32210594 PMCID: PMC7071855 DOI: 10.2147/idr.s243334] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/02/2020] [Indexed: 12/13/2022] Open
Abstract
Purpose Pandrug-resistant K. pneumoniae is still rare in China, and the lack of studies limits our understanding of the emergence mechanism of pandrug-resistant K. pneumoniae. Here, we report the rapid emergence of a pandrug-resistant K. pneumoniae ST11 strain in an inpatient after treatment with multiple broad-spectrum antibiotics in China. Patients and Methods K. pneumoniae strain KP65 was isolated from a 55-year-old male patient hospitalized in the Department of Intensive Care Unit (ICU) of a teaching hospital in China. Antimicrobial susceptibility testing was conducted according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). The complete genome sequence of the strain was determined using the Illumina NovaSeq 6000 platform and long-read MinION sequencer. Genomic features and resistance mechanisms of the strain were comprehensively analysed using various bioinformatics approaches. Results K. pneumoniae strain KP65 was found to be resistant to all antibiotics tested, including beta-lactams, aminoglycosides, quinolones, tigecycline and colistin. Seven resistance genes were identified in the genome. The carbapenem-resistant gene blaKPC-2 and extended-spectrum β-lactamase (ESBL)-producing gene blaCTX-M-65 are located on the IncFII-type plasmid pKPC-2-KP65. No mcr genes were detected in the genome, but an IS5 insertion element was found at position 117 of the mgrB gene. Regarding the rpsJ gene, single-base substitution, G169C, leading to the amino acid substitution V57L was also identified. According to in silico MLST analysis, K. pneumoniae KP65 belongs to sequence type ST11. The closest relative of K. pneumoniae KP65 is another ST11 K. pneumoniae strain, which was isolated from a bloodstream infection in Hangzhou, differing by only 53 cgMLST loci. Conclusion Under the selective pressure of antibiotics, the KPC-2-producing K. pneumoniae ST11 strain can easily evolve pandrug resistance through chromosomal mutations. More attention is required to monitor the prevalence of the KPC-2-producing K. pneumoniae ST11 strain in China.
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Affiliation(s)
- Juan Xu
- Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang 310013, People's Republic of China
| | - Zhao Zhao
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, People's Republic of China
| | - Yumei Ge
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, People's Republic of China
| | - Fang He
- Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang 310014, People's Republic of China
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Inactivation of mgrB gene regulator and resistance to colistin is becoming endemic in carbapenem-resistant Klebsiella pneumoniae in Greece: A nationwide study from 2014 to 2017. Int J Antimicrob Agents 2020; 55:105930. [PMID: 32130981 DOI: 10.1016/j.ijantimicag.2020.105930] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 02/24/2020] [Indexed: 01/13/2023]
Abstract
INTRODUCTION In Greece, the spread of carbapenem-resistant Enterobacteriaceae in humans has led to the reintroduction of colistin as a therapeutic agent. Unfortunately, colistin resistance with different mechanisms has emerged. The present work aims to determine the prevalence of carbapenem and colistin resistance and the corresponding mechanisms in Klebsiella pneumoniae clinical isolates from Greece. METHODS From 2014 to 2017, 288 carbapenem-resistant K. pneumoniae clinical strains were gathered from a collection of 973 isolates from eight different hospitals in Greece. Antibiotic susceptibility testing was performed using three different methods. Screening of carbapenem and colistin resistance genes was conducted using polymerase chain reaction (PCR) amplification and sequencing. RESULTS Among the 288 (29.6 %) carbapenem-resistant isolates, 213 (73.9%) were colistin-resistant (minimum inhibitory concentration [MIC] >2 mg/L). The KPC type was the most common carbapenemase gene (116; 40.3%), followed by VIM (41; 14.2%), NDM (33; 11.5%) and OXA-48 (22; 7.6%). Moreover, 44 (15.3%) strains co-produced two types of carbapenemases. No mcr genes were detected for colistin resistance but mutations in chromosomal genes were found. These included inactivation of the mgrB gene for 148 (69.5%) strains, including insertion sequences for 94 (44.1%), nonsense mutations for 4 (1.9%) and missense mutations for 24 (11.3%). Moreover, PCR amplification of mgrB gene was negative for 26 (12.2%) strains. Finally, 65 (30.5%) colistin-resistant strains exhibited a wild-type mgrB, the mechanisms of which remain to be elucidated. CONCLUSION This study shows that K. pneumoniae clinical strains in Greece are resistant to both carbapenems and colistin and this is endemic and is likely chromosomally encoded.
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Palmieri M, D'Andrea MM, Pelegrin AC, Mirande C, Brkic S, Cirkovic I, Goossens H, Rossolini GM, van Belkum A. Genomic Epidemiology of Carbapenem- and Colistin-Resistant Klebsiella pneumoniae Isolates From Serbia: Predominance of ST101 Strains Carrying a Novel OXA-48 Plasmid. Front Microbiol 2020; 11:294. [PMID: 32153554 PMCID: PMC7047997 DOI: 10.3389/fmicb.2020.00294] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
Klebsiella pneumoniae is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Carbapenem resistance is frequent, and colistin represents a key molecule to treat infections caused by such isolates. Here we evaluated the antimicrobial resistance (AMR) mechanisms and the genomic epidemiology of clinical K. pneumoniae isolates from Serbia. Consecutive non-replicate K. pneumoniae clinical isolates (n = 2,298) were collected from seven hospitals located in five Serbian cities and tested for carbapenem resistance by disk diffusion. Isolates resistant to at least one carbapenem (n = 426) were further tested for colistin resistance with Etest or Vitek2. Broth microdilution (BMD) was performed to confirm the colistin resistance phenotype, and colistin-resistant isolates (N = 45, 10.6%) were characterized by Vitek2 and whole genome sequencing. Three different clonal groups (CGs) were observed: CG101 (ST101, N = 38), CG258 (ST437, N = 4; ST340, N = 1; ST258, N = 1) and CG17 (ST336, N = 1). mcr genes, encoding for acquired colistin resistance, were not observed, while all the genomes presented mutations previously associated with colistin resistance. In particular, all strains had a mutated MgrB, with MgrBC28S being the prevalent mutation and associated with ST101. Isolates belonging to ST101 harbored the carbapenemase OXA-48, which is generally encoded by an IncL/M plasmid that was no detected in our isolates. MinION sequencing was performed on a representative ST101 strain, and the obtained long reads were assembled together with the Illumina high quality reads to decipher the bla OXA- 48 genetic background. The bla OXA- 48 gene was located in a novel IncFIA-IncR hybrid plasmid, also containing the extended spectrum β-lactamase-encoding gene bla CTX-M-15 and several other AMR genes. Non-ST101 isolates presented different MgrB alterations (C28S, C28Y, K2∗, K3∗, Q30∗, adenine deletion leading to frameshift and premature termination, IS5-mediated inactivation) and expressed different carbapenemases: OXA-48 (ST437 and ST336), NDM-1 (ST437 and ST340) and KPC-2 (ST258). Our study reports the clonal expansion of the newly emerging ST101 clone in Serbia. This high-risk clone appears adept at acquiring resistance, and efforts should be made to contain the spread of such clone.
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Affiliation(s)
- Mattia Palmieri
- bioMérieux, Data Analytics Unit, La Balme-les-Grottes, France
| | - Marco Maria D'Andrea
- Department of Biology, University of "Tor Vergata", Rome, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | | | - Snezana Brkic
- Institute for Laboratory Diagnostics Konzilijum, Belgrade, Serbia
| | - Ivana Cirkovic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Gian Maria Rossolini
- Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alex van Belkum
- bioMérieux, Data Analytics Unit, La Balme-les-Grottes, France
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Mavroidi A, Katsiari M, Likousi S, Palla E, Roussou Z, Nikolaou C, Mathas C, Merkouri E, Platsouka ED. Changing Characteristics and In Vitro Susceptibility to Ceftazidime/Avibactam of Bloodstream Extensively Drug-Resistant Klebsiella pneumoniae from a Greek Intensive Care Unit. Microb Drug Resist 2020; 26:28-37. [DOI: 10.1089/mdr.2019.0090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Angeliki Mavroidi
- Department of Microbiology, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Maria Katsiari
- Intensive Care Unit, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Sofia Likousi
- Department of Microbiology, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Eleftheria Palla
- Department of Microbiology, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Zoi Roussou
- Department of Microbiology, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Charikleia Nikolaou
- Intensive Care Unit, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Christos Mathas
- Intensive Care Unit, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Eleni Merkouri
- Department of Microbiology, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
| | - Evangelia D. Platsouka
- Department of Microbiology, Konstantopouleio-Patission, General Hospital of N. Ionias, Athens, Greece
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Martín-Galiano AJ, McConnell MJ. Using Omics Technologies and Systems Biology to Identify Epitope Targets for the Development of Monoclonal Antibodies Against Antibiotic-Resistant Bacteria. Front Immunol 2019; 10:2841. [PMID: 31921119 PMCID: PMC6914692 DOI: 10.3389/fimmu.2019.02841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022] Open
Abstract
Over the past few decades, antimicrobial resistance has emerged as an important threat to public health due to the global dissemination of multidrug-resistant strains from several bacterial species. This worrisome trend, in addition to the paucity of new antibiotics with novel mechanisms of action in the development pipeline, warrants the development of non-antimicrobial approaches to combating infection caused by these isolates. Monoclonal antibodies (mAbs) have emerged as highly effective molecules for the treatment of multiple diseases. However, in spite of the fact that antibodies play an important role in protective immunity against bacteria, only three mAb therapies have been approved for clinical use in the treatment of bacterial infections. In the present review, we briefly outline the therapeutic potential of mAbs in the treatment of bacterial diseases and discuss how their development can be facilitated when assisted by “omics” technologies and interpreted under a systems biology paradigm. Specifically, methods employing large genomic, transcriptomic, structural, and proteomic datasets allow for the rational identification of epitopes. Ideally, these include those that are present in the majority of circulating isolates, highly conserved at the amino acid level, surface-exposed, located on antigens essential for virulence, and expressed during critical stages of infection. Therefore, these knowledge-based approaches can contribute to the identification of high-value epitopes for the development of effective mAbs against challenging bacterial clones.
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Affiliation(s)
- Antonio J Martín-Galiano
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Michael J McConnell
- Intrahospital Infections Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain
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Abstract
Surveillance studies have shown that OXA-48-like carbapenemases are the most common carbapenemases in Enterobacterales in certain regions of the world and are being introduced on a regular basis into regions of nonendemicity, where they are responsible for nosocomial outbreaks. OXA-48, OXA-181, OXA-232, OXA-204, OXA-162, and OXA-244, in that order, are the most common enzymes identified among the OXA-48-like carbapenemase group. OXA-48 is associated with different Tn1999 variants on IncL plasmids and is endemic in North Africa and the Middle East. OXA-162 and OXA-244 are derivatives of OXA-48 and are present in Europe. OXA-181 and OXA-232 are associated with ISEcp1, Tn2013 on ColE2, and IncX3 types of plasmids and are endemic in the Indian subcontinent (e.g., India, Bangladesh, Pakistan, and Sri Lanka) and certain sub-Saharan African countries. Overall, clonal dissemination plays a minor role in the spread of OXA-48-like carbapenemases, but certain high-risk clones (e.g., Klebsiella pneumoniae sequence type 147 [ST147], ST307, ST15, and ST14 and Escherichia coli ST38 and ST410) have been associated with the global dispersion of OXA-48, OXA-181, OXA-232, and OXA-204. Chromosomal integration of bla OXA-48 within Tn6237 occurred among E. coli ST38 isolates, especially in the United Kingdom. The detection of Enterobacterales with OXA-48-like enzymes using phenotypic methods has improved recently but remains challenging for clinical laboratories in regions of nonendemicity. Identification of the specific type of OXA-48-like enzyme requires sequencing of the corresponding genes. Bacteria (especially K. pneumoniae and E. coli) with bla OXA-48, bla OXA-181, and bla OXA-232 are emerging in different parts of the world and are most likely underreported due to problems with the laboratory detection of these enzymes. The medical community should be aware of the looming threat that is posed by bacteria with OXA-48-like carbapenemases.
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Perdigão J, Modesto A, Pereira AL, Neto O, Matos V, Godinho A, Phelan J, Charleston J, Spadar A, de Sessions PF, Hibberd M, Campino S, Costa A, Fernandes F, Ferreira F, Correia AB, Gonçalves L, Clark TG, Duarte A. Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital. Microb Genom 2019; 7:000349. [PMID: 32234124 PMCID: PMC8627661 DOI: 10.1099/mgen.0.000349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/14/2020] [Indexed: 01/08/2023] Open
Abstract
Klebsiella pneumoniae has emerged as an important nosocomial pathogen, with whole-genome sequencing (WGS) significantly improving our ability to characterize associated outbreaks. Our study sought to perform a genome-wide analysis of multiclonal K. pneumoniae isolates (n=39; 23 patients) producing extended spectrum beta-lactamases and/or carbapenemases sourced between 2011 and 2016 in a Portuguese tertiary-care hospital. All isolates showed resistance to third-generation cephalosporins and six isolates (five patients) were also carbapenem resistant. Genome-wide-based phylogenetic analysis revealed a topology representing ongoing dissemination of three main sequence-type (ST) clades (ST15, ST147 and ST307) and transmission across different wards, compatible with missing links that can take the form of undetected colonized patients. Two carbapenemase-coding genes were detected: blaKPC-3, located on a Tn4401d transposon, and blaGES-5 on a novel class 3 integron. Additionally, four genes coding for ESBLs (blaBEL-1, blaCTX-M-8, blaCTX-M-15 and blaCTX-M-32) were also detected. ESBL horizontal dissemination across five clades is highlighted by the similar genetic environments of blaCTX-M-15 gene upstream of ISEcp1 on a Tn3-like transposon. Overall, this study provides a high-resolution genome-wide perspective on the epidemiology of ESBL and carbapenemase-producing K. pneumoniae in a healthcare setting while contributing for the adoption of appropriate intervention and prevention strategies.
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Affiliation(s)
- João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - A. L. Pereira
- Clinical Pathology Unit. Hospital SAMS, Lisboa, Portugal
| | - O. Neto
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - V. Matos
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - A. Godinho
- Infection Control Commission, Hospital SAMS, Lisboa, Portugal
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Martin Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - A. Costa
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - F. Fernandes
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - F. Ferreira
- Intensive Care Medicine Unit, Hospital SAMS, Lisboa, Portugal
| | - A. B. Correia
- Clinical Pathology Unit. Hospital SAMS, Lisboa, Portugal
| | | | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Portugal
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Lee YL, Lu MC, Shao PL, Lu PL, Chen YH, Cheng SH, Ko WC, Lin CY, Wu TS, Yen MY, Wang LS, Liu CP, Lee WS, Shi ZY, Chen YS, Wang FD, Tseng SH, Lin CN, Chen YH, Sheng WH, Lee CM, Liao MH, Hsueh PR. Nationwide surveillance of antimicrobial resistance among clinically important Gram-negative bacteria, with an emphasis on carbapenems and colistin: Results from the Surveillance of Multicenter Antimicrobial Resistance in Taiwan (SMART) in 2018. Int J Antimicrob Agents 2019; 54:318-328. [PMID: 31202925 DOI: 10.1016/j.ijantimicag.2019.06.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 06/10/2019] [Indexed: 11/29/2022]
Abstract
Multicentre surveillance of antimicrobial susceptibility of clinically important Gram-negative bacteria (GNB) from 16 Taiwanese hospitals was performed. Escherichia coli (n = 398), Klebsiella pneumoniae (n = 346), Pseudomonas aeruginosa (n = 252) and Acinetobacter baumannii complex (ABC) (n = 188) bloodstream isolates, non-typhoidal Salmonella (n = 230) and Shigella flexneri (n = 18) from various sources were collected. Antimicrobial MICs were determined using broth microdilution. Genes encoding K. pneumoniae carbapenemases (KPCs), New Delhi metallo-β-lactamases (NDMs), Verona integron-encoded metallo-β-lactamase (VIM), OXA-48-like carbapenemase (OXA-48) as well as mcr-1-5 genes were detected by molecular methods. Rates of carbapenem non-susceptibility were 2.8%, 9.0%, 0.4%, 0%, 10.3% and 48.8% for E. coli, K. pneumoniae, Salmonella, Shigella, P. aeruginosa and ABC, respectively. For carbapenemases, one (0.3%) E. coli harboured blaNDM-1. Fifteen (4.3%), two (0.6%) and two (0.6%) K. pneumoniae contained blaKPC, blaOXA-48 and blaVIM, respectively. Two (0.5%) E. coli and fourteen (4.0%) K. pneumoniae were non-wild-type according to the colistin MIC. Among Enterobacteriaceae with a colistin MIC ≥ 2 mg/L, mcr-1 was detected in one E. coli, two K. pneumoniae and three Salmonella spp. All three mcr-1-positive Salmonella isolates were collected from community-acquired infections; none of the six mcr-1-positive Enterobacteriaceae were carbapenem-resistant. Carbapenem resistance has increased among clinically important GNB, especially among hospital-acquired infections. blaKPC, especially the blaKPC-2 variant, was detected in approximately one-half of the carbapenem-resistant K. pneumoniae isolates in this study. Although resistance rates to colistin remained low among Enterobacteriaceae, the finding of mcr-1 from different species raises concern of potential dissemination.
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Affiliation(s)
- Yu-Lin Lee
- Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan, and Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Min-Chi Lu
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Pei-Lan Shao
- Department of Pediatrics, Hsin-Chu Branch, National Taiwan University Hospital, Hsin-Chu, Taiwan
| | - Po-Liang Lu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yen-Hsu Chen
- Department of Internal Medicine, Kaohsiung Medical University Hospital, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Hsing Cheng
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan, and School of Public Health, College of Public Health and Nutrition, Taipei Medical University, Taipei, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Medical College and Hospital, Tainan, Taiwan
| | - Chi-Ying Lin
- Department of Internal Medicine, National Taiwan University Hospital Yun-Lin Branch, Yun-Lin, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Muh-Yong Yen
- Division of Infectious Diseases, Taipei City Hospital, and National Yang-Ming University, School of Medicine, Taipei, Taiwan
| | - Lih-Shinn Wang
- Division of Infectious Diseases, Department of Internal Medicine, Buddhist Tzu Chi General Hospital and Tzu Chi University, Hualien, Taiwan
| | - Chang-Pan Liu
- Division of Infectious Diseases, Department of Internal Medicine, MacKay Memorial Hospital, Taipei, Taiwan, and MacKay Medical College, New Taipei City, Taiwan
| | - Wen-Sen Lee
- Division of Infectious Diseases, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, and Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Zhi-Yuan Shi
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Shen Chen
- Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan, and School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Fu-Der Wang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, and School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Shu-Hui Tseng
- Center for Disease Control and Prevention, Ministry of Health and Welfare, Taiwan
| | - Chao-Nan Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, and Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yu-Hui Chen
- Infection Control Center, Chi Mei Hospital, Liouying, Taiwan
| | - Wang-Huei Sheng
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chun-Ming Lee
- Department of Internal Medicine, St Joseph's Hospital, Yunlin County, Taiwan, and MacKay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Ming-Huei Liao
- National Pingtung University of Science and Technology, Neipu, Taiwan
| | - Po-Ren Hsueh
- Division of Infectious Diseases, Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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42
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Perdigão Neto LV, Corscadden L, Martins RCR, Nagano DS, Cunha MPV, Neves PR, Franco LAM, Moura MLN, Rizek CF, Guimarães T, Boszczowski Í, Rossi F, Levin AS, Stabler RA, Costa SF. Simultaneous colonization by Escherichia coli and Klebsiella pneumoniae harboring mcr-1 in Brazil. Infection 2019; 47:661-664. [PMID: 31025216 DOI: 10.1007/s15010-019-01309-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/17/2019] [Indexed: 10/27/2022]
Abstract
CASE PRESENTATION We present a case report of a woman, concurrently colonized by polymyxin-resistant E. coli and K. pneumoniae. A Brazilian female patient, in her mid-fifties, was hospitalized with schistosomiasis. During hospitalization, polymyxin-resistant E. coli and K. pneumoniae were isolated from surveillance cultures. METHODS Identification, antimicrobial susceptibility testings, PCR for mcr-1, plasmid transfer by conjugation and whole genome sequencing were performed. RESULTS E. coli ST744 and K. pneumoniae ST101 carrying mcr-1 gene were described. Transconjugant E. coli was positive for mcr-1 and IncX4 by PCR. The plasmid is a 33,304-base pair plasmid, and the mcr-1 gene was the only antimicrobial resistance gene present in the plasmid. CONCLUSIONS This study presents a case report of a hospitalized woman, concurrently colonized by mcr-1-harboring E. coli ST744, a different ST from previously described in Brazil, and a K. pneumoniae ST101.
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Affiliation(s)
- Lauro Vieira Perdigão Neto
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil.
- , Rua Arruda Alvim, 107, #142, São Paulo, SP, 05410-020, Brazil.
| | - Louise Corscadden
- Department of Infectious and Tropical Diseases, School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Roberta Cristina Ruedas Martins
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Débora Satie Nagano
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Marcos Paulo Vieira Cunha
- School of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo, SP, 05508-270, Brazil
| | - Patrícia Regina Neves
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Lucas Augusto Moyses Franco
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Maria Luísa Nascimento Moura
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Camila Fonseca Rizek
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Thais Guimarães
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Ícaro Boszczowski
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
| | - Flávia Rossi
- Microbiology Laboratory, Hospital das Clínicas, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 155, São Paulo, SP, 05403-000, Brazil
| | - Anna S Levin
- Hospital das Clínicas, University of São Paulo, Rua Dr. Ovídio Pires de Campos, 225, Sala 629, São Paulo, SP, 05403-010, Brazil
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
| | - Richard A Stabler
- Department of Infectious and Tropical Diseases, School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Silvia F Costa
- Department of Infectious Diseases and LIM-54, University of São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 470, São Paulo, SP, 05403-000, Brazil
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43
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Roe CC, Vazquez AJ, Esposito EP, Zarrilli R, Sahl JW. Diversity, Virulence, and Antimicrobial Resistance in Isolates From the Newly Emerging Klebsiella pneumoniae ST101 Lineage. Front Microbiol 2019; 10:542. [PMID: 31001209 PMCID: PMC6454207 DOI: 10.3389/fmicb.2019.00542] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/01/2019] [Indexed: 11/13/2022] Open
Abstract
The global dissemination of Klebsiella pneumoniae and Klebsiella pneumoniae carbapenemase (KPC) has been largely attributed to a few high-risk sequence types (STs) (ST258, ST11, ST512) associated with human disease. ST101 is an emerging clone that has been identified in different parts of the world with the potential to become a global, persistent public health threat. Recent research suggests the ST101 lineage is associated with an 11% increase in mortality rate in comparison to non-ST101 infections. In this study, we generated a high-quality, near-finished genome assembly of a multidrug-resistant (MDR) isolate from Italy (isolate 4743) that is a single locus variant of ST101 (ST1685). We demonstrate that the 4743 genome contains virulence features such as an integrative conjugative element carrying the yersiniabactin siderophore (ICEKp3), the mannose-resistant Klebsiella-like (type III) fimbriae cluster (mrkABCDFHIJ), the ferric uptake system (kfuABC), the yersiniabactin receptor gene fyuA, a capsular K type K17, and an O antigen type of O1. K. pneumoniae 4743 carries the blaKPC-2 carbapenemase gene along with genes conferring resistance to aminoglycosides, beta-lactams, fluoroquinolones, fosfomycin, macrolides, lincosamides, and streptogramin B. A comparative genomics analysis of 44 ST101 genomes as well as newly sequenced isolate 4743 identified variable antimicrobial resistance (AMR) resistance profiles and incompatibility plasmid types, but similar virulence factor profiles. Using Bayesian methodologies, we estimate the common ancestor for the ST101 lineage emerged in 1990 (95% HPD: 1965 to 2007) and isolates within the lineage acquired bla KPC after the divergence from its parental clonal group and dissemination. The identification of virulence factors and antibiotic resistance genes acquired by this newly emerging clone provides insight into the reported increased mortality rates and highlights its potential success as a persistent nosocomial pathogen. With a combination of both colistin resistance, carbapenem resistance, and several known virulence factors, the ST101 genetic repertoire may be a "perfect storm" allowing for a newly emerging, high-risk, extensively antibiotic resistant clone. This high-risk clone appears adept at acquiring resistance and may perpetuate the dissemination of extensive antimicrobial resistance. Greater focus on the acquisition of virulence factors and antibiotic resistance genes is crucial for understanding the spread of antibiotic resistance.
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Affiliation(s)
- Chandler C. Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Adam J. Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Eliana Pia Esposito
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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44
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Chi X, Berglund B, Zou H, Zheng B, Börjesson S, Ji X, Ottoson J, Lundborg CS, Li X, Nilsson LE. Characterization of Clinically Relevant Strains of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Occurring in Environmental Sources in a Rural Area of China by Using Whole-Genome Sequencing. Front Microbiol 2019; 10:211. [PMID: 30809212 PMCID: PMC6379450 DOI: 10.3389/fmicb.2019.00211] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Klebsiella pneumoniae is a gram-negative, opportunistic pathogen, and a common cause of healthcare-associated infections such as pneumonia, septicemia, and urinary tract infection. The purpose of this study was to survey the occurrence of and characterize K. pneumoniae in different environmental sources in a rural area of Shandong province, China. Two hundred and thirty-one samples from different environmental sources in 12 villages were screened for extended-spectrum β-lactamase-(ESBL)-producing K. pneumoniae, and 14 (6%) samples were positive. All isolates were multidrug-resistant and a few of them belonged to clinically relevant strains which are known to cause hospital outbreaks worldwide. Serotypes, virulence genes, serum survival, and phagocytosis survival were analyzed and the results showed the presence of virulence factors associated with highly virulent clones and a high degree of phagocytosis survivability, indicating the potential virulence of these isolates. These results emphasize the need for further studies designed to elucidate the role of the environment in transmission and dissemination of ESBL-producing K. pneumoniae and the potential risk posed to human and environmental health.
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Affiliation(s)
- Xiaohui Chi
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Björn Berglund
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.,State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Huiyun Zou
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Stefan Börjesson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.,Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, Uppsala, Sweden
| | - Xiang Ji
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Jakob Ottoson
- Department of Risk and Benefit Assessment, National Food Agency, Uppsala, Sweden
| | - Cecilia Stålsby Lundborg
- Department of Public Health Sciences, Global Health-Health Systems and Policy, Medicines, Focusing Antibiotics, Karolinska Institutet, Stockholm, Sweden
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Shandong University, Jinan, China
| | - Lennart E Nilsson
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
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