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Biedrzycka M, Urbanowicz P, Żabicka D, Hryniewicz W, Gniadkowski M, Izdebski R. Country-wide expansion of a VIM-1 carbapenemase-producing Klebsiella oxytoca ST145 lineage in Poland, 2009-2019. Eur J Clin Microbiol Infect Dis 2023; 42:1449-1457. [PMID: 37857919 PMCID: PMC10651708 DOI: 10.1007/s10096-023-04682-x] [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: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
PURPOSE To elucidate the role of the Klebsiella oxytoca species complex (KoSC) in epidemiology of VIM-type MBL-producing Enterobacterales in Poland. METHODS The study comprised all 106 VIM-positive KoSC isolates collected by the Polish National Reference Centre for Susceptibility Testing during 2009-2019 from 60 institutions in 35 towns. All isolates were sequenced by Illumina MiSeq, followed by MinION sequencing of selected organisms. Genomes were subjected to bioinformatic analysis, addressing taxonomy, clonality, phylogeny and structural characterisation of key resistance determinants within their chromosomal and plasmidic loci. RESULTS Among five species identified, K. oxytoca was predominant (n = 92), followed by Klebsiella michiganensis (n = 11). MLST distinguished 18 STs, with the most prevalent Klebsiella oxytoca ST145 (n = 83). The clone segregated a lineage with the In237-like integron [blaVIM-1-aacA4 genes; n = 78], recorded in 28 cities almost all over the country. The integron was located in a ~ 49-50 kb chromosomal mosaic region with multiple other resistance genes, linked to a ~ 51 kb phage-like element. The organism might have originated from Greece, and its evolution in Poland included several events of chromosomal ~ 54-258 kb deletions, comprising the natural β-lactamase blaOXY gene. A group of other isolates of various species and clones (n = 12) carried the integron In916 on self-transmissible IncA-type plasmids, effectively spreading in Italy, France and Poland. CONCLUSION KoSC has been one of the major VIM producers in Poland, owing largely to clonal expansion of the specific K. oxytoca-In237-like lineage. Its apparently enhanced epidemic potential may create a danger on international scale.
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Affiliation(s)
- M Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
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Izdebski R, Biedrzycka M, Urbanowicz P, Żabicka D, Gniadkowski M. Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp., Poland. Emerg Infect Dis 2023; 29:1618-1626. [PMID: 37486192 PMCID: PMC10370858 DOI: 10.3201/eid2908.230199] [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: 07/25/2023] Open
Abstract
We sequenced all nonduplicate 934 VIM/IMP carbapenemase-producing Enterobacterales (CPE) reported in Poland during 2006-2019 and found ≈40% of the isolates (n = 375) were Enterobacter spp. During the study period, incidence of those bacteria gradually grew in nearly the entire country. The major factor affecting the increase was clonal spread of several E. hormaechei lineages responsible for multiregional and interregional outbreaks (≈64% of all isolates), representing mainly the pandemic sequence type (ST) 90 or the internationally rare ST89 and ST121 clones. Three main VIM-encoding integron types efficiently disseminated across the clone variants (subclones) with various molecular platforms. Those variants were predominantly Pseudomonas aeruginosa-derived In238-like elements, present with IncHI2+HI2A, IncFII+FIA, IncFIB, or IncN3 plasmids, or chromosomal genomic islands in 30 Enterobacter STs. Another prevalent type, found in 34 STs, were In916-like elements, spreading in Europe recently with a lineage of IncA-like plasmids.
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Slimene K, Salabi AE, Dziri O, Mathlouthi N, Diene SM, Mohamed EA, Amhalhal JMA, Aboalgasem MO, Alrjael JF, Rolain JM, Chouchani C. Epidemiology, Phenotypic and Genotypic Characterization of Carbapenem-Resistant Gram-Negative Bacteria from a Libyan Hospital. Microb Drug Resist 2023. [PMID: 37145891 DOI: 10.1089/mdr.2022.0060] [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: 05/07/2023] Open
Abstract
Antimicrobial resistance, particularly resistance to carbapenems, has become one of the major threats to public health. Seventy-two isolates were collected from patients and hospital environment of Ibn Sina Hospital, Sirte, Libya. Antibiotic susceptibility tests, using the disc diffusion method and E-Test strips, were performed to select carbapenem-resistant strains. The colistin (CT) resistance was also tested by determining the minimum inhibitory concentration (MIC). RT-PCR was conducted to identify the presence of carbapenemase encoding genes and plasmid-mediated mcr CT resistance genes. Standard PCR was performed for positive RT-PCR and the chromosome-mediated CT resistance genes (mgrB, pmrA, pmrB, phoP, phoQ). Gram-negative bacteria showed a low susceptibility to carbapenems. Molecular investigations indicated that the metallo-β-lactamase New Delhi metallo-beta-lactamases-1 was the most prevalent (n = 13), followed by Verona integron-encoded metallo-beta-lactamase (VIM) enzyme (VIM-2 [n = 6], VIM-1 [n = 1], and VIM-4 [n = 1]) that mainly detected among Pseudomonas spp. The oxacillinase enzyme OXA-23 was detected among six Acinetobacter baumannii, and OXA-48 was detected among one Citrobacter freundii and three Klebsiella pneumoniae, in which one coharbored the Klebsiella pneumoniae carbapenemase enzyme and showed resistance to CT (MIC = 64 μg/mL) by modification in pmrB genes. In this study, we report for the first time the emergence of Pseudomonas aeruginosa carrying the blaNDM-1 gene and belonging to sequence type773 in Libya. Our study reported also for the first time CT resistance by mutation in the pmrB gene among Enterobacteriaceae isolates in Libya.
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Affiliation(s)
- Khouloud Slimene
- Faculté de Médecine et de Pharmacie, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille Cedex 05, France
- IHU Méditerranée Infection, Marseille Cedex 05, France
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
- Unité de Service en Commun Pour la Recherche « Plateforme Génomique » Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
| | - Allaaeddin El Salabi
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya
| | - Olfa Dziri
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
- Unité de Service en Commun Pour la Recherche « Plateforme Génomique » Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
| | - Najla Mathlouthi
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
- Unité de Service en Commun Pour la Recherche « Plateforme Génomique » Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
| | - Seydina M Diene
- Faculté de Médecine et de Pharmacie, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille Cedex 05, France
- IHU Méditerranée Infection, Marseille Cedex 05, France
| | | | - Jadalla M A Amhalhal
- Department of Anesthesia and Surgical Intensive Care, Faculty of Medicine, Sirte University, Sirte, Libya
- ICU Department, Ibn Sina Hospital, Sirte, Libya
| | - Mohammed O Aboalgasem
- Department of Internal Medicine, Faculty of Medicine, University of Sirte, Sirte, Libya
- Infection Prevention and Patient Safety Office, Ibn Sina Hospital, Sirte, Libya
| | - Jomaa F Alrjael
- ICU Department, Ibn Sina Hospital, Sirte, Libya
- Department of Anesthesia, Ibn Sina Hospital, Sirte, Libya
| | - Jean-Marc Rolain
- Faculté de Médecine et de Pharmacie, Aix-Marseille Université, IRD, APHM, MEPHI, Marseille Cedex 05, France
- IHU Méditerranée Infection, Marseille Cedex 05, France
| | - Chedly Chouchani
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l'Environnement, Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
- Unité de Service en Commun Pour la Recherche « Plateforme Génomique » Institut Supérieur des Sciences et Technologies de l'Environnement de Borj-Cedria, Université de Carthage, Tunis, Tunisie
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Biedrzycka M, Izdebski R, Urbanowicz P, Polańska M, Hryniewicz W, Gniadkowski M, Literacka E. MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009-19. J Antimicrob Chemother 2022; 77:3367-3375. [PMID: 36177793 DOI: 10.1093/jac/dkac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/05/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To characterize carbapenemase-producing isolates of the Klebsiella pneumoniae hypervirulent (hvKp) clone ST23 in Poland. METHODS Fifteen K. pneumoniae ST23 isolates were identified by the Polish surveillance of carbapenemase-producing Enterobacterales. These comprised a cluster with KPC-2 + NDM-1 (n = 7), KPC-2 (n = 1) or NDM-1 (n = 1) enzymes from one hospital from 2018, and sporadic isolates with KPC-2 (n = 1), NDM-1 (n = 1), VIM-1 (n = 1) or OXA-48 (n = 3), recovered from 2009 to 2019 in different towns. The isolates were sequenced by Illumina MiSeq, followed by MinION for six representatives. Clonality, phylogeny, serotypes, virulomes, resistomes and plasmids of the isolates were analysed and compared with international ST23 strains, using various bioinformatic tools. RESULTS Only two diverse isolates with KPC-2 or VIM-1 were of typical hvKp ST23 serotypes K1 and O1v.2, and its predominant phylogenetic clade. These contained multiple chromosomal (ybt, clb) and pK2044/KpVP-1 plasmid (iuc, iro, rmpADC, rmpA2) virulence loci, whereas carbapenemase and other antimicrobial resistance (AMR) genes were on single additional plasmids. All remaining isolates were of K57 and O2v.2 serotypes, and a minor, distant clade of unclear phylogeny, including also ∼10 isolates from other European countries. These had fewer virulence loci (ybt, iuc, rmpADC, rmpA2) but abounded in plasmids, which with several chromosomal AMR mutations conferred more extensive MDR phenotypes than in K1 O1v.2. Lower clonal diversity than in K1, and numerous common characteristics of the isolates supported the hypothesis of the emerging character of the ST23 K57 clade. CONCLUSIONS A new MDR ST23 lineage has emerged in Europe, causing a potential threat to public health.
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Affiliation(s)
| | - R Izdebski
- National Medicines Institute, Warsaw, Poland
| | | | - M Polańska
- Faculty of Biology, Warsaw University, Warsaw, Poland
| | | | | | - E Literacka
- National Medicines Institute, Warsaw, Poland
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Chi X, Meng X, Xiong L, Chen T, Zhou Y, Ji J, Zheng B, Xiao Y. Small wards in the ICU: a favorable measure for controlling the transmission of carbapenem-resistant Klebsiella pneumoniae. Intensive Care Med 2022; 48:1573-1581. [PMID: 36129475 PMCID: PMC9592670 DOI: 10.1007/s00134-022-06881-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE Carbapenem-resistant Klebsiella pneumoniae (CRKP) is one of the leading causes of healthcare-associated infections (HAIs) and is particularly pervasive in intensive care units (ICUs). This study takes ICU layout as the research object, and integrates clinical data and bacterial genome analysis to clarify the role of separate, small wards within the ICU in controlling the transmission of CRKP. METHODS This study prospectively observed the carriage and spread of CRKP from a long-term in-hospital patient (hereafter called the Patient) colonized with CRKP in the gut and located in a separate, small ward within the ICU. The study also retrospectively investigated CRKP-HAIs in the same ICU. The relationship and transmission between CRKP isolates from the Patient and HAI events in the ICU were explored with comparative genomics. RESULTS In this study, 65 CRKP-HAI cases occurred during the investigation period. Seven CRKP-HAI outbreaks were also observed. A total of 95 nonrepetitive CRKP isolates were collected, including 32 strains from the Patient in the separate small ward. Phylogenetic analysis based on core genome single-nucleotide polymorphism (cgSNP) showed that there were five possible CRKP clonal transmission events and two clonal outbreaks (A1, A2) during the study. CRKP strains from the Patient did not cause CRKP between-patient transmission or outbreaks in the ICU during the 5-year study period. CONCLUSION The presence of a long-term hospitalized patient carrying CRKP and positioned in a separate, small ward did not lead to CRKP transmission or infection outbreaks in the ICU. Combining a small-ward ICU layout with normative HAI control measures for multidrug-resistant pathogen infection was effective in reducing CRKP transmission.
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Affiliation(s)
- Xiaohui Chi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China
| | - Xiaohua Meng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China
| | - Luying Xiong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China
| | - Tao Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China
| | - Yanzi Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China
| | - Jinru Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China.
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China.
- Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, 310003, China.
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China.
- Research Units of Infectious Disease and Microecology, Chinese Academy of Medical Sciences, Beijing, China.
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Emeraud C, Petit C, Gauthier L, Bonnin RA, Naas T, Dortet L. Emergence of VIM-producing Enterobacter cloacae complex in France between 2015 and 2018. J Antimicrob Chemother 2022; 77:944-951. [PMID: 35045171 DOI: 10.1093/jac/dkab471] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES To genetically characterize VIM-producing Enterobacter cloacae complex (ECC) isolates recovered in France from 2015 to 2018. METHODS WGS, species determination, MLST, clonal relationship and genetic characterization were performed on 149 VIM-producing ECC isolates. RESULTS Among VIM-producing Enterobacterales, the prevalence of ECC increased drastically from 6% in 2012 to 52% in 2018. The most prevalent species were Enterobacter hormaechei subsp. hoffmannii (40.9%), E. hormaechei subsp. steigerwaltii (21.5%), E. hormaechei subsp. xiangfangensis (14.8%) and ECC clade S (17.4%). Major STs were ST-873 (17.5%), ST-66 (12.1%), ST-78 (9.4%), ST-419 (8.1%), ST-145 (4.7%), ST-50 (4.0%), ST-118 (4.0%) and ST-168 (4.0%). Finally, six different integrons were identified, with some being specific to a given blaVIM variant (In916 with blaVIM-1-aacA4'-aphA15-aadA1-catB2 and In416 with blaVIM-4-aacA7-dfrA1b-aadA1b-smr2 genes). CONCLUSIONS This study demonstrated the genetic diversity among VIM-producing ECC isolates, indicating that their spread is not linked to a single clone.
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Affiliation(s)
- Cécile Emeraud
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Caroline Petit
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Lauraine Gauthier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Team "Resist", UMR1184, Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB), INSERM, Paris-Saclay University, Faculty of Medicine, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacteriaceae, Le Kremlin-Bicêtre, France
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1561-1569. [DOI: 10.1093/jac/dkac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/16/2022] [Indexed: 11/14/2022] Open
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Biedrzycka M, Urbanowicz P, Guzek A, Brisse S, Gniadkowski M, Izdebski R. Dissemination of Klebsiella pneumoniae ST147 NDM-1 in Poland, 2015-19. J Antimicrob Chemother 2021; 76:2538-2545. [PMID: 34164678 DOI: 10.1093/jac/dkab207] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/29/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To assess the spread of New Delhi metallo-β-lactamase-1 (NDM-1)-producing Klebsiella pneumoniae ST147 organisms in Poland since an introduction from Tunisia in March 2015, including their phylogenetic position in the global population of the high-risk clone. METHODS Out of 8925 unique NDM-positive K. pneumoniae isolates identified in Poland from April 2015 till December 2019, 126 isolates, including the Tunisian imports, were related by PFGE and blaNDM gene-carrying Tn125 transposon derivatives. Forty-seven representative isolates were sequenced by Illumina MiSeq. The phylogeny, resistome, virulome and plasmid replicons were analysed and compared with the international ST147 strains. Plasmids of six isolates were studied by the MinION sequencing. RESULTS A high homogeneity of the 47 isolates was observed, with minor variations in their resistomes and plasmid replicon profiles. However, the detailed SNP comparison discerned a strict outbreak cluster of 40 isolates. All of the organisms were grouped within the ST147 phylogenetic international lineage, and four NDM-1 producers from Tunisia, Egypt and France were the closest relatives of the Polish isolates. Yersiniabactin genes (YbST280 type) were located within the ICEKpn12-like element in most of the outbreak isolates, characterized by O2v1 and KL64 antigen loci. The blaNDM-1 genes were located in double-replicon IncFIIK2+IncFIBK plasmids. CONCLUSIONS The continuous spread of K. pneumoniae ST147 NDM-1 in Poland since 2015, largely in the Warsaw area, is demonstrated by this genomic analysis. The isolates showed a high degree of homogeneity, and close relatedness to organisms spreading in the Mediterranean region.
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Affiliation(s)
- M Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - A Guzek
- Department of Laboratory Diagnostics, Section of Microbiology, Military Institute of Medicine, Warsaw, Poland
| | - S Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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Spread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study. Microbiol Spectr 2021; 9:e0005821. [PMID: 34259540 PMCID: PMC8552774 DOI: 10.1128/spectrum.00058-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The aim of this study was to determine the contribution of the contamination of the health care environment in the acquisition of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a CRKP-prevalent setting. We performed a 3-month prospective study in a 20-bed medical intensive care unit (ICU) by collecting rectal/oral swabs from patients within 3 days of ICU admission and weekly thereafter. We also comprehensively sampled the beds and rooms of patients and instruments for patient care every week. CRKP were detected, genome sequenced, and assigned to clones based on core genome analyses. The survival of four CRKP clones was determined under ICU conditions. Seventeen patients were in the ICU at the start of the study, and 99 were admitted afterwards. Six were positive patients, with four detected on initial screening and two during weekly monitoring. CRKP was detected from 76 of 3,699 (2.1%) environment samples, including from the immediate surroundings of 21 patients (five had CRKP from clinical samples and 16 did not). CRKP was not detected outside patient care areas. Among 49 CRKP sequenced isolates (nine from swabs, five from clinical samples, and 35 from environment) from 21 patients, 45 were ST11 and had blaKPC-2. These could be assigned to four clones, with either KL47 (n = 22) or KL64 (n = 23) capsular type. The two dominant clones survived >30 days under ICU conditions. In conclusion, environmental contamination of CRKP was extensive but usually transient. It had little impact on CRKP acquisition by ICU patients, highlighting the ability to control CRKP transmission through infection prevention efforts even in high-prevalence settings. IMPORTANCEKlebsiella pneumoniae can be an opportunistic pathogen with the oral cavity and gut the main origin. However, carbapenem-resistant Klebsiella pneumoniae (CRKP) can be found in patient surroundings and is a serious threat for human infections. Although the hospital environment, particularly sinks, has long been considered a potential reservoir of CRKP, the exact role of environmental contamination contributing to the acquisition and transmission of CRKP among patients remains largely unknown. To understand the link between environmental contamination in health care settings and colonization and infection of patients by CRKP, we performed a 3-month prospective study in a 20-bed medical ICU. Isolates were collected by active patient screening and were subsequently genome sequenced to describe the diversity of CRKP and the linkage of patients and environmental reservoirs. We found that the environmental contamination of CRKP was extensive, and CRKP clones were freely circulating in the ICU. Environmental contamination was not due to sharing the bed unit or sharing contaminated instruments but more likely resulted from the movement of health care workers. Very few patients acquired CRKP in the ICU, which is likely due to the fact that environmental contamination was usually transient when a routine cleaning protocol was complied. Although CRKP contamination in patient surroundings may be extensive, as long as routine environment cleaning protocols are appropriate and well implemented, the health care environment is unlikely to be a major source of CRKP colonization and infection in ICU patients. Reducing the high workload for ICU nurses may help minimize CRKP environmental contamination.
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Chudejova K, Kraftova L, Mattioni Marchetti V, Hrabak J, Papagiannitsis CC, Bitar I. Genetic Plurality of OXA/NDM-Encoding Features Characterized From Enterobacterales Recovered From Czech Hospitals. Front Microbiol 2021; 12:641415. [PMID: 33633720 PMCID: PMC7900173 DOI: 10.3389/fmicb.2021.641415] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/20/2021] [Indexed: 01/24/2023] Open
Abstract
The aim of this study was to characterize four Enterobacterales co-producing NDM- and OXA-48-like carbapenemases from Czech patients with travel history or/and previous hospitalization abroad. Klebsiella pneumoniae isolates belonged to “high risk” clones ST147, ST11, and ST15, while the Escherichia coli isolate was assigned to ST167. All isolates expressed resistance against most β-lactams, including carbapenems, while retaining susceptibility to colistin. Furthermore, analysis of WGS data showed that all four isolates co-produced OXA-48- and NDM-type carbapenemases, in different combinations (Kpn47733: blaNDM–5 + blaOXA–181; Kpn50595: blaNDM–1 + blaOXA–181; Kpn51015: blaNDM–1 + blaOXA–244; Eco52418: blaNDM–5 + blaOXA–244). In Kpn51015, the blaOXA–244 was found on plasmid p51015_OXA-244, while the respective gene was localized in the chromosomal contig of E. coli Eco52418. On the other hand, blaOXA–181 was identified on a ColKP3 plasmid in isolate Kpn47733, while a blaOXA–181-carrying plasmid being an IncX3-ColKP3 fusion was identified in Kpn50595. The blaNDM–1 gene was found on two different plasmids, p51015_NDM-1 belonging to a novel IncH plasmid group and p51015_NDM-1 being an IncFK1-FIB replicon. Furthermore, the blaNDM–5 was found in two IncFII plasmids exhibiting limited nucleotide similarity to each other. In both plasmids, the genetic environment of blaNDM–5 was identical. Finally, in all four carbapenemase-producing isolates, a diverse number of additional replicons, some of these associated with important resistance determinants, like blaCTX–M–15, arr-2 and ermB, were identified. In conclusion, this study reports the first description of OXA-244-producing Enterobacterales isolated from Czech hospitals. Additionally, our findings indicated the genetic plurality involved in the acquisition and dissemination of determinants encoding OXA/NDM carbapenemases.
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Affiliation(s)
- Katerina Chudejova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Lucie Kraftova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Vittoria Mattioni Marchetti
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Costas C Papagiannitsis
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia.,Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia.,Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
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11
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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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12
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Abstract
Infections caused by carbapenemase-producing bacteria have led to the revival of polymyxins as the “last-resort” antibiotic. Since 2016, several reports describing the presence of plasmid-mediated colistin resistance genes, mcr, in different host species and geographic areas were published. The aim of this study was to report the characterization of the first mcr-positive Enterobacterales isolated from Czech hospitals. In 2019, one Citrobacter freundii and four Enterobacter isolates were recovered from Czech hospitals. The production of carbapenemases was examined by a matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) imipenem hydrolysis assay. Additionally, bacteria were screened for the presence of carbapenemase-encoding genes and plasmid-mediated colistin resistance genes by PCR. To define the genetic units carrying mcr genes, the genomic DNAs of mcr-carrying clinical isolates were sequenced on the PacBio Sequel I platform. Results showed that all isolates carried blaVIM- and mcr-like genes. Analysis of whole-genome sequencing (WGS) data revealed that all isolates carried mcr-9-like alleles. Furthermore, the three sequence type 106 (ST106) Enterobacter hormaechei isolates harbored the blaVIM-1 gene, while the ST764 E. hormaechei and ST95 C. freundii included blaVIM-4. Analysis of plasmid sequences showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. Additionally, at least one multidrug resistance (MDR) region was identified in each mcr-9-carrying IncHI2 plasmid. The blaVIM-4 gene was found in the MDR regions of p48880_MCR_VIM and p51929_MCR_VIM. In the three remaining isolates, blaVIM-1 was localized on plasmids (∼55 kb) exhibiting repA-like sequences 99% identical to the respective gene of pKPC-CAV1193. In conclusion, to the best of our knowledge, these 5 isolates were the first mcr-9-positive bacteria of clinical origin identified in the Czech Republic. Additionally, the carriage of the blaVIM-1 on pKPC-CAV1193-like plasmids is described for the first time. Thus, our findings underline the ongoing evolution of mobile elements implicated in the dissemination of clinically important resistance determinants. IMPORTANCE Infections caused by carbapenemase-producing bacteria have led to the revival of polymyxins as the “last-resort” antibiotic. Since 2016, several reports describing the presence of plasmid-mediated colistin resistance genes, mcr, in different host species and geographic areas were published. Here, we report the first detection of Enterobacterales carrying mcr-9-like alleles isolated from Czech hospitals in 2019. Furthermore, the three ST106 Enterobacter hormaechei isolates harbored blaVIM-1, while the ST764 E. hormaechei and ST95 Citrobacter freundii isolates included blaVIM-4. Analysis of WGS data showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. blaVIM-4 was found in the MDR regions of IncHI2 plasmids, while blaVIM-1 was localized on pKPC-CAV1193-like plasmids, described here for the first time. These findings underline the ongoing evolution of mobile elements implicated in dissemination of clinically important resistance determinants. Thus, WGS characterization of MDR bacteria is crucial to unravel the mechanisms involved in dissemination of resistance mechanisms.
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13
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Genetic diversity of carbapenem-resistant Klebsiella Pneumoniae causing neonatal sepsis in intensive care unit, Cairo, Egypt. Eur J Clin Microbiol Infect Dis 2019; 39:583-591. [PMID: 31773363 DOI: 10.1007/s10096-019-03761-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/30/2019] [Indexed: 12/26/2022]
Abstract
Neonatal sepsis is a great challenge for clinicians and infection control practitioners, especially in facilities with limited resources. Carbapenem-resistant Klebsiella pneumoniae (CRKP) is rapidly increasing and carriages a major threat to neonates. We aimed to examine phenotypes causing neonatal late onset sepsis (NLOS) in comparison with neonatal early onset sepsis (NEOS) with further investigations of genotypes, and genetic relatedness of CRKP in neonatal late-onset sepsis. Our study included 88 neonates diagnosed with sepsis: 58 with (NLOS) and 30 with (NEOS) from November 2015 to April 2016, at neonatal intensive care unit (NICU) of Cairo University Hospital. K. pneumoniae was the most common encountered pathogen in the NLOS group (37.9%) with a mean sepsis score of 6.39 when compared to the NEOS group (p < 0.05). In Klebsiella group, C-reactive protein and interleukin-6 levels were significantly high (p ˂ 0.001) and 56.5% of the isolates were meropenem resistant. The most prevalent carbapenemase gene was OXA-48 which was identified in 14/23 (60.8%) followed by NDM-1 which was identified in 12/23 (52.2%) as detected by multiplex PCR. Coexistence of both carbapenemases was found in 52.2% (12/23). The blaKPC, blaIMP, and blaVIM genes were not harbored in the isolates. By investigating the genetic relatedness of CRKP by pulsed-field gel electrophoresis, 23 isolates of K. pneumoniae revealed various pulsed-field gel electrophoresis (PFGE) patterns, demonstrating that the isolates were non-clonal. Awareness of the existing phenotypes and genotypes is important for proper treatment and infection control practices.
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14
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Gurieva T, Dautzenberg MJD, Gniadkowski M, Derde LPG, Bonten MJM, Bootsma MCJ. The Transmissibility of Antibiotic-Resistant Enterobacteriaceae in Intensive Care Units. Clin Infect Dis 2019; 66:489-493. [PMID: 29020273 PMCID: PMC5850446 DOI: 10.1093/cid/cix825] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/13/2017] [Indexed: 11/23/2022] Open
Abstract
Background The global emergence of infections caused by Enterobacteriaceae resistant to expanded-spectrum cephalosporins (ESCs) in intensive care units (ICUs) is, at least partly, driven by cross-transmission. Yet, individual transmission capacities of bacterial species have not been quantified. Methods In this post hoc analysis of a multicenter study in 13 European ICUs, prospective surveillance data and a mathematical model were used to estimate transmission capacities and single-admission reproduction numbers (RA) of Escherichia coli and non–E. coli Enterobacteriaceae (non-EcE), all being ESC resistant. Surveillance was based on a chromogenic selective medium for ESC-resistant Enterobacteriaceae, allowing identification of E. coli and of Klebsiella, Enterobacter, Serratia, and Citrobacter species, grouped as non-EcE. Results Among 11420 patients included, the admission prevalence was 3.8% for non-EcE (74% being Klebsiella pneumoniae) and 3.3% for E. coli. Acquisition rates were 7.4 and 2.6 per 100 admissions at risk for non-EcE and E. coli, respectively. The estimated transmission capacity of non-EcE was 3.7 (95% credibility interval [CrI], 1.4–11.3) times higher than that of E. coli, yielding single-admission reproduction numbers (RA) of 0.17 (95% CrI, .094–.29) for non-EcE and 0.047 (95% CrI, .018–.098) for E. coli. Conclusions In ICUs, non-EcE, mainly K. pneumoniae, are 3.7 times more transmissible than E. coli. Estimated RA values of these bacteria were below the critical threshold of 1, suggesting that in these ICUs outbreaks typically remain small with current infection control policies.
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Affiliation(s)
| | - Mirjam J D Dautzenberg
- Julius Center for Health Sciences and Primary Care.,Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Lennie P G Derde
- Julius Center for Health Sciences and Primary Care.,Department of Intensive Care Medicine, University Medical Center Utrecht
| | - Marc J M Bonten
- Julius Center for Health Sciences and Primary Care.,Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Martin C J Bootsma
- Julius Center for Health Sciences and Primary Care.,Faculty of Sciences, Department of Mathematics, Utrecht University, The Netherlands
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15
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Izdebski R, Baraniak A, Zabicka D, Sekowska A, Gospodarek-Komkowska E, Hryniewicz W, Gniadkowski M. VIM/IMP carbapenemase-producing Enterobacteriaceae in Poland: epidemic Enterobacter hormaechei and Klebsiella oxytoca lineages. J Antimicrob Chemother 2019; 73:2675-2681. [PMID: 29986025 DOI: 10.1093/jac/dky257] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/06/2018] [Indexed: 12/23/2022] Open
Abstract
Objectives To analyse VIM/IMP-type MBL-producing Enterobacteriaceae isolates identified in Poland during 2006-12. Methods Isolates were typed by PFGE, followed by MLST. blaVIM/IMP genes were amplified and sequenced within class 1 integrons. Their plasmidic versus chromosomal location was assessed by nuclease S1 and I-CeuI plus hybridization experiments. Plasmids were characterized by transfer assays and PCR-based replicon typing. Results One hundred and nineteen VIM/IMP-positive Enterobacteriaceae cases were reported in Poland from the first case in 2006 until 2012. The patients were in 54 hospitals and were infected or colonized by 121 organisms, including Enterobacter cloacae complex (n = 64), Klebsiella oxytoca (n = 23), Serratia marcescens (n = 20) and Klebsiella pneumoniae (n = 11). The isolates represented numerous pulsotypes and mainly original STs, and carried eight integrons with blaVIM-1-like genes (blaVIM-1/-4/-28/-37/-40; n = 101), three with blaVIM-2 variants (blaVIM-2/-20; n = 17) and one with blaIMP-19 (n = 3). Six integrons were new, and five and two formed prevalent families of In238-like (n = 96) and In1008-like (n = 16) elements, respectively. In238 (aacA4-blaVIM-4rpt) and In1008 (blaVIM-2-aacA4) had been originally observed in Polish Pseudomonas aeruginosa, suggestive of their transfer to enterobacteria, followed by spread and diversification. Four organisms have disseminated inter-regionally, i.e. Enterobacter hormaechei ST90 with plasmidic In238/In238a integrons (n = 36), K. oxytoca ST145 with a chromosomal In237-like element (n = 18) and two subclones of E. hormaechei ST89 with In1008- or In238-type variants (n = 8 and n = 7, respectively). Conclusions The epidemiology of VIM/IMP-producing Enterobacteriaceae in Poland has revealed a remarkable number of specific or novel characteristics of the organisms, with some possible links to other mid-southern European countries.
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Affiliation(s)
- R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - D Zabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - A Sekowska
- Department of Microbiology, Nicolas Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - E Gospodarek-Komkowska
- Department of Microbiology, Nicolas Copernicus University, Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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16
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Messaoudi A, Haenni M, Bouallègue O, Saras E, Chatre P, Chaouch C, Boujâafar N, Mansour W, Madec JY. Dynamics and molecular features of OXA-48-like-producing Klebsiella pneumoniae lineages in a Tunisian hospital. J Glob Antimicrob Resist 2019; 20:87-93. [PMID: 31306816 DOI: 10.1016/j.jgar.2019.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/18/2019] [Accepted: 07/03/2019] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES The aim of this study was to elucidate the molecular features of genes, plasmids and clones of OXA-48-like producingKlebsiella pneumoniae isolates recovered in Sahloul Hospital (Sousse, Tunisia) in the period 2012-2014. METHODS In vitro antimicrobial susceptibility testing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blotting and PCR-based replicon typing (PBRT) were performed. Extended-spectrum β-lactamase (ESBL) and carbapenemases genes were detected by PCR and sequencing. The clonality of isolates was assessed by PFGE and multilocus sequence typing (MLST). RESULTS Klebsiella pneumoniae accounted for 26.8% (1095/4083) of clinical Enterobacterales isolates identified during 2012-2014, of which 21.9% (240/1095) were resistant to carbapenems, mostly harbouring blaOXA-48-like genes (196/240; 81.7%). Plasmid analysis showed that blaOXA-204 and blaOXA-48 were mostly carried by IncA/C and IncL plasmids, respectively. The current data highlight the dominance of two ST101 and ST147 lineages spreading OXA-48 and OXA-204, respectively, through successive clonal spreads at this hospital. In addition, a large diversity of other K. pneumoniae lineages was also identified, such as ST15, ST36 and ST525 spreading OXA-48 as well as ST340, ST2032, ST301, ST199 and ST1561 spreading OXA-48 or OXA-204, constituting a reservoir of possible dominant clones in the future. CONCLUSION This study reports the full molecular characterisation of carbapenem resistance in K. pneumoniae and the predominance of a few clones responsible for the dissemination of OXA-48 and OXA-204 enzymes in a Tunisian hospital.
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Affiliation(s)
- Aziza Messaoudi
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia
| | - Marisa Haenni
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Olfa Bouallègue
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Medicine Ibn Al Jazzar Sousse, University of Sousse, Sousse, Tunisia
| | - Estelle Saras
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Pierre Chatre
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Cherifa Chaouch
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Noureddine Boujâafar
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Wejdene Mansour
- Research Unit: Emergent Bacterial Resistance and Safety of Care (UR12SP37), Laboratory of Microbiology, University Hospital Sahloul, Sousse, Tunisia; Faculty of Medicine Ibn Al Jazzar Sousse, University of Sousse, Sousse, Tunisia; Laboratory of Metabolic Biophysics and Applied Pharmacology (LR12ES02), Department of Biophysics, Faculty of Medicine Ibn El Jazzar Sousse, University of Sousse, Sousse, Tunisia.
| | - Jean-Yves Madec
- Université de Lyon-French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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17
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Papagiannitsis CC, Bitar I, Malli E, Tsilipounidaki K, Hrabak J, Petinaki E. IncC bla KPC-2-positive plasmid characterised from ST648 Escherichia coli. J Glob Antimicrob Resist 2019; 19:73-77. [PMID: 31077860 DOI: 10.1016/j.jgar.2019.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 10/26/2022] Open
Abstract
OBJECTIVES This study describes the characterisation of type 2 IncC plasmids pC-Ec20-KPC and pC-Ec2-KPC, carrying theblaKPC-2 gene, from two multiresistant Escherichia coli recovered in University Hospital of Larissa (Greece) in 2018. METHODS E. coli strains Ec-2Lar and Ec-20Lar were recovered from rectal swabs of two patients during monthly surveillance cultures. Transfer experiments by conjugation were carried out using rifampicin-resistant E. coli A15 laboratory strain as recipient. blaKPC-carrying plasmids were characterised by S1 profiling. Isolates were typed by MLST. Whole-genome sequencing was performed using the Sequel platform. RESULTS Both E. coli isolates, belonging to ST648, transferred blaKPC-2 to E. coli A15 by conjugation. Plasmid analysis revealed that the transconjugants harboured blaKPC-positive plasmids of different sizes. Analysis of plasmid sequences showed that in both isolates the blaKPC-2 gene was carried on a type 2 IncC plasmid (pC-Ec20-KPC and pC-Ec2-KPC, respectively). Both plasmids carried the ARI-B resistance island consisting of several resistance genes, intact and truncated copies of several mobile elements, and a 25 571-bp segment harbouring coding sequences for an iron transporter. The blaKPC-2 gene was part of transposon Tn4401a, which was bounded by 5-bp direct repeats (TCCTT) suggesting its transposition into the IncC plasmids. CONCLUSION To our knowledge, this is the first report on complete nucleotide sequences of type 2 IncC plasmids. These findings, which hypothesise the acquisition of KPC-2-encoding transposon Tn4401a by an IncC replicon, indicate the ongoing need for molecular surveillance studies of multidrug-resistant pathogens. In addition, they underline the increasing clinical importance of the IncC plasmid family.
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Affiliation(s)
| | - Ibrahim Bitar
- Biomedical Center, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic
| | - Ergina Malli
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | | | - Jaroslav Hrabak
- Biomedical Center, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic
| | - Efthimia Petinaki
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece.
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18
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Kontopoulou K, Iosifidis E, Antoniadou E, Tasioudis P, Petinaki E, Malli E, Metallidis S, Vatopoulos A, Malisiovas N. The clinical significance of carbapenem-resistant Klebsiella pneumoniae rectal colonization in critically ill patients: from colonization to bloodstream infection. J Med Microbiol 2019; 68:326-335. [PMID: 30688629 DOI: 10.1099/jmm.0.000921] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
PURPOSE To highlight the clinical significance of carbapenem-resistant Klebsiella pneumoniae (CRKP) rectal colonization by examining the risk factors for CRKP rectal colonization and subsequent bloodstream infection (BSI) in critically ill patients. METHODOLOGY Prospective study of CRKP rectal colonization in an intensive care unit (ICU) during a 39-month period. CRKP strains isolated from both the blood cultures and corresponding rectal specimens (n=96) of patients were screened by PCR for the presence of antibiotic resistance-associated genes. Molecular analyses were conducted to investigate the clonal relatedness of CRKP strains from the rectal and blood specimens. RESULTS Among the 498 patients, 226 were rectally colonized by CRKP, 48 of whom developed a CRKP BSI. The median time from hospital admission to the detection of CRKP rectal colonization was 8 days, while the median time from colonization to BSI was 4 days. The duration of ICU stay, patient/nurse ratio and prior use of antianaerobic antimicrobials were associated with CRKP rectal colonization. No specific factor was associated with BSIs in the colonized patients. The blaKPC-2 gene was detected in all 96 strains, which were all classified as sequence type ST-258. Representative pairs (n=48) of CRKP strains colonizing and infecting the same patient shared the same pulsotype. CONCLUSION Our results indicate that hospitalized patients become infected with their colonizing strains, supporting the strong association between colonization and BSI. Limiting antianaerobic antimicrobial administration, reducing the duration of ICU stay and maintaining a low patient/nurse ratio are possible strategies to restrict rectal CRKP colonization in ICUs.
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Affiliation(s)
| | - Elias Iosifidis
- 2 3rd Department of Pediatrics, Hippokration Hospital, Aristotle University, Thessaloniki, Greece
| | | | | | - Efthymia Petinaki
- 4 Department of Microbiology, Medical School, University of Thessaly, Larissa, Greece
| | - Ergina Malli
- 4 Department of Microbiology, Medical School, University of Thessaly, Larissa, Greece
| | - Symeon Metallidis
- 5 1st Internal Medicine Department, Infectious Diseases Division, AHEPA Hospital, Medical School, Aristotle University of Thessaloniki, Greece
| | | | - Nicolaos Malisiovas
- 7 Department of Microbiology, Aristotle University of Thessaloniki Medical School, Thessaloniki, Greece
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19
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Salimraj R, Hinchliffe P, Kosmopoulou M, Tyrrell JM, Brem J, van Berkel SS, Verma A, Owens RJ, McDonough MA, Walsh TR, Schofield CJ, Spencer J. Crystal structures of VIM-1 complexes explain active site heterogeneity in VIM-class metallo-β-lactamases. FEBS J 2019; 286:169-183. [PMID: 30430727 PMCID: PMC6326847 DOI: 10.1111/febs.14695] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/06/2018] [Accepted: 11/02/2018] [Indexed: 12/12/2022]
Abstract
Metallo-β-Lactamases (MBLs) protect bacteria from almost all β-lactam antibiotics. Verona integron-encoded MBL (VIM) enzymes are among the most clinically important MBLs, with VIM-1 increasing in carbapenem-resistant Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae) that are among the hardest bacterial pathogens to treat. VIM enzymes display sequence variation at residues (224 and 228) that in related MBLs are conserved and participate in substrate binding. How they accommodate this variability, while retaining catalytic efficiency against a broad substrate range, has remained unclear. Here, we present crystal structures of VIM-1 and its complexes with a substrate-mimicking thioenolate inhibitor, ML302F, that restores meropenem activity against a range of VIM-1 producing clinical strains, and the hydrolysed product of the carbapenem meropenem. Comparison of these two structures identifies a water-mediated hydrogen bond, between the carboxylate group of substrate/inhibitor and the backbone carbonyl of the active site zinc ligand Cys221, that is common to both complexes. Structural comparisons show that the responsible Cys221-bound water is observed in all known VIM structures, participates in carboxylate binding with other inhibitor classes, and thus effectively replicates the role of the conserved Lys224 in analogous complexes with other MBLs. These results provide a mechanism for substrate binding that permits the variation at positions 224 and 228 that is a hallmark of VIM MBLs. ENZYMES: EC 3.5.2.6 DATABASES: Co-ordinates and structure factors for protein structures described in this manuscript have been deposited in the Protein Data Bank (www.rcsb.org/pdb) with accession codes 5N5G (VIM-1), 5N5H (VIM-1:ML302F complex) and 5N5I (VIM-1-hydrolysed meropenem complex).
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Affiliation(s)
- Ramya Salimraj
- School of Cellular and Molecular MedicineUniversity of BristolUK
| | | | | | | | - Jürgen Brem
- Department of ChemistryUniversity of OxfordUK
| | | | - Anil Verma
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | - Raymond J. Owens
- Oxford Protein Production Facility UKRutherford Appleton LaboratoryOxfordshireUK
| | | | | | | | - James Spencer
- School of Cellular and Molecular MedicineUniversity of BristolUK
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20
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Malli E, Florou Z, Tsilipounidaki K, Voulgaridi I, Stefos A, Xitsas S, Papagiannitsis CC, Petinaki E. Evaluation of rapid polymyxin NP test to detect colistin-resistant Klebsiella pneumoniae isolated in a tertiary Greek hospital. J Microbiol Methods 2018; 153:35-39. [DOI: 10.1016/j.mimet.2018.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/20/2018] [Accepted: 08/20/2018] [Indexed: 11/30/2022]
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21
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Wilson H, Török ME. Extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacteriaceae. Microb Genom 2018; 4:e000197. [PMID: 30035710 PMCID: PMC6113871 DOI: 10.1099/mgen.0.000197] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global public-health emergency, which threatens the advances made by modern medical care over the past century. The World Health Organization has recently published a global priority list of antibiotic-resistant bacteria, which includes extended-spectrum β-lactamase-producing Enterobacteriaceae and carbapenemase-producing Enterobacteriaceae. In this review, we highlight the mechanisms of resistance and the genomic epidemiology of these organisms, and the impact of AMR.
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Affiliation(s)
- Hayley Wilson
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
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22
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Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae of Sequence Type 36. Antimicrob Agents Chemother 2018; 62:AAC.02644-17. [PMID: 29712659 DOI: 10.1128/aac.02644-17] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/05/2018] [Indexed: 02/06/2023] Open
Abstract
Sequence type 36 (ST36) Klebsiella pneumoniae is distributed worldwide. We found an ST36 K. pneumoniae clinical isolate that was carbapenem resistant, carried blaKPC-2, had mucoid regulator gene rmpA, and exhibited high virulence. The finding suggests the emergence of carbapenem-resistant hypervirulent K. pneumoniae of ST36, and surveillance of carbapenem-resistant hypervirulent K. pneumoniae is required.
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23
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Hinchliffe P, Tanner CA, Krismanich AP, Labbé G, Goodfellow VJ, Marrone L, Desoky AY, Calvopiña K, Whittle EE, Zeng F, Avison MB, Bols NC, Siemann S, Spencer J, Dmitrienko GI. Structural and Kinetic Studies of the Potent Inhibition of Metallo-β-lactamases by 6-Phosphonomethylpyridine-2-carboxylates. Biochemistry 2018; 57:1880-1892. [PMID: 29485857 PMCID: PMC6007964 DOI: 10.1021/acs.biochem.7b01299] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There are currently no clinically available inhibitors of metallo-β-lactamases (MBLs), enzymes that hydrolyze β-lactam antibiotics and confer resistance to Gram-negative bacteria. Here we present 6-phosphonomethylpyridine-2-carboxylates (PMPCs) as potent inhibitors of subclass B1 (IMP-1, VIM-2, and NDM-1) and B3 (L1) MBLs. Inhibition followed a competitive, slow-binding model without an isomerization step (IC50 values of 0.3-7.2 μM; Ki values of 0.03-1.5 μM). Minimum inhibitory concentration assays demonstrated potentiation of β-lactam (Meropenem) activity against MBL-producing bacteria, including clinical isolates, at concentrations at which eukaryotic cells remain viable. Crystal structures revealed unprecedented modes of binding of inhibitor to B1 (IMP-1) and B3 (L1) MBLs. In IMP-1, binding does not replace the nucleophilic hydroxide, and the PMPC carboxylate and pyridine nitrogen interact closely (2.3 and 2.7 Å, respectively) with the Zn2 ion of the binuclear metal site. The phosphonate group makes limited interactions but is 2.6 Å from the nucleophilic hydroxide. Furthermore, the presence of a water molecule interacting with the PMPC phosphonate and pyridine N-C2 π-bond, as well as the nucleophilic hydroxide, suggests that the PMPC binds to the MBL active site as its hydrate. Binding is markedly different in L1, with the phosphonate displacing both Zn2, forming a monozinc enzyme, and the nucleophilic hydroxide, while also making multiple interactions with the protein main chain and Zn1. The carboxylate and pyridine nitrogen interact with Ser221 and -223, respectively (3 Å distance). The potency, low toxicity, cellular activity, and amenability to further modification of PMPCs indicate these and similar phosphonate compounds can be further considered for future MBL inhibitor development.
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Affiliation(s)
- Philip Hinchliffe
- School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K
| | - Carol A Tanner
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Anthony P Krismanich
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Geneviève Labbé
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Valerie J Goodfellow
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Laura Marrone
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Ahmed Y Desoky
- Department of Chemistry, College of Science , University of Hail , Saudi Arabia
| | - Karina Calvopiña
- School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K
| | - Emily E Whittle
- School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K
| | - Fanxing Zeng
- Department of Biology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Matthew B Avison
- School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K
| | - Niels C Bols
- Department of Biology , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
| | - Stefan Siemann
- Department of Chemistry and Biochemistry , Laurentian University , Sudbury , Ontario , Canada P3E 2C6
| | - James Spencer
- School of Cellular & Molecular Medicine , University of Bristol , Bristol BS8 1TD , U.K
| | - Gary I Dmitrienko
- Department of Chemistry , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1.,School of Pharmacy , University of Waterloo , Waterloo , Ontario , Canada N2L 3G1
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24
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Kukla R, Chudejova K, Papagiannitsis CC, Medvecky M, Habalova K, Hobzova L, Bolehovska R, Pliskova L, Hrabak J, Zemlickova H. Characterization of KPC-Encoding Plasmids from Enterobacteriaceae Isolated in a Czech Hospital. Antimicrob Agents Chemother 2018; 62:e02152-17. [PMID: 29263065 PMCID: PMC5826142 DOI: 10.1128/aac.02152-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/02/2017] [Indexed: 12/29/2022] Open
Abstract
Ten Enterobacteriaceae isolates collected in a Czech hospital carried blaKPC-positive plasmids of different sizes (∼30, ∼45, and ∼80 kb). Sequencing revealed three types of plasmids (A to C) with the Tn4401a transposon. Type A plasmids comprised an IncR backbone and a KPC-2-encoding multidrug resistance (MDR) region. Type B plasmids were derivatives of type A plasmids carrying an IncN3-like segment, while type C plasmids were IncP6 plasmids sharing the same KPC-2-encoding MDR region with type A and B plasmids.
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Affiliation(s)
- Rudolf Kukla
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, 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
| | - Costas C Papagiannitsis
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
- 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
| | - Matej Medvecky
- Veterinary Research Institute, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Katerina Habalova
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Lenka Hobzova
- Department of Hospital Hygiene, University Hospital, Hradec Kralove, Czech Republic
| | - Radka Bolehovska
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Kralove, Czech Republic
| | - Lenka Pliskova
- Department of Clinical Biochemistry and Diagnostics, University Hospital, Hradec Kralove, 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
| | - Helena Zemlickova
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
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25
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Matsumura Y, Peirano G, Devinney R, Bradford PA, Motyl MR, Adams MD, Chen L, Kreiswirth B, Pitout JDD. Genomic epidemiology of global VIM-producing Enterobacteriaceae. J Antimicrob Chemother 2018; 72:2249-2258. [PMID: 28520983 DOI: 10.1093/jac/dkx148] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/19/2017] [Indexed: 12/21/2022] Open
Abstract
Background International data on the molecular epidemiology of Enterobacteriaceae with VIM carbapenemases are limited. Methods We performed short read (Illumina) WGS on a global collection of 89 VIM-producing clinical Enterobacteriaceae (2008-14). Results VIM-producing (11 varieties within 21 different integrons) isolates were mostly obtained from Europe. Certain integrons with bla VIM were specific to a country in different species and clonal complexes (CCs) (In 87 , In 624 , In 916 and In 1323 ), while others had spread globally among various Enterobacteriaceae species (In 110 and In 1209 ). Klebsiella pneumoniae was the most common species ( n = 45); CC147 from Greece was the most prevalent clone and contained In 590 -like integrons with four different bla VIM s. Enterobacter cloacae complex was the second most common species and mainly consisted of Enterobacter hormaechei ( Enterobacter xiangfangensis , subsp. steigerwaltii and Hoffmann cluster III). CC200 (from Croatia and Turkey), CC114 (Croatia, Greece, Italy and the USA) and CC78 (from Greece, Italy and Spain) containing bla VIM-1 were the most common clones among the E. cloacae complex. Conclusions This study highlights the importance of surveillance programmes using the latest molecular techniques in providing insight into the characteristics and global distribution of Enterobacteriaceae with bla VIM s.
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Affiliation(s)
- Yasufumi Matsumura
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Gisele Peirano
- Departments of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.,Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada
| | - Rebekah Devinney
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Mark D Adams
- Department of Medical Microbiology, J. Craig Venter Institute, La Jolla, CA, USA
| | - Liang Chen
- Public Research Institute TB Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Barry Kreiswirth
- Public Research Institute TB Center, New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Johann D D Pitout
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.,Departments of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.,Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
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26
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Comparison of imipenem and meropenem antibiotics for the MALDI-TOF MS detection of carbapenemase activity. J Microbiol Methods 2017; 137:30-33. [DOI: 10.1016/j.mimet.2017.04.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 11/18/2022]
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27
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Baraniak A, Izdebski R, Żabicka D, Bojarska K, Górska S, Literacka E, Fiett J, Hryniewicz W, Gniadkowski M. Multiregional dissemination of KPC-producing Klebsiella pneumoniae ST258/ST512 genotypes in Poland, 2010–14. J Antimicrob Chemother 2017; 72:1610-1616. [DOI: 10.1093/jac/dkx054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/29/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Anna Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw 00-725, Poland
| | - Radosław Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw 00-725, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Center for Susceptibility Testing, National Medicines Institute, Warsaw 00-725, Poland
| | - Katarzyna Bojarska
- Department of Epidemiology and Clinical Microbiology, The National Reference Center for Susceptibility Testing, National Medicines Institute, Warsaw 00-725, Poland
| | - Sandra Górska
- Department of Molecular Microbiology, National Medicines Institute, Warsaw 00-725, Poland
| | - Elżbieta Literacka
- Department of Epidemiology and Clinical Microbiology, The National Reference Center for Susceptibility Testing, National Medicines Institute, Warsaw 00-725, Poland
| | - Janusz Fiett
- Department of Molecular Microbiology, National Medicines Institute, Warsaw 00-725, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Center for Susceptibility Testing, National Medicines Institute, Warsaw 00-725, Poland
| | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw 00-725, Poland
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28
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Prevalence of Extended-Spectrum-β-Lactamase- and/or Carbapenemase-Producing Escherichia coli Isolated from Yellow-Legged Gulls from Barcelona, Spain. Antimicrob Agents Chemother 2017; 61:AAC.02071-16. [PMID: 27919890 DOI: 10.1128/aac.02071-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/25/2016] [Indexed: 11/20/2022] Open
Abstract
Seventy-two (54.5%) out of 132 fecal samples from a group of yellow-legged gulls in Barcelona, Spain, were positive for Escherichia coli producing either extended-spectrum β-lactamases (ESBL) (51.5%), carbapenemase (1.5%), or cephamycinase (1.5%). The isolation of two carbapenemase-producing E. coli strains is a matter of concern.
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29
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Papagiannitsis CC, Malli E, Florou Z, Sarrou S, Hrabak J, Mantzarlis K, Zakynthinos E, Petinaki E. Emergence of sequence type 11 Klebsiella pneumoniae coproducing NDM-1 and VIM-1 metallo-β-lactamases in a Greek hospital. Diagn Microbiol Infect Dis 2016; 87:295-297. [PMID: 27993422 DOI: 10.1016/j.diagmicrobio.2016.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/06/2016] [Accepted: 12/11/2016] [Indexed: 11/24/2022]
Abstract
Sequence type 11 Klebsiella pneumoniae, coproducing NDM-1 and VIM-1 metallo-β-lactamases, were isolated in a Greek hospital. blaNDM-1 was part of a Tn125 derivative, located on an ~90-kb plasmid similar to the NDM-1-encoding plasmid pB-3002cz. blaVIM-1 was located in an In-e541-like integron, carried on a multireplicon (IncA/C and IncR) plasmid of ~180kb.
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Affiliation(s)
- C C Papagiannitsis
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece; Biomedical Center, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic
| | - E Malli
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - Z Florou
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - S Sarrou
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece
| | - J Hrabak
- Biomedical Center, Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic
| | - K Mantzarlis
- Department of Critical Care, Medical School, University of Thessaly, Larissa, Greece
| | - E Zakynthinos
- Department of Critical Care, Medical School, University of Thessaly, Larissa, Greece
| | - E Petinaki
- Department of Microbiology, University Hospital of Larissa, Larissa, Greece.
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30
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Salimraj R, Zhang L, Hinchliffe P, Wellington EMH, Brem J, Schofield CJ, Gaze WH, Spencer J. Structural and Biochemical Characterization of Rm3, a Subclass B3 Metallo-β-Lactamase Identified from a Functional Metagenomic Study. Antimicrob Agents Chemother 2016; 60:5828-40. [PMID: 27431213 PMCID: PMC5038237 DOI: 10.1128/aac.00750-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 07/08/2016] [Indexed: 11/20/2022] Open
Abstract
β-Lactamase production increasingly threatens the effectiveness of β-lactams, which remain a mainstay of antimicrobial chemotherapy. New activities emerge through both mutation of previously known β-lactamases and mobilization from environmental reservoirs. The spread of metallo-β-lactamases (MBLs) represents a particular challenge because of their typically broad-spectrum activities encompassing carbapenems, in addition to other β-lactam classes. Increasingly, genomic and metagenomic studies have revealed the distribution of putative MBLs in the environment, but in most cases their activity against clinically relevant β-lactams and, hence, the extent to which they can be considered a resistance reservoir remain uncharacterized. Here we characterize the product of one such gene, blaRm3, identified through functional metagenomic sampling of an environment with high levels of biocide exposure. blaRm3 encodes a subclass B3 MBL that, when expressed in a recombinant Escherichia coli strain, is exported to the bacterial periplasm and hydrolyzes clinically used penicillins, cephalosporins, and carbapenems with an efficiency limited by high Km values. An Rm3 crystal structure reveals the MBL superfamily αβ/βα fold, which more closely resembles that in mobilized B3 MBLs (AIM-1 and SMB-1) than other chromosomal enzymes (L1 or FEZ-1). A binuclear zinc site sits in a deep channel that is in part defined by a relatively extended N terminus. Structural comparisons suggest that the steric constraints imposed by the N terminus may limit its affinity for β-lactams. Sequence comparisons identify Rm3-like MBLs in numerous other environmental samples and species. Our data suggest that Rm3-like enzymes represent a distinct group of B3 MBLs with a wide distribution and can be considered an environmental reservoir of determinants of β-lactam resistance.
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Affiliation(s)
- Ramya Salimraj
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Lihong Zhang
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | | | - Jürgen Brem
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - William H Gaze
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
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Potter RF, D'Souza AW, Dantas G. The rapid spread of carbapenem-resistant Enterobacteriaceae. Drug Resist Updat 2016; 29:30-46. [PMID: 27912842 DOI: 10.1016/j.drup.2016.09.002] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/23/2016] [Accepted: 09/07/2016] [Indexed: 02/07/2023]
Abstract
Carbapenems, our one-time silver bullet for multidrug resistant bacterial infections, are now threatened by widespread dissemination of carbapenem-resistant Enterobacteriaceae (CRE). Successful expansion of Enterobacteriaceae clonal groups and frequent horizontal gene transfer of carbapenemase expressing plasmids are causing increasing carbapenem resistance. Recent advances in genetic and phenotypic detection facilitate global surveillance of CRE diversity and prevalence. In particular, whole genome sequencing enabled efficient tracking, annotation, and study of genetic elements colocalized with carbapenemase genes on chromosomes and on plasmids. Improved characterization helps detail the co-occurrence of other antibiotic resistance genes in CRE isolates and helps identify pan-drug resistance mechanisms. The novel β-lactamase inhibitor, avibactam, combined with ceftazidime or aztreonam, is a promising CRE treatment compared to current colistin or tigecycline regimens. To halt increasing CRE-associated morbidity and mortality, we must continue quality, cooperative monitoring and urgently investigate novel treatments.
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Affiliation(s)
- Robert F Potter
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Alaric W D'Souza
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences and System Biology, Washington University School of Medicine, 4515 McKinley Avenue, Campus Box 8510, St. Louis, MO 63110, USA; Department of Pathology & Immunology, Washington University School of Medicine, 660 South Euclid Ave, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in Saint Louis, 1 Brookings Drive, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, 660 S. Euclid Ave, St. Louis, MO 63110, USA.
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32
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Nosocomial Outbreak of OXA-48-Producing Klebsiella pneumoniae in a Chinese Hospital: Clonal Transmission of ST147 and ST383. PLoS One 2016; 11:e0160754. [PMID: 27490695 PMCID: PMC4973971 DOI: 10.1371/journal.pone.0160754] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/25/2016] [Indexed: 02/05/2023] Open
Abstract
Background In China, the spread and outbreak of OXA-48-producing Enterobacteriaceae remains largely unknown. Methods OXA-48-producing isolates were analyzed for genetic relatedness by pulsed-field gel electrophoresis (PFGE), antimicrobial susceptibility by E-test, and sequence type (ST) by multilocus sequence typing. S1-PFGE and southern blotting were used for plasmid profiling, and PCR and subsequent sequencing were performed to determine the genetic environment of blaOXA-48 gene. Results In total, 37 non-duplicated OXA-48-producing K. pneumoniae (OXAKp) isolates were recovered. From December 2013 to August 2014, an outbreak was observed at a respiratory ICU. The 37 isolates of K. pneumoniae were categorized into four PFGE types (A, B, C, and D). The predominant strains associated with the outbreak were strains with PFGE type A and B, which belonged to ST383 and ST147, respectively. Plasmid sequencing revealed that the blaOXA-48-carrying plasmid is 69,069 bp in length and belongs to the IncL/M incompatibility group. Sequence analysis revealed that the IS1999 element was located upstream of the blaOXA-48 gene and was truncated by IS1R. Conclusions In this study, the dissemination and outbreak of OXAKp isolates were clonal, and ST147 and ST383 K. pneumoniae were the predominant clones that were associated with the outbreak. Meanwhile, the horizontal transfer of plasmids potentially mediate the spread of blaOXA-48 gene between different K. pneumoniae strains.
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Reinheimer C, Kempf VAJ, Göttig S, Hogardt M, Wichelhaus TA, O'Rourke F, Brandt C. Multidrug-resistant organisms detected in refugee patients admitted to a University Hospital, Germany June‒December 2015. ACTA ACUST UNITED AC 2016; 21:30110. [PMID: 26794850 DOI: 10.2807/1560-7917.es.2016.21.2.30110] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 01/14/2016] [Indexed: 11/20/2022]
Abstract
Multidrug-resistant Gram-negative bacteria (MDR GNB) were found to colonise 60.8% (95% confidence interval: 52.3-68.9) of 143 refugee patients mainly from Syria (47), Afghanistan (29), and Somalia (14) admitted to the University Hospital Frankfurt, Germany, between June and December 2015. This percentage exceeds the prevalence of MDR GNB in resident patients four-fold. Healthcare personnel should be aware of this and the need to implement or adapt adequate infection control measures.
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Affiliation(s)
- Claudia Reinheimer
- Institute for Medical Microbiology and Infection Control, University Hospital Frankfurt am Main, Germany
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Karampatakis T, Antachopoulos C, Iosifidis E, Tsakris A, Roilides E. Molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae in Greece. Future Microbiol 2016; 11:809-23. [PMID: 27206024 DOI: 10.2217/fmb-2016-0042] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Hospital infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) constitute a worldwide problem associated with high rates of treatment failure and mortality. In Greece, CRKP have emerged in 2002 due to VIM carbapenemase production and later due to KPC, NDM and OXA-48-like carbapenemases that have become endemic. The molecular epidemiology of CRKP strains is dynamic, as antibiotic consumption and worldwide traveling are strongly associated with global spread of CRKP isolates. Lately, porin defects, such as disruption of OmpK35 and production of OmpK36 variant, have also contributed to carbapenem resistance. In the coming years, the high prevalence of CRKP will require intense infection control measures, while novel molecular patterns may appear. To our knowledge, this is the first review analyzing the molecular epidemiology of CRKP strains in Greece.
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Affiliation(s)
- Theodoros Karampatakis
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Aristotle University, Hippokration General Hospital, Thessaloniki, Greece
| | - Charalampos Antachopoulos
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Aristotle University, Hippokration General Hospital, Thessaloniki, Greece
| | - Elias Iosifidis
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Aristotle University, Hippokration General Hospital, Thessaloniki, Greece
| | - Athanassios Tsakris
- Microbiology Department, Athens University School of Medicine, Athens, Greece
| | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Department of Pediatrics, Medical Faculty, School of Health Sciences, Aristotle University, Hippokration General Hospital, Thessaloniki, Greece
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Sabirova JS, Xavier BB, Coppens J, Zarkotou O, Lammens C, Janssens L, Burggrave R, Wagner T, Goossens H, Malhotra-Kumar S. Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS. J Antimicrob Chemother 2016; 71:1501-9. [PMID: 26968884 DOI: 10.1093/jac/dkw003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 12/30/2015] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical carbapenem-resistant Klebsiella pneumoniae strains (TGH1-TGH12). METHODS All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII) (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen; BioNumerics, Applied Maths). RESULTS All 12 strains were ST383. Of the 12 strains, 11 were carbapenem resistant, 7 harboured blaKPC-2 and 11 harboured blaVIM-19. Varying the parameters for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or ≥10 unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a difference of three or more bands between PFGE profiles, the Simpson's diversity indices (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883-0.996) and PFGE (0.93, Jackknife pseudo-values CI: 0.828-1.000) were similar (P = 0.649). However, the discriminatory power of WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883-0.996) than that of PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values CI: 0.212-0.849) (P = 0.007). CONCLUSIONS This study demonstrates the application of WGM to understanding the epidemiology of hospital-associated K. pneumoniae. Utilizing a combination of WGM and WGS, we also present here the first longitudinal genomic characterization of the highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining importance in Europe.
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Affiliation(s)
- Julia S Sabirova
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Basil Britto Xavier
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Jasmine Coppens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Olympia Zarkotou
- Department of Microbiology, Tzaneio General Hospital, Piraeus, Greece
| | - Christine Lammens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Lore Janssens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | | | | | - Herman Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
| | - Surbhi Malhotra-Kumar
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, Universiteit Antwerpen, Antwerp, Belgium
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Rossini A, Di Santo S, Libori M, Tiracchia V, Balice M, Salvia A. Risk factors for carbapenemase-producing Enterobacteriaceae colonization of asymptomatic carriers on admission to an Italian rehabilitation hospital. J Hosp Infect 2016; 92:78-81. [DOI: 10.1016/j.jhin.2015.10.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/26/2015] [Indexed: 10/22/2022]
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KPC-Like Carbapenemase-Producing Enterobacteriaceae Colonizing Patients in Europe and Israel. Antimicrob Agents Chemother 2015; 60:1912-7. [PMID: 26711772 DOI: 10.1128/aac.02756-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/18/2015] [Indexed: 01/03/2023] Open
Abstract
In a 2008-2011 survey, 17,945 patients in 18 hospital units in Europe and Israel were screened for carriage of Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae, resulting in identification of 124 positive patients. The isolates were dominated by Klebsiella pneumoniae sequence type 258 (ST258) KPC-2 and ST512 KPC-3, mainly from Greece and Italy, respectively, whereas Israeli isolates were of diverse species, clones, and KPC variants. Various blaKPC platforms were observed, among which IncFIIK-FIBK plasmids with blaKPC-2/-3 genes in the Tn4401a transposon prevailed.
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Papagiannitsis CC, Dolejska M, Izdebski R, Giakkoupi P, Skálová A, Chudějová K, Dobiasova H, Vatopoulos AC, Derde LPG, Bonten MJM, Gniadkowski M, Hrabák J. Characterisation of IncA/C2 plasmids carrying an In416-like integron with the blaVIM-19 gene from Klebsiella pneumoniae ST383 of Greek origin. Int J Antimicrob Agents 2015; 47:158-62. [PMID: 26795022 DOI: 10.1016/j.ijantimicag.2015.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/29/2015] [Accepted: 12/01/2015] [Indexed: 11/30/2022]
Abstract
The complete nucleotide sequences of three multidrug resistance (MDR) IncA/C-like plasmids from Enterobacteriaceae isolates carrying the VIM-type carbapenemase-encoding integrons In4863 (blaVIM-19-aacA7-dfrA1-ΔaadA1-smr2) or In4873 (blaVIM-1-aacA7-dfrA1-ΔaadA1-smr2) were determined, which are the first In416-like elements identified in Greece. Plasmids pKP-Gr642 and pKP-Gr8143 were from Klebsiella pneumoniae ST383 isolates, whereas plasmid pEcl-Gr4873 was from an Enterobacter cloacae ST88 isolate. Sequencing showed that pKP-Gr642 (162787bp) and pKP-Gr8143 (154395bp) consisted of the type 1 IncA/C2 conserved backbone, the blaCMY-2-like gene-containing region, and the ARI-B (with the sul2 gene) and ARI-A (with a class 1 integron) resistance islands, like the plasmid pUMNK88_161 from the USA. The third plasmid, pEcl-Gr4873 (153958bp), exhibited extensive similarity with the type 2 IncA/C2 plasmid pR55 from France. pEcl-Gr4873 carried only one resistance island of a hybrid transposon structure inserted in a different location to ARI-A in type 1 A/C2 plasmids. In all three plasmids, the In416-like integrons In4863 or In4873 were identified within non-identical class II transposon structures. All three In416-like-carrying regions presented significant similarities with the MDR region of the IncA/C2 plasmid pCC416 from Italy, carrying the prototype In416 integron (blaVIM-4-aacA7-dfrA1-ΔaadA1-smr2). These findings provided the basis for speculations regarding the evolution of IncA/C2 plasmids with In416-like integrons, and confirmed the rapid evolution of some IncA/C2 plasmid lineages. Considering the broad host range of IncA/C2 molecules, it seems that pKP-Gr642, pKP-Gr8143 and pEcl-Gr4873 plasmids might support the diffusion of In416-like integrons among Enterobacteriaceae.
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Affiliation(s)
- Costas C Papagiannitsis
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic; Biomedical Center, Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic.
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | | | - Panagiota Giakkoupi
- Department of Microbiology, National School of Public Health, Athens, Greece
| | - Anna Skálová
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic
| | - Kateřina Chudějová
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic
| | - Hana Dobiasova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic; CEITEC, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | | | | | | | | | - Jaroslav Hrabák
- Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic; Biomedical Center, Faculty of Medicine and University Hospital in Plzeň, Charles University in Prague, Plzeň, Czech Republic
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Papagiannitsis CC, Pollini S, De Luca F, Rossolini GM, Docquier JD, Hrabák J. Biochemical Characterization of VIM-39, a VIM-1-Like Metallo-β-Lactamase Variant from a Multidrug-Resistant Klebsiella pneumoniae Isolate from Greece. Antimicrob Agents Chemother 2015; 59:7811-4. [PMID: 26369975 PMCID: PMC4649142 DOI: 10.1128/aac.01935-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/08/2015] [Indexed: 11/20/2022] Open
Abstract
VIM-39, a VIM-1-like metallo-β-lactamase variant (VIM-1 Thr33Ala His224Leu) was identified in a clinical isolate of Klebsiella pneumoniae belonging to sequence type 147. VIM-39 hydrolyzed ampicillin, cephalothin, and imipenem more efficiently than did VIM-1 and VIM-26 (a VIM-1 variant with the His224Leu substitution) because of higher turnover rates.
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Affiliation(s)
- Costas C Papagiannitsis
- Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic Biomedical Center, Faculty of Medicine in Plzen, Charles University in Prague, Plzen, Czech Republic
| | - Simona Pollini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Filomena De Luca
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gian Maria Rossolini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | | | - Jaroslav Hrabák
- Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic Biomedical Center, Faculty of Medicine in Plzen, Charles University in Prague, Plzen, Czech Republic
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Izdebski R, Fiett J, Urbanowicz P, Baraniak A, Derde LPG, Bonten MJM, Carmeli Y, Goossens H, Hryniewicz W, Brun-Buisson C, Brisse S, Gniadkowski M. Phylogenetic lineages, clones and β-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins. J Antimicrob Chemother 2015; 70:3230-7. [PMID: 26318191 DOI: 10.1093/jac/dkv273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/10/2015] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES The objective of this study was to examine Klebsiella oxytoca clonal and phylogenetic diversity, based on an international collection of carriage isolates non-susceptible to expanded-spectrum cephalosporins (ESCs). METHODS The study material comprised 68 rectal carriage K. oxytoca isolates non-susceptible to ESCs recovered in 2008-11 from patients in 14 hospitals across Europe and Israel. ESC resistance was tested phenotypically; genes encoding ESBLs, AmpC cephalosporinases and carbapenemases were amplified and sequenced. The isolates were typed by PFGE and MLST, followed by sequencing of blaOXY genes. RESULTS MLST and PFGE distinguished 34 STs and 47 pulsotypes among the isolates, respectively. Six STs were split into several pulsotypes each. Five STs were more prevalent (n = 2-9) and occurred in several countries each, including ST2, ST9 and ST141, which belong to a growing international clonal complex (CC), CC2. Four phylogenetic lineages were distinguished, each with another type of chromosomal OXY-type β-lactamase. Three of these, with OXY-1/-5, OXY-2 types and OXY-4, corresponded to previously described phylogroups KoI, KoII and KoIV, respectively. A single isolate from Israel represented a distinct lineage with a newly defined OXY-7 type. The phylogroups showed interesting differences in mechanisms of ESC resistance; KoI strains rarely overexpressed the OXY enzymes but commonly produced ESBLs, whereas KoII strains often were OXY hyperproducers and carried ESBLs much less frequently. AmpCs (DHA-1) and carbapenemases (VIM-1) occurred sporadically. CONCLUSIONS The study confirmed the high genetic diversity of the collection of K. oxytoca ESC-non-susceptible isolates, composed of phylogroups with distinct types of OXY-type β-lactamases, and revealed some STs of broad geographical distribution.
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Affiliation(s)
- R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - J Fiett
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - L P G Derde
- Department of Medical Microbiology and Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M J M Bonten
- Department of Medical Microbiology and Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Y Carmeli
- Division of Epidemiology and Preventive Medicine, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - H Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - W Hryniewicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - C Brun-Buisson
- Service de reanimation médicale, INSERM, U957 & Université Paris-Est, Créteil, France
| | - S Brisse
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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Papagiannitsis CC, Dolejska M, Izdebski R, Dobiasova H, Studentova V, Esteves FJ, Derde LPG, Bonten MJM, Hrabák J, Gniadkowski M. Characterization of pKP-M1144, a Novel ColE1-Like Plasmid Encoding IMP-8, GES-5, and BEL-1 β-Lactamases, from a Klebsiella pneumoniae Sequence Type 252 Isolate. Antimicrob Agents Chemother 2015; 59:5065-8. [PMID: 26033721 PMCID: PMC4505226 DOI: 10.1128/aac.00937-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/29/2015] [Indexed: 11/20/2022] Open
Abstract
IMP-8 metallo-β-lactamase was identified in Klebsiella pneumoniae sequence type 252 (ST252), isolated in a Portuguese hospital in 2009. blaIMP-8 was the first gene cassette of a novel class 3 integron, In1144, also carrying the blaGES-5, blaBEL-1, and aacA4 cassettes. In1144 was located on a ColE1-like plasmid, pKP-M1144 (12,029 bp), with a replication region of limited nucleotide similarity to those of other RNA-priming plasmids, such as pJHCMW1. In1144 and pKP-M1144 represent an interesting case of evolution of resistance determinants in Gram-negative bacteria.
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Affiliation(s)
- Costas C Papagiannitsis
- Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic National Medicines Institute, Warsaw, Poland
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | | | - Hana Dobiasova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic CEITEC VFU, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Vendula Studentova
- Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic
| | | | | | | | - Jaroslav Hrabák
- Faculty of Medicine and University Hospital in Plzen, Charles University in Prague, Plzen, Czech Republic Biomedical Center, Faculty of Medicine in Plzen, Charles University in Prague, Plzen, Czech Republic
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