1
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Cai M, Song K, Wang R, Wang S, Chen H, Wang H. Tracking intra-species and inter-genus transmission of KPC through global plasmids mining. Cell Rep 2024; 43:114351. [PMID: 38923465 DOI: 10.1016/j.celrep.2024.114351] [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: 03/21/2024] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC) poses a major public health risk. Understanding its transmission dynamics requires examining the epidemiological features of related plasmids. Our study compiled 15,660 blaKPC-positive isolates globally over the past two decades. We found extensive diversity in the genetic background of KPC, with 23 Tn4401-related and 341 non-Tn4401 variants across 163 plasmid types in 14 genera. Intra-K. pneumoniae and cross-genus KPC transmission patterns varied across four distinct periods. In the initial periods, plasmids with narrow host ranges gradually established a survival advantage. In later periods, broad-host-range plasmids became crucial for cross-genera transmission. In total, 61 intra-K. pneumoniae and 66 cross-genus transmission units have been detected. Furthermore, phylogenetic reconstruction dated the origin of KPC transmission back to 1991 and revealed frequent exchanges across countries. Our research highlights the frequent and transient spread events of KPC mediated by plasmids across multiple genera and offers theoretical support for high-risk plasmid monitoring.
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Affiliation(s)
- Meng Cai
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Kaiwen Song
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China; Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Shuyi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China; Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China.
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Yao Y, Falgenhauer L, Rezazadeh Y, Falgenhauer J, Imirzalioglu C, Chakraborty T. Predominant transmission of KPC-2 carbapenemase in Germany by a unique IncN plasmid variant harboring a novel non-transposable element (NTE KPC -Y). Microbiol Spectr 2024; 12:e0256423. [PMID: 38084979 PMCID: PMC10790570 DOI: 10.1128/spectrum.02564-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/30/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Current infection control protocols assume that the spread of KPC-2 carbapenemase-producing Enterobacterales (KPC2-CPE) by detected carriers to other in-house patients is through clonal transmission and can be restricted by implementing containment measures. We examined the presence of the bla KPC-2 gene in different genera and species of Enterobacterales isolated from humans at different hospitals and surface waters between 2013 and 2019 in Germany. We found that a single IncN[pMLST15] plasmid carrying the bla KPC-2 gene on a novel non-Tn4401-element (NTEKPC-Y), flanked by an adjacent region encoding 12 other antibiotic resistance genes, was uniquely present in multiple species of KPC2-CPE isolates. These findings demonstrate the selective impact of specific IncN plasmids as major drivers of carbapenemase dissemination and suggest "plasmid-based endemicity" for KPC2-CPE. Studies on the dynamics of plasmid-based KPC2-CPE transmission and its presence in persistent reservoirs need to be urgently considered to implement effective surveillance and prevention measures in healthcare institutions.
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Affiliation(s)
- Yancheng Yao
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Linda Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Yalda Rezazadeh
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Jane Falgenhauer
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - the IncN Study GroupHauriAnja M.1HeinmüllerPetra1DomannEugen2GhoshHiren2GoesmannAlexander2JanssenStefan2GatermannSören3KaaseMartin3PfennigwerthNiels3ExnerMartin4OvermannJörg5BunkBoyke5SpröerCathrin5Hessisches Landesprüfungs- und Untersuchungsamt im Gesundheitswesen - HLPUG, Dillenburg, GermanyJustus Liebig University Giessen, Giessen, GermanyGerman National Reference Centre for Multidrug-Resistant Gram-negative Bacteria, Ruhr-University Bochum, Bochum, GermanyUniversity of Bonn, Bonn, GermanyLeibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
- Institute for Hygiene and Environmental Medicine, Justus Liebig University Giessen, Giessen, Germany
| | - Can Imirzalioglu
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Trinad Chakraborty
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Partner Site Giessen-Marburg-Langen, Giessen, Germany
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Lerminiaux N, Mitchell R, Bartoszko J, Davis I, Ellis C, Fakharuddin K, Hota SS, Katz K, Kibsey P, Leis JA, Longtin Y, McGeer A, Minion J, Mulvey M, Musto S, Rajda E, Smith SW, Srigley JA, Suh KN, Thampi N, Tomlinson J, Wong T, Mataseje L. Plasmid genomic epidemiology of blaKPC carbapenemase-producing Enterobacterales in Canada, 2010-2021. Antimicrob Agents Chemother 2023; 67:e0086023. [PMID: 37971242 PMCID: PMC10720558 DOI: 10.1128/aac.00860-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/07/2023] [Indexed: 11/19/2023] Open
Abstract
Carbapenems are considered last-resort antibiotics for the treatment of infections caused by multidrug-resistant Enterobacterales, but carbapenem resistance due to acquisition of carbapenemase genes is a growing threat that has been reported worldwide. Klebsiella pneumoniae carbapenemase (blaKPC) is the most common type of carbapenemase in Canada and elsewhere; it can hydrolyze penicillins, cephalosporins, aztreonam, and carbapenems and is frequently found on mobile plasmids in the Tn4401 transposon. This means that alongside clonal expansion, blaKPC can disseminate through plasmid- and transposon-mediated horizontal gene transfer. We applied whole genome sequencing to characterize the molecular epidemiology of 829 blaKPC carbapenemase-producing isolates collected by the Canadian Nosocomial Infection Surveillance Program from 2010 to 2021. Using a combination of short-read and long-read sequencing, we obtained 202 complete and circular blaKPC-encoding plasmids. Using MOB-suite, 10 major plasmid clusters were identified from this data set which represented 87% (175/202) of the Canadian blaKPC-encoding plasmids. We further estimated the genomic location of incomplete blaKPC-encoding contigs and predicted a plasmid cluster for 95% (603/635) of these. We identified different patterns of carbapenemase mobilization across Canada related to different plasmid clusters, including clonal transmission of IncF-type plasmids (108/829, 13%) in K. pneumoniae clonal complex 258 and novel repE(pEh60-7) plasmids (44/829, 5%) in Enterobacter hormaechei ST316, and horizontal transmission of IncL/M (142/829, 17%) and IncN-type plasmids (149/829, 18%) across multiple genera. Our findings highlight the diversity of blaKPC genomic loci and indicate that multiple, distinct plasmid clusters have contributed to blaKPC spread and persistence in Canada.
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Affiliation(s)
| | | | | | - Ian Davis
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
| | - Chelsey Ellis
- The Moncton Hospital, Moncton, New Brunswick, Canada
| | - Ken Fakharuddin
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Susy S. Hota
- University Health Network, Toronto, Ontario, Canada
| | - Kevin Katz
- North York General Hospital, Toronto, Ontario, Canada
| | - Pamela Kibsey
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
| | - Jerome A. Leis
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Yves Longtin
- Jewish General Hospital, Montréal, Québec, Canada
| | | | - Jessica Minion
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
| | - Michael Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - Sonja Musto
- Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - Ewa Rajda
- McGill University Health Centre, Montréal, Québec, Canada
| | | | - Jocelyn A. Srigley
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
| | | | - Nisha Thampi
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | | | - Titus Wong
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Laura Mataseje
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - on behalf of the Canadian Nosocomial Infection Surveillance Program
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
- Public Health Agency of Canada, Ottawa, Ontario, Canada
- QEII Health Sciences Centre, Halifax, Nova Scotia, Canada
- The Moncton Hospital, Moncton, New Brunswick, Canada
- University Health Network, Toronto, Ontario, Canada
- North York General Hospital, Toronto, Ontario, Canada
- Royal Jubilee Hospital, Victoria, British Columbia, Canada
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Jewish General Hospital, Montréal, Québec, Canada
- Sinai Health, Toronto, Ontario, Canada
- Saskatchewan Health Authority, Regina, Saskatchewan, Canada
- Health Sciences Centre, Winnipeg, Manitoba, Canada
- McGill University Health Centre, Montréal, Québec, Canada
- University of Alberta Hospital, Edmonton, Alberta, Canada
- BC Women’s and BC Children’s Hospital, Vancouver, British Columbia, Canada
- The Ottawa Hospital, Ottawa, Ontario, Canada
- Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
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4
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Rodrigues C, Lanza VF, Peixe L, Coque TM, Novais Â. Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0339522. [PMID: 37098951 PMCID: PMC10269502 DOI: 10.1128/spectrum.03395-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/26/2023] [Indexed: 04/27/2023] Open
Abstract
Klebsiella pneumoniae sequence type 14 (ST14) and ST15 caused outbreaks of CTX-M-15 and/or carbapenemase producers worldwide, but their phylogeny and global dynamics remain unclear. We clarified the evolution of K. pneumoniae clonal group 14 (CG14) and CG15 by analyzing the capsular locus (KL), resistome, virulome, and plasmidome of public genomes (n = 481) and de novo sequences (n = 9) representing main sublineages circulating in Portugal. CG14 and CG15 evolved independently within 6 main subclades defined according to the KL and the accessory genome. The CG14 (n = 65) clade was structured in two large monophyletic subclades, CG14-I (KL2, 86%) and CG14-II (KL16, 14%), whose emergences were dated to 1932 and 1911, respectively. Genes encoding extended-spectrum β-lactamase (ESBL), AmpC, and/or carbapenemases were mostly observed in CG14-I (71% versus 22%). CG15 clade (n = 170) was segregated into subclades CG15-IA (KL19/KL106, 9%), CG15-IB (variable KL types, 6%), CG15-IIA (KL24, 43%) and CG15-IIB (KL112, 37%). Most CG15 genomes carried specific GyrA and ParC mutations and emerged from a common ancestor in 1989. CTX-M-15 was especially prevalent in CG15 (68% CG15 versus 38% CG14) and in CG15-IIB (92%). Plasmidome analysis revealed 27 predominant plasmid groups (PG), including particularly pervasive and recombinant F-type (n = 10), Col (n = 10), and new plasmid types. While blaCTX-M-15 was acquired multiple times by a high diversity of F-type mosaic plasmids, other antibiotic resistance genes (ARGs) were dispersed by IncL (blaOXA-48) or IncC (blaCMY/TEM-24) plasmids. We first demonstrate an independent evolutionary trajectory for CG15 and CG14 and how the acquisition of specific KL, quinolone-resistance determining region (QRDR) mutations (CG15), and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-I and CG15-IIA/IIB). IMPORTANCE Klebsiella pneumoniae represents a major threat in the burden of antibiotic resistance (ABR). Available studies to explain the origin, the diversity, and the evolution of certain ABR K. pneumoniae populations have mainly been focused on a few clonal groups (CGs) using phylogenetic analysis of the core genome, the accessory genome being overlooked. Here, we provide unique insights into the phylogenetic evolution of CG14 and CG15, two poorly characterized CGs which have contributed to the global dissemination of genes responsible for resistance to first-line antibiotics such as β-lactams. Our results point out an independent evolution of these two CGs and highlight the existence of different subclades structured by the capsular type and the accessory genome. Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome reflect the exposure and adaptation of K. pneumoniae under different selective pressures.
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Affiliation(s)
- Carla Rodrigues
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Val F. Lanza
- Unidad de Genómica Traslacional Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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5
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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: 16] [Impact Index Per Article: 16.0] [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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6
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Hendrickx APA, Schade RP, Landman F, Bosch T, Schouls LM, van Dijk K. Comparative analysis of IMP-4- and OXA-58-containing plasmids of three carbapenemase-producing Acinetobacter ursingii strains in the Netherlands. J Glob Antimicrob Resist 2022; 31:207-211. [PMID: 36184039 DOI: 10.1016/j.jgar.2022.09.006] [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: 07/18/2022] [Revised: 09/10/2022] [Accepted: 09/15/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES A recent occurrence of carbapenemase-producing Acinetobacter ursingii was reported in the Netherlands and comprised three unrelated strains carrying the blaIMP-4 and blaOXA-58 encoding genes. The objective was to investigate a putative common source of the carbapenemase resistance genes and plasmids in these A. ursingii strains. METHODS Hybrid assembly of short-read and long-read sequencing data was performed using Unicycler and assembled genomes were analysed by ResFinder and PlasmidFinder. RESULTS Hybrid assemblies of A. ursingii genomes yielded a circular chromosome, a large plasmid harboring blaIMP-4 and blaOXA-58 genes (sizes 259-317kb), and four to five other smaller plasmids. ResFinder analyses revealed 16 other acquired resistance genes on the plasmids carrying the blaIMP-4 and blaOXA-58 genes. These 18 genes encode resistance towards eight antibiotic classes. The smaller plasmids did not carry acquired resistance genes. Comparative analysis showed that the three blaIMP-4/blaOXA-58 plasmids were similar (61%-83%) and shared 13 to 17 of the 18 resistance genes. BLAST analysis showed that the blaIMP-4/blaOXA-58 plasmids were not reported before. However, a close match with a 399 kb plasmid from Acinetobacter johnsonii was found (99% similarity, 80% coverage). This A. johnsonii plasmid contains the blaOXA-58 gene, but lacks blaIMP-4, and it shares eight other resistance genes with those present on the A. ursingii blaIMP-4/blaOXA-58 plasmids. CONCLUSION Three blaIMP-4/blaOXA-58-carrying plasmids were characterized in three carbapenemase-producing A. ursingii strains. The plasmids were highly similar, suggesting a putative common source or co-selection of resistance genes from A. johnsonii. These results provide initial insights in the dissemination of carbapenem-resistance in A. ursingii in the Netherlands.
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Affiliation(s)
- Antoni P A Hendrickx
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - Rogier P Schade
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Fabian Landman
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Thijs Bosch
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Leo M Schouls
- Centre for Infectious Diseases Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Karin van Dijk
- Department of Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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7
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Schouls LM, Veldman K, Brouwer MSM, Dierikx C, Witteveen S, van Santen-Verheuvel M, Hendrickx APA, Landman F, Hengeveld P, Wullings B, Rapallini M, Wit B, van Duijkeren E. cfr and fexA genes in methicillin-resistant Staphylococcus aureus from humans and livestock in the Netherlands. COMMUNICATIONS MEDICINE 2022; 2:135. [PMID: 36317053 PMCID: PMC9616846 DOI: 10.1038/s43856-022-00200-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2022] Open
Abstract
Background Although the Netherlands is a country with a low endemic level of methicillin-resistant Staphylococcus aureus (MRSA), a national MRSA surveillance has been in place since 1989. In 2003 livestock emerged as a major reservoir of MRSA and currently livestock-associated MRSA (clonal complex CC398) make up 25% of all surveillance isolates. To assess possible transfer of resistant strains or resistance genes, MRSA obtained from humans and animals were characterized in detail. Methods The sequenced genomes of 6327 MRSA surveillance isolates from humans and from 332 CC398 isolates from livestock-related samples were analyzed and resistance genes were identified. Several isolates were subjected to long-read sequencing to reconstruct chromosomes and plasmids. Results Here we show the presence of the multi-resistance gene cfr in seven CC398 isolates obtained from humans and in one CC398 isolate from a pig-farm dust sample. Cfr induces resistance against five antibiotic classes, which is true for all but two isolates. The isolates are genetically unrelated, and in seven of the isolates cfr are located on distinct plasmids. The fexA gene is found in 3.9% surveillance isolates and in 7.5% of the samples from livestock. There is considerable sequence variation of fexA and geographic origin of the fexA alleles. Conclusions The rare cfr and fexA resistance genes are found in MRSA from humans and animals in the Netherlands, but there is no evidence for spread of resistant strains or resistance plasmids. The proportion of cfr-positive MRSA is low, but its presence is worrying and should be closely monitored.
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Affiliation(s)
- Leo M. Schouls
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Kees Veldman
- grid.4818.50000 0001 0791 5666Wageningen Bioveterinary Research (WBVR), Bacteriology, Host Pathogen Interaction & Diagnostics, Lelystad, The Netherlands
| | - Michael S. M. Brouwer
- grid.4818.50000 0001 0791 5666Wageningen Bioveterinary Research (WBVR), Bacteriology, Host Pathogen Interaction & Diagnostics, Lelystad, The Netherlands
| | - Cindy Dierikx
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Zoonoses and Environmental Microbiology (Z&O), Bilthoven, The Netherlands
| | - Sandra Witteveen
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Marga van Santen-Verheuvel
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Antoni P. A. Hendrickx
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Fabian Landman
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Infectious Diseases Research, Diagnostics and laboratory Surveillance (IDS), Bilthoven, The Netherlands
| | - Paul Hengeveld
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Zoonoses and Environmental Microbiology (Z&O), Bilthoven, The Netherlands
| | - Bart Wullings
- grid.4818.50000 0001 0791 5666Wageningen Food Safety Research, Team Bacteriology, Molecular Biology & AMR, Wageningen, The Netherlands
| | - Michel Rapallini
- grid.4818.50000 0001 0791 5666Wageningen Food Safety Research, Team Bacteriology, Molecular Biology & AMR, Wageningen, The Netherlands
| | - Ben Wit
- grid.435742.30000 0001 0726 7822Netherlands Food and Consumer Product Safety Authority (NVWA), Food safety, Apeldoorn, The Netherlands
| | - Engeline van Duijkeren
- grid.31147.300000 0001 2208 0118National Institute for Public Health and the Environment (RIVM), Zoonoses and Environmental Microbiology (Z&O), Bilthoven, The Netherlands
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Gaibani P, Amadesi S, Lazzarotto T, Ambretti S. Complete Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Strain Carrying blaOXA181 and blaKPC-125 Carbapenemase. Microb Drug Resist 2022; 28:916-920. [PMID: 36112395 DOI: 10.1089/mdr.2022.0143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Carbapenemase-producing Enterobacterales (CPEs) strains represent a serious threat to public health. The rapid diffusion of CPEs is of particular concern due to the limited effective treatments available against these multidrug resistant microorganisms. In this study, we characterized the complete genome sequence of Klebsiella pneumoniae strain BO714 coproducing KPC and OXA-181 carbapenemase conferring resistance to all β-lactam/β-lactamase inhibitor combinations (βL-βLICs) and siderophore cephalosporin cefiderocol (CFD). The genome of BO714 has a length of 5,876,068 bp with an average G + C content of 56.96% and a total of 5,878 open reading frames. The KPC-Kp strain BO714 was classified as ST512 and contained a circular chromosome of 5,348,787 bp and three different plasmids, respectively, of 363,560, 112,243, and 51,478 bp. Resistome analysis showed that BO714 harbored different β-lactamase genes including blaCMY-16, blaOXA-10, blaTEM-1, blaSHV-11, blaOXA181, and a novel blaKPC-3 variant named blaKPC-125. KPC-125 differed to KPC-3 by Asp to Ala at position 179 within the Ω-loop region. The genomic characterization of a K. pneumoniae cross-resistant to novel βL-βLICs and CFD improves knowledge regarding the emergence of novel traits of multidrug resistance in CPEs.
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Affiliation(s)
- Paolo Gaibani
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Stefano Amadesi
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tiziana Lazzarotto
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Section of Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Simone Ambretti
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Bello Gonzalez TD, Kant A, Dijkstra Q, Marcato F, van Reenen K, Veldman KT, Brouwer MSM. Changes in Fecal Carriage of Extended-Spectrum β-Lactamase Producing Enterobacterales in Dutch Veal Calves by Clonal Spread of Klebsiella pneumoniae. Front Microbiol 2022; 13:866674. [PMID: 35814663 PMCID: PMC9260047 DOI: 10.3389/fmicb.2022.866674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/31/2022] [Indexed: 01/14/2023] Open
Abstract
This study aimed to characterize the changes in fecal carriage of Extended-Spectrum β-Lactamase (ESBL) producing Enterobacterales (ESBL-PE) in a single Dutch veal calves. During the rearing period at the Dutch veal farm, a decrease in fecal carriage of cefotaxime-resistant Escherichia coli isolates was observed after 2 weeks at the veal farm, while an increase of cefotaxime-resistant Klebsiella pneumoniae isolates was demonstrated. E. coli and K. pneumoniae were isolated from rectal swabs collected from 110 veal calves in week 2, 6, 10, 18, and 24 after their arrival at the farm. ESBL-PE isolates were selectively cultured and identified by MALDI-TOF. ESBL genes were characterized by RT-PCR, PCRs, and amplicon sequencing. A total of 80 E. coli and 174 K. pneumoniae strains were isolated from 104 out of 110 veal calves. The prevalence of ESBL-E. coli decreased from week 2 (61%) to week 6 (7%), while an unexpected increase in ESBL-K. pneumoniae colonization was detected in week 6 (80%). The predominant ESBL genes detected in E. coli isolates were blaCTX-M-15 and the non-ESBL gene blaTEM-1a, while in K. pneumoniae blaCTX-M-14 gene was detected in all isolates. Four cefotaxime-resistant K. pneumoniae isolates were randomly selected and characterized in deep by transformation, PCR-based replicon typing, and whole-genome sequencing (WGS). The clonal relatedness of a subgroup of nine animals carrying K. pneumoniae ESBL genes was investigated by Multi Locus sequence typing (MLST). In four ESBL-K. pneumoniae isolates, blaCTX-M-14 was located on IncFIIK and IncFIINK plasmid replicons and the isolates were multi-drug resistant (MDR). MLST demonstrated a clonal spread of ESBL-K. pneumoniae ST107. To the best of our knowledge, this is the first study to report a change in fecal carriage of ESBL-PE over time in the same veal calf during the rearing period.
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Affiliation(s)
- Teresita d.J. Bello Gonzalez
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
- *Correspondence: Teresita d.J. Bello Gonzalez,
| | - Arie Kant
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Quillan Dijkstra
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Francesca Marcato
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Kees van Reenen
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Kees T. Veldman
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Michael S. M. Brouwer
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
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A prospective matched case-control study on the genomic epidemiology of colistin-resistant Enterobacterales from Dutch patients. COMMUNICATIONS MEDICINE 2022; 2:55. [PMID: 35607432 PMCID: PMC9122983 DOI: 10.1038/s43856-022-00115-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/20/2022] [Indexed: 11/08/2022] Open
Abstract
Abstract
Background
Colistin is a last-resort treatment option for infections with multidrug-resistant Gram-negative bacteria. However, colistin resistance is increasing.
Methods
A six-month prospective matched case-control study was performed in which 22 Dutch laboratories with 32 associated hospitals participated. Laboratories were invited to send a maximum of five colistin-resistant Escherichia coli or Klebsiella pneumoniae (COLR-EK) isolates and five colistin-susceptible isolates (COLS-EK) to the reference laboratory, matched for patient location, material of origin and bacterial species. Epidemiological/clinical data were collected and included in the analysis. Characteristics of COLR-EK/COLS-EK isolates were compared using logistic regression with correction for variables used for matching. Forty-six ColR-EK/ColS-EK pairs were analysed by next-generation sequencing (NGS) for whole-genome multi-locus sequence typing and identification of resistance genes, including mcr genes. To identify chromosomal mutations potentially leading to colistin resistance, NGS reads were mapped against gene sequences of pmrAB, phoPQ, mgrB and crrB.
Results
In total, 72 COLR-EK/COLS-EK pairs (75% E. coli and 25% K. pneumoniae) were included. Twenty-one percent of COLR-EK patients had received colistin, in contrast to 3% of COLS-EK patients (OR > 2.9). Of COLR-EK isolates, five contained mcr-1 and two mcr-9. One isolate lost mcr-9 after repeated sub-culturing, but retained colistin resistance. Among 46 sequenced COLR-EK isolates, genetic diversity was large and 19 (41.3%) isolates had chromosomal mutations potentially associated with colistin resistance.
Conclusions
Colistin resistance is present but uncommon in the Netherlands and caused by the mcr gene in a minority of COLR-EK isolates. There is a need for surveillance of colistin resistance using appropriate susceptibility testing methods.
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11
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Dierikx CM, Meijs AP, Hengeveld PD, van der Klis FRM, van Vliet J, Gijsbers EF, Rozwandowicz M, van Hoek AHAM, Hendrickx APA, Hordijk J, Van Duijkeren E. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac041. [PMID: 35445193 PMCID: PMC9015910 DOI: 10.1093/jacamr/dlac041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives Plasmid-mediated colistin resistance can be transferred from animals to humans. We investigated the prevalence of carriage of mcr-mediated colistin-resistant Escherichia coli and Klebsiella pneumoniae (ColR-E/K) in veterinary healthcare workers and in the general population in the Netherlands. Methods Two cross-sectional population studies were performed: one among veterinary healthcare workers and one in the general population. Participants sent in a faecal sample and filled in a questionnaire. Samples were analysed using selective enrichment and culture. Mobile colistin resistance genes (mcr) were detected by PCR and ColR-E/K were sequenced using Illumina and Nanopore technologies. Results The prevalence of mcr-mediated ColR-E/K was 0.2% (1/482, 95% CI 0.04%–1.17%) among veterinary personnel and 0.8% (5/660, 95% CI 0.3%–1.8%) in the population sample. mcr-1 was found in E. coli from four persons, mcr-8 in K. pneumoniae from one person and another person carried both mcr-1 and mcr-8 in a K. pneumoniae isolate. mcr-1 was found on different plasmid types (IncX4, IncI1 and IncI2), while mcr-8 was found on IncF plasmids only. Conclusions mcr-mediated ColR-E/K resistance was uncommon in both populations. Professional contact with animals does not increase the chance of carriage of these bacteria in the Netherlands at present. mcr-8 was found for the first time in the Netherlands. Surveillance of colistin resistance and its underlying mechanisms in humans, livestock and food is important in order to identify emerging trends in time.
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Affiliation(s)
- C. M. Dierikx
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
- Corresponding author. E-mail:
| | - A. P. Meijs
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - P. D. Hengeveld
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - F. R. M. van der Klis
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - J. van Vliet
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - E. F. Gijsbers
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - M. Rozwandowicz
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - A. H. A. M. van Hoek
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - A. P. A. Hendrickx
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - J. Hordijk
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
| | - E. Van Duijkeren
- National Institute for Public Health and the Environment (RIVM), Centrum for Infectious Disease Control, Bilthoven, The Netherlands
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12
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Ares-Arroyo M, Rocha EPC, Gonzalez-Zorn B. Evolution of ColE1-like plasmids across γ-Proteobacteria: From bacteriocin production to antimicrobial resistance. PLoS Genet 2021; 17:e1009919. [PMID: 34847155 PMCID: PMC8683028 DOI: 10.1371/journal.pgen.1009919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 12/17/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
Antimicrobial resistance is one of the major threats to Public Health worldwide. Understanding the transfer and maintenance of antimicrobial resistance genes mediated by mobile genetic elements is thus urgent. In this work, we focus on the ColE1-like plasmid family, whose distinctive replication and multicopy nature has given rise to key discoveries and tools in molecular biology. Despite being massively used, the hosts, functions, and evolutionary history of these plasmids remain poorly known. Here, we built specific Hidden Markov Model (HMM) profiles to search ColE1 replicons within genomes. We identified 1,035 ColE1 plasmids in five Orders of γ-Proteobacteria, several of which are described here for the first time. The phylogenetic analysis of these replicons and their characteristic MOBP5/HEN relaxases suggest that ColE1 plasmids have diverged apart, with little transfer across orders, but frequent transfer across families. Additionally, ColE1 plasmids show a functional shift over the last decades, losing their characteristic bacteriocin production while gaining several antimicrobial resistance genes, mainly enzymatic determinants and including several extended-spectrum betalactamases and carbapenemases. Furthermore, ColE1 plasmids facilitate the intragenomic mobilization of these determinants, as various replicons were identified co-integrated with large non-ColE1 plasmids, mostly via transposases. These results illustrate how families of plasmids evolve and adapt their gene repertoires to bacterial adaptive requirements. The extraordinary adaptability of bacteria and the massive prevalence of mobile genetic elements within populations has turned antimicrobial resistance into a growing threat to Public Health. Among all the mobile genetic elements, plasmids have been the focus of attention as these extrachromosomal molecules of DNA are able to mobilize several antimicrobial resistance genes at once through conjugation. However, although small mobilizable and non-conjugative replicons have been traditionally overlooked when analyzing plasmid-mediated antimicrobial resistance, they have recently been described as important carriers of AMR genes. In this work, we have analyzed the ColE1-like plasmid family, whose study has been neglected even if they are one of the main groups of small plasmids in natural populations of Proteobacteria. We observed that these plasmids have evolved for a long time within γ-Proteobacteria acquiring different genetic features in specific hosts, being major players in the spread of antimicrobial resistance determinants.
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Affiliation(s)
- Manuel Ares-Arroyo
- Antimicrobial Resistance Unit (ARU), Faculty of Veterinary Medicine and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université de Paris, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit (ARU), Faculty of Veterinary Medicine and VISAVET, Complutense University of Madrid, Madrid, Spain
- * E-mail:
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13
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Within patient genetic diversity of bla KPC harboring Klebsiella pneumoniae in a Colombian hospital and identification of a new NTE KPC platform. Sci Rep 2021; 11:21409. [PMID: 34725422 PMCID: PMC8560879 DOI: 10.1038/s41598-021-00887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022] Open
Abstract
Resistance to carbapenems in Klebsiellapneumoniae has been mostly related with the worldwide dissemination of KPC, largely due to the pandemic clones belonging to the complex clonal (CC) 258. To unravel blaKPC post-endemic clinical impact, here we describe clinical characteristics of 68 patients from a high complexity hospital, and the molecular and genetic characteristics of their 139 blaKPC—K.pneumoniae (KPC-Kp) isolates. Of the 26 patients that presented relapses or reinfections, 16 had changes in the resistance profiles of the isolates recovered from the recurrent episodes. In respect to the genetic diversity of KPC-Kp isolates, PFGE revealed 45 different clonal complexes (CC). MLST for 12 representative clones showed ST258 was present in the most frequent CC (23.0%), however, remaining 11 representative clones belonged to non-CC258 STs (77.0%). Interestingly, 16 patients presented within-patient genetic diversity of KPC-Kp clones. In one of these, three unrelated KPC-Kp clones (ST258, ST504, and ST846) and a blaKPC—K.variicola isolate (ST182) were identified. For this patient, complete genome sequence of one representative isolate of each clone was determined. In K.pneumoniae isolates blaKPC was mobilized by two Tn3-like unrelated platforms: Tn4401b (ST258) and Tn6454 (ST504 and ST846), a new NTEKPC-IIe transposon for first time characterized also determined in the K.variicola isolate of this study. Genome analysis showed these transposons were harbored in different unrelated but previously reported plasmids and in the chromosome of a K.pneumoniae (for Tn4401b). In conclusion, in the blaKPC post-endemic dissemination in Colombia, different KPC-Kp clones (mostly non-CC258) have emerged due to integration of the single blaKPC gene in new genetic platforms. This work also shows the intra-patient resistant and genetic diversity of KPC-Kp isolates. This circulation dynamic could impact the effectiveness of long-term treatments.
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14
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Interactions between Viral Regulatory Proteins Ensure an MOI-Independent Probability of Lysogeny during Infection by Bacteriophage P1. mBio 2021; 12:e0101321. [PMID: 34517752 PMCID: PMC8546580 DOI: 10.1128/mbio.01013-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phage P1 is a temperate phage which makes the lytic or lysogenic decision upon infecting bacteria. During the lytic cycle, progeny phages are produced and the cell lyses, and in the lysogenic cycle, P1 DNA exists as a low-copy-number plasmid and replicates autonomously. Previous studies at the bulk level showed that P1 lysogenization was independent of multiplicity of infection (MOI; the number of phages infecting a cell), whereas lysogenization probability of the paradigmatic phage λ increases with MOI. However, the mechanism underlying the P1 behavior is unclear. In this work, using a fluorescent reporter system, we demonstrated this P1 MOI-independent lysogenic response at the single-cell level. We further observed that the activity of the major repressor of lytic functions (C1) is a determining factor for the final cell fate. Specifically, the repression activity of P1, which arises from a combination of C1, the anti-repressor Coi, and the corepressor Lxc, remains constant for different MOI, which results in the MOI-independent lysogenic response. Additionally, by increasing the distance between phages that infect a single cell, we were able to engineer a λ-like, MOI-dependent lysogenization upon P1 infection. This suggests that the large separation of coinfecting phages attenuates the effective communication between them, allowing them to make decisions independently of each other. Our work establishes a highly quantitative framework to describe P1 lysogeny establishment. This system plays an important role in disseminating antibiotic resistance by P1-like plasmids and provides an alternative to the lifestyle of phage λ.
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15
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Yoon EJ, Jeong SH. MALDI-TOF Mass Spectrometry Technology as a Tool for the Rapid Diagnosis of Antimicrobial Resistance in Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10080982. [PMID: 34439032 PMCID: PMC8388893 DOI: 10.3390/antibiotics10080982] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
Species identification by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a routine diagnostic process for infectious diseases in current clinical settings. The rapid, low-cost, and simple to conduct methodology is expanding its application in clinical microbiology laboratories to diagnose the antimicrobial resistance (AMR) in microorganisms. Primarily, antimicrobial susceptibility testing is able to be carried out either by comparing the area under curve of MALDI spectra of bacteria grown in media with antimicrobial drugs or by identifying the shift peaks of bacteria grown in media including 13C isotope with antimicrobial drugs. Secondly, the antimicrobial resistance is able to be determined through identifying (i) the antimicrobial-resistant clonal groups based on the fingerprints of the clone, (ii) the shift peak of the modified antimicrobial drug, which is inactivated by the resistance determinant, (iii) the shift peak of the modified antimicrobial target, (iv) the peak specific for the antimicrobial determinant, and (v) the biomarkers that are coproduced proteins with AMR determinants. This review aims to present the current usage of the MALDI-TOF MS technique for diagnosing antimicrobial resistance in bacteria, varied approaches for AMR diagnostics using the methodology, and the future applications of the methods for the accurate and rapid identification of AMR in infection-causing bacterial pathogens.
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Affiliation(s)
- Eun-Jeong Yoon
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Korea;
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
- Correspondence:
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16
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Kraftova L, Finianos M, Studentova V, Chudejova K, Jakubu V, Zemlickova H, Papagiannitsis CC, Bitar I, Hrabak J. Evidence of an epidemic spread of KPC-producing Enterobacterales in Czech hospitals. Sci Rep 2021; 11:15732. [PMID: 34344951 PMCID: PMC8333104 DOI: 10.1038/s41598-021-95285-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022] Open
Abstract
The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018–2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the presence of several types of blaKPC-carrying plasmids; 19 out of 25 blaKPC-carrying plasmids could be assigned to R (n = 12), N (n = 5), C (n = 1) and P6 (n = 1) incompatibility (Inc) groups. Five of the remaining blaKPC-carrying plasmids were multireplicon, while one plasmid couldn’t be typed. Additionally, phylogenetic analysis confirmed the spread of blaKPC-carrying plasmids among different clones of diverse Enterobacterales species. Our findings demonstrated that the increased prevalence of KPC-producing isolates was due to plasmids spreading among different species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC-carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC-producing strains.
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Affiliation(s)
- Lucie Kraftova
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Marc Finianos
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Vendula Studentova
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - Vladislav Jakubu
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Pilsen, Czech Republic.,Department of Microbiology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
| | - Helena Zemlickova
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Pilsen, Czech Republic.,Department of Microbiology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
| | | | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic. .,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic.
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
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17
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Huang QS, Liao W, Xiong Z, Li D, Du FL, Xiang TX, Wei D, Wan LG, Liu Y, Zhang W. Prevalence of the NTE KPC-I on IncF Plasmids Among Hypervirulent Klebsiella pneumoniae Isolates in Jiangxi Province, South China. Front Microbiol 2021; 12:622280. [PMID: 34234750 PMCID: PMC8256152 DOI: 10.3389/fmicb.2021.622280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/03/2021] [Indexed: 12/18/2022] Open
Abstract
Infection caused by carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) has become a tricky health care threat in China and KPC-2 enzyme is a main factor mediating resistance to carbapenems of K. pneumoniae. Here, we report the characterization of the genetic environment of the blaKPC-2 gene in CR-hvKP clinical isolates from South China. Forty-five non-duplicated CR-hvKP isolates collected in Jiangxi Province from 2018 to 2019 were analyzed. Each of them were multidrug-resistant due to the presence not only of blaKPC-2 gene but also of other resistance determinants, including Metallo-β-lactamases (NDM-1), extended-spectrum β-lactamases (TEM-1, CTX-M-14, SHV-1), and plasmid-mediated quinolone resistance determinants (qnrS, aac(6′)-Ib-cr). After plasmid analyses of PCR-based replicon typing (PBRT), mapping PCR, amplicon sequencing, and whole-genome sequencing (WGS) were used to analyze the genetic environment of the blaKPC-2 gene. PCR analysis of pLVPK-like plasmids, Southern Blot, and mouse lethality assay were used to characterize the virulence phenotype of K. pneumoniae. Multilocus sequence typing (MLST) analysis showed ST11 CR-hvKP was the predominant clone. In conclusion, this is the first analysis of diverse genetic structures blaKPC-2 gene in CR-hvKP isolates from south China. Both the NTEKPC-I on the IncF plasmids and pLVPK-like virulence plasmids make contributions to the formation of CR-hvKP especially ST11 which need more attention.
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Affiliation(s)
- Qi-Sen Huang
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Wenjian Liao
- Department of Respiratory and Critical Care, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Zhijuan Xiong
- Department of Respiratory and Critical Care, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Dan Li
- Department of Respiratory and Critical Care, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Fang-Ling Du
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Tian-Xin Xiang
- Department of Infectious Disease, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - DanDan Wei
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - La-Gen Wan
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Yang Liu
- Department of Clinical Microbiology, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
| | - Wei Zhang
- Department of Respiratory and Critical Care, First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
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18
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Hendrickx APA, Debast S, Pérez-Vázquez M, Schoffelen AF, Notermans DW, Landman F, Wielders CCH, Cañada Garcia JE, Flipse J, de Haan A, Witteveen S, van Santen-Verheuvel M, de Greeff SC, Kuijper E, Schouls LM. A genetic cluster of MDR Enterobacter cloacae complex ST78 harbouring a plasmid containing bla VIM-1 and mcr-9 in the Netherlands. JAC Antimicrob Resist 2021; 3:dlab046. [PMID: 34223115 PMCID: PMC8210100 DOI: 10.1093/jacamr/dlab046] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/14/2021] [Indexed: 11/23/2022] Open
Abstract
Background Carbapenemases produced by Enterobacterales are often encoded by genes on transferable plasmids and represent a major healthcare problem, especially if the plasmids contain additional antibiotic resistance genes. As part of Dutch national surveillance, 50 medical microbiological laboratories submit their Enterobacterales isolates suspected of carbapenemase production to the National Institute for Public Health and the Environment for characterization. All isolates for which carbapenemase production is confirmed are subjected to next-generation sequencing. Objectives To study the molecular characteristics of a genetic cluster of Enterobacter cloacae complex isolates collected in Dutch national surveillance in the period 2015–20 in the Netherlands. Methods Short- and long-read genome sequencing was used in combination with MLST and pan-genome MLST (pgMLST) analyses. Automated antimicrobial susceptibility testing (AST), the Etest for meropenem and the broth microdilution test for colistin were performed. The carbapenem inactivation method was used to assess carbapenemase production. Results pgMLST revealed that nine E. cloacae complex isolates from three different hospitals in the Netherlands differed by <20 alleles and grouped in a genetic cluster termed EclCluster-013. Seven isolates were submitted by one hospital in 2016–20. EclCluster-013 isolates produced carbapenemase and were from ST78, a globally disseminated lineage. EclCluster-013 isolates harboured a 316 078 bp IncH12 plasmid carrying the blaVIM-1 carbapenemase and the novel mcr-9 colistin resistance gene along with genes encoding resistance to different antibiotic classes. AST showed that EclCluster-013 isolates were MDR, but susceptible to meropenem (<2 mg/L) and colistin (<2 mg/L). Conclusions The EclCluster-013 reported here represents an MDR E. cloacae complex ST78 strain containing an IncH12 plasmid carrying both the blaVIM-1 carbapenemase and the mcr-9 colistin resistance gene.
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Affiliation(s)
- Antoni P A Hendrickx
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sylvia Debast
- Isala, Laboratory for Medical Microbiology and Infectious Diseases, Zwolle, The Netherlands
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Annelot F Schoffelen
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Daan W Notermans
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Fabian Landman
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Cornelia C H Wielders
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Javier E Cañada Garcia
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Jacky Flipse
- Isala, Laboratory for Medical Microbiology and Infectious Diseases, Zwolle, The Netherlands
| | - Angela de Haan
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sandra Witteveen
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marga van Santen-Verheuvel
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sabine C de Greeff
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Ed Kuijper
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Leo M Schouls
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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Hendrickx APA, Landman F, de Haan A, Witteveen S, van Santen-Verheuvel MG, Schouls LM. blaOXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands. Microb Genom 2021; 7:000512. [PMID: 33961543 PMCID: PMC8209719 DOI: 10.1099/mgen.0.000512] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/01/2021] [Indexed: 11/29/2022] Open
Abstract
Carbapenem-hydrolysing enzymes belonging to the OXA-48-like group are encoded by blaOXA-48-like alleles and are abundant among Enterobacterales in the Netherlands. Therefore, the objective here was to investigate the characteristics, gene content and diversity of the blaOXA-48-like carrying plasmids and chromosomes of Escherichia coli and Klebsiella pneumoniae collected in the Dutch national surveillance from 2014 to 2019 in comparison with genome sequences from 29 countries. A combination of short-read genome sequencing with long-read sequencing enabled the reconstruction of 47 and 132 complete blaOXA-48-like plasmids for E. coli and K. pneumoniae, respectively. Seven distinct plasmid groups designated as pOXA-48-1 to pOXA-48-5, pOXA-181 and pOXA-232 were identified in the Netherlands which were similar to internationally reported plasmids obtained from countries from North and South America, Europe, Asia and Oceania. The seven plasmid groups varied in size, G+C content, presence of antibiotic resistance genes, replicon family and gene content. The pOXA-48-1 to pOXA-48-5 plasmids were variable, and the pOXA-181 and pOXA-232 plasmids were conserved. The pOXA-48-1, pOXA-48-2, pOXA-48-3 and pOXA-48-5 groups contained a putative conjugation system, but this was absent in the pOXA-48-4, pOXA-181 and pOXA-232 plasmid groups. pOXA-48 plasmids contained the PemI antitoxin, while the pOXA-181 and pOXA-232 plasmids did not. Furthermore, the pOXA-181 plasmids carried a virB2-virB3-virB9-virB10-virB11 type IV secretion system, while the pOXA-48 plasmids and pOXA-232 lacked this system. A group of non-related pOXA-48 plasmids from the Netherlands contained different resistance genes, non-IncL-type replicons or no replicons. Whole genome multilocus sequence typing revealed that the blaOXA-48-like plasmids were found in a wide variety of genetic backgrounds in contrast to chromosomally encoded blaOXA-48-like alleles. Chromosomally localized blaOXA-48 and blaOXA-244 alleles were located on genetic elements of variable sizes and comprised regions of pOXA-48 plasmids. The blaOXA-48-like genetic element was flanked by a direct repeat upstream of IS1R, and was found at multiple locations in the chromosomes of E. coli. Lastly, K. pneumoniae isolates carrying blaOXA-48 or blaOXA-232 were mostly resistant for meropenem, whereas E. coli blaOXA-48, blaOXA-181 and chromosomal blaOXA-48 or blaOXA-244 isolates were mostly sensitive. In conclusion, the overall blaOXA-48-like plasmid population in the Netherlands is conserved and similar to that reported for other countries, confirming global dissemination of blaOXA-48-like plasmids. Variations in size, presence of antibiotic resistance genes and gene content impacted pOXA-48, pOXA-181 and pOXA-232 plasmid architecture.
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Affiliation(s)
- Antoni P. A. Hendrickx
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Fabian Landman
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Angela de Haan
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sandra Witteveen
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marga G. van Santen-Verheuvel
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Leo M. Schouls
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - the Dutch CPE surveillance Study Group
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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