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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: 4] [Impact Index Per Article: 4.0] [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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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: 8] [Impact Index Per Article: 4.0] [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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Sarowska J, Choroszy-Krol I, Jama-Kmiecik A, Mączyńska B, Cholewa S, Frej-Madrzak M. Occurrence and Characteristics of Carbapenem-Resistant Klebsiella pneumoniae Strains Isolated from Hospitalized Patients in Poland-A Single Centre Study. Pathogens 2022; 11:859. [PMID: 36014980 PMCID: PMC9416609 DOI: 10.3390/pathogens11080859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 12/10/2022] Open
Abstract
The global emergence and spread of genes responsible for the production of ESBL (extended-spectrum beta-lactamases) and carbapenemases in Klebsiella pneumoniae isolates poses a serious threat to public health. The aim of this study was to retrospectively analyze the frequency of occurrence and drug resistance of selected alarm agents isolated from patients of the specialist hospital in Wrocław. A total of 13,528 clinical materials collected from patients of a specialist hospital in Wrocław were analyzed in the period from 1 January 2020 to 31 December 2020. Overall, 3894 bacterial strains were isolated from clinical materials, including 416 K. pneumoniae isolates. K. pneumoniae that showed resistance to ETP (ertapenem) and/or MEM (meropenem) were tested using phenotypic tests for the detection of KPC (carbapenemase-producing Klebsiella), MBL (metallo-β-lactamase) and OXA-48 (oxacilinase-48) carbapenemases. In the case of a positive or doubtful result of the phenotypic test, immunochromatographic tests and the CarbaNP test were performed. In total, 58 K. pneumoniae isolates resistant to 1 or more carbapenem antibiotics were isolated. Of the 58 strains, 16 (27.6%) were isolated from rectal swabs conducted on CPE (carbapenemase-producing Enterobacteriaceae) carriers. In the case of CRE (carbapenem-resistant Enterobacteriaceae) K. pneumoniae, carbapenemases were detected in 28/58 (48.3%) isolates. Notably, 23/28 K. pneumoniae isolates produced MBL/NDM (New Delhi metallo-β-lactamase) (82.1%), 5/28 produced VIM (Verona-intergon-encoded metallo-β-lactamase) (14.3%), and one produced MBL/NDM + OXA-48. Carbapenemases were detected in 13 of 16 (81.3%) carbapenem-resistant K. pneumoniae isolates derived from rectal swabs. The significant participation of CRE and CPE isolates in the infections proves the need to test patients admitted to hospital wards for their status as a CPE carrier in order to limit the emergence of new epidemic outbreaks.
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Affiliation(s)
- Jolanta Sarowska
- Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland; (J.S.); (I.C.-K.); (M.F.-M.)
| | - Irena Choroszy-Krol
- Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland; (J.S.); (I.C.-K.); (M.F.-M.)
| | - Agnieszka Jama-Kmiecik
- Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland; (J.S.); (I.C.-K.); (M.F.-M.)
| | - Beata Mączyńska
- Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Medical University, 50-367 Wroclaw, Poland;
| | - Sylwia Cholewa
- Medical Laboratory Synevo, Fieldorfa 2, 50-049 Wroclaw, Poland;
| | - Magdalena Frej-Madrzak
- Department of Basic Sciences, Faculty of Health Sciences, Wroclaw Medical University, Chalubinskiego 4, 50-368 Wroclaw, Poland; (J.S.); (I.C.-K.); (M.F.-M.)
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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: 11] [Impact Index Per Article: 3.7] [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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Tompkins K, van Duin D. Treatment for carbapenem-resistant Enterobacterales infections: recent advances and future directions. Eur J Clin Microbiol Infect Dis 2021; 40:2053-2068. [PMID: 34169446 DOI: 10.1007/s10096-021-04296-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/15/2021] [Indexed: 12/16/2022]
Abstract
Carbapenem-resistant Enterobacterales (CRE) are a growing threat to human health worldwide. CRE often carry multiple resistance genes that limit treatment options and require longer durations of therapy, are more costly to treat, and necessitate therapies with increased toxicities when compared with carbapenem-susceptible strains. Here, we provide an overview of the mechanisms of resistance in CRE, the epidemiology of CRE infections worldwide, and available treatment options for CRE. We review recentlyapproved agents for the treatment of CRE, including ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, cefiderocol, and novel aminoglycosides and tetracyclines. We also discuss recent advances in phage therapy and antibiotics that are currently in development targeted to CRE. The potential for the development of resistance to these therapies remains high, and enhanced antimicrobial stewardship is imperative both to reduce the spread of CRE worldwide and to ensure continued access to efficacious treatment options.
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Affiliation(s)
- Kathleen Tompkins
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.
| | - David van Duin
- Division of Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
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Kazmierczak KM, de Jonge BLM, Stone GG, Sahm DF. Longitudinal analysis of ESBL and carbapenemase carriage among Enterobacterales and Pseudomonas aeruginosa isolates collected in Europe as part of the International Network for Optimal Resistance Monitoring (INFORM) global surveillance programme, 2013-17. J Antimicrob Chemother 2021; 75:1165-1173. [PMID: 32040168 DOI: 10.1093/jac/dkz571] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/21/2019] [Accepted: 12/24/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To determine the spread of ESBLs and carbapenemases in Enterobacterales and Pseudomonas aeruginosa in Europe. METHODS 45 335 Gram-negative bacilli were collected in 18 European countries as part of the International Network for Optimal Resistance Monitoring (INFORM) global surveillance programme from 2013 to 2017. Antimicrobial susceptibility was determined using broth microdilution, and 9546 isolates were screened for β-lactamase genes by PCR and sequencing. RESULTS ESBLs were identified in 35.5% of Klebsiella pneumoniae and 18.5% of Escherichia coli. ESBL carriage was lowest among isolates in Northern/Western Europe and highest in Eastern Europe. CTX-M-15 was the dominant ESBL in all countries except Greece, where SHV-type ESBLs were more common. Carbapenemases (KPC, OXA-48-like, GES, NDM and VIM) were found in 3.4% of Enterobacterales and were most common among K. pneumoniae (10.5% of those collected). Carbapenemase carriage was lowest in Northern/Western and highest in Southern Europe. KPC-positive Enterobacterales were most abundant but the percentages of OXA-48-like-, NDM- and VIM-positive isolates increased over time and were correlated with an increase in meropenem non-susceptibility. Carbapenemases (VIM, IMP, NDM and GES) were also identified in 5.1% of P. aeruginosa and were commonly found in Eastern Europe. Carbapenemase carriage and meropenem non-susceptibility among P. aeruginosa fluctuated over the 5 years studied and were not well correlated. CONCLUSIONS ESBL and carbapenemase carriage varied by species and European subregion. Meropenem non-susceptibility in European isolates of Enterobacterales can be attributed to carbapenemase carriage and is increasingly caused by MBLs and OXA-48-like carbapenemases. Carbapenemases or other β-lactamases are not a common cause of meropenem non-susceptibility in P. aeruginosa in Europe.
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Affiliation(s)
| | | | | | - Daniel F Sahm
- International Health Management Associates, Inc., Schaumburg, IL, USA
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Hansen GT. Continuous Evolution: Perspective on the Epidemiology of Carbapenemase Resistance Among Enterobacterales and Other Gram-Negative Bacteria. Infect Dis Ther 2021; 10:75-92. [PMID: 33492641 PMCID: PMC7954928 DOI: 10.1007/s40121-020-00395-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/22/2020] [Indexed: 12/20/2022] Open
Abstract
The global emergence of carbapenemase-producing bacteria capable of hydrolyzing the once effective carbapenem antibiotics is considered a contemporary public health concern. Carbapenemase enzymes, once constrained to isolates of Klebsiella pneumoniae, are now routinely reported in different bacteria within the Enterobacterales order of bacteria, creating the acronym CRE which now defines Carbapenem-Resistant Enterobacterales. CRE harboring different types of enzymes, including the most prevalent types KPC, VIM, IMP, NDM, and OXA-48, are now routinely reported and more importantly, are now frequently present in many infections world-wide. Defining and updating the contemporary epidemiology of both the US and global burden of carbapenem-resistant infections is now more important than ever. This review describes the global distribution and continued evolution of carbapenemases which continue to spread at alarming rates. Informed understanding of the current epidemiology of CRE, coupled with advances in antibiotic options, and the use rapid diagnostics offers the potential for rapid identification and management of carbapenem-resistant infections.
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Affiliation(s)
- Glen T Hansen
- Department of Pathology and Laboratory Medicine, Hennepin County Medical Center, Minneapolis, MN, USA.
- Department of Pathology and Laboratory Medicine, University of Minnesota, School of Medicine, Minneapolis, MN, USA.
- Department of Medicine, Infectious Disease, University of Minnesota, School of Medicine, Minneapolis, MN, USA.
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The Impact of Insertion Sequences on O-Serotype Phenotype and Its O-Locus-Based Prediction in Klebsiella pneumoniae O2 and O1. Int J Mol Sci 2020; 21:ijms21186572. [PMID: 32911792 PMCID: PMC7556023 DOI: 10.3390/ijms21186572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/14/2022] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen, pointed out by the World Helth Organisation (WHO) as “critical” regarding the highly limited options of treatment. Lipopolysaccharide (LPS, O-antigen) and capsular polysaccharide (K-antigen) are its virulence factors and surface antigens, determining O- and K-serotypes and encoded by O- or K-loci. They are promising targets for antibody-based therapies (vaccines and passive immunization) as an alternative to antibiotics. To make such immunotherapy effective, knowledge about O/K-antigen structures, drift, and distribution among clinical isolates is needed. At present, the structural analysis of O-antigens is efficiently supported by bioinformatics. O- and K-loci-based genotyping by polymerase chain reaction (PCR) or whole genome sequencing WGS has been proposed as a diagnostic tool, including the Kaptive tool available in the public domain. We analyzed discrepancies for O2 serotyping between Kaptive-based predictions (O2 variant 2 serotype) and the actual phenotype (O2 variant 1) for two K. pneumoniae clinical isolates. Identified length discrepancies from the reference O-locus resulted from insertion sequences (ISs) within rfb regions of the O-loci. In silico analysis of 8130 O1 and O2 genomes available in public databases indicated a broader distribution of ISs in rfbs that may influence the actual O-antigen structure. Our results show that current high-throughput genotyping algorithms need to be further refined to consider the effects of ISs on the LPS O-serotype.
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Pranavathiyani G, Prava J, Rajeev AC, Pan A. Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction. Front Cell Infect Microbiol 2020; 10:109. [PMID: 32318354 PMCID: PMC7146069 DOI: 10.3389/fcimb.2020.00109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 11/13/2022] Open
Abstract
The opportunistic pathogen Klebsiella pneumoniae is a causative agent of several hospital-acquired infections. It has become resistant to a wide range of currently available antibiotics, leading to high mortality rates among patients; this has further led to a demand for novel therapeutic intervention to treat such infections. Using a series of in silico analyses, the present study aims to explore novel drug/vaccine candidates from the hypothetical proteins of K. pneumoniae. A total of 540 proteins were found to be hypothetical in this organism. Analysis of these 540 hypothetical proteins revealed 30 pathogen-specific proteins essential for pathogen survival. A motifs/domain family analysis, similarity search against known proteins, gene ontology, and protein–protein interaction analysis of the shortlisted 30 proteins led to functional assignment for 17 proteins. They were mainly cataloged as enzymes, lipoproteins, stress-induced proteins, transporters, and other proteins (viz., two-component proteins, skeletal proteins and toxins). Among the annotated proteins, 16 proteins, located in the cytoplasm, periplasm, and inner membrane, were considered as potential drug targets, and one extracellular protein was considered as a vaccine candidate. A druggability analysis indicated that the identified 17 drug/vaccine candidates were “novel”. Furthermore, a host–pathogen interaction analysis of these identified target candidates revealed a betaine/carnitine/choline transporters (BCCT) family protein showing interactions with five host proteins. Structure prediction and validation were carried out for this protein, which could aid in structure-based inhibitor design.
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Affiliation(s)
- G Pranavathiyani
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Jyoti Prava
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Athira C Rajeev
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Archana Pan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Abstract
β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics. Critical β-lactamases are those enzymes whose genes are encoded on mobile elements that are transferable among species. Major β-lactamase families include plasmid-mediated extended-spectrum β-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases now appearing globally, with geographic preferences for specific variants. CTX-M enzymes include the most common ESBLs that are prevalent in all areas of the world. In contrast, KPC serine carbapenemases are present more frequently in the Americas, the Mediterranean countries, and China, whereas NDM metallo-β-lactamases are more prevalent in the Indian subcontinent and Eastern Europe. As selective pressure from β-lactam use continues, multiple β-lactamases per organism are increasingly common, including pathogens carrying three different carbapenemase genes. These organisms may be spread throughout health care facilities as well as in the community, warranting close attention to increased infection control measures and stewardship of the β-lactam-containing drugs in an effort to control selection of even more deleterious pathogens.
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Gauthier L, Dortet L, Jousset AB, Mihaila L, Golse N, Naas T, Bonnin RA. Molecular characterization of plasmid-encoded Tripoli MBL 1 (TMB-1) in Enterobacteriaceae. J Antimicrob Chemother 2020; 74:42-47. [PMID: 30252055 DOI: 10.1093/jac/dky372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/17/2018] [Indexed: 01/15/2023] Open
Abstract
Objectives Available commercial tools (molecular methods or immunochromatographic assays) usually allow the detection of the five most prevalent carbapenemases (KPC, NDM, VIM, IMP and OXA-48-like), but miss minor carbapenemases. Here, we characterize two enterobacterial isolates with reduced susceptibility to carbapenems and negative for the most commonly encountered carbapenemase genes. Methods Enterobacter hormaechei and Citrobacter freundii isolates were recovered from a bile sample and rectal screening, respectively. Both isolates were investigated by WGS. Resistance genes were detected using ResFinder. The blaTMB-1-harbouring plasmid was reconstructed using CLC genomic workbench 10.0 and was annotated using the RAST tool. Transfer frequency was determined by conjugation experiments using the laboratory strain Escherichia coli J53. Results The two isolates were resistant to broad-spectrum cephalosporins and carbapenems. WGS revealed the presence of blaTMB-1, which has previously only been described in non-fermenters. blaTMB-1 was located within an ISKpn19-based composite class 1 transposon. Comparative genomics revealed that this structure was carried on a conjugative IncN-type plasmid within an integration hotspot. Conjugation experiments revealed high transfer frequencies of ∼1 × 10-3. Conclusions To the best of our knowledge, this study corresponds to the first report of Tripoli MBL 1-producing Enterobacteriaceae. Despite always being described as likely to be chromosomally located in non-fermenters, the blaTMB-1 gene is now found to be carried by a conjugative plasmid among Enterobacteriaceae, raising concern about the possible dissemination of this carbapenemase. The blaTMB-1 gene should now be suspected when PCRs targeting the main carbapenemases remain negative.
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Affiliation(s)
- Lauraine Gauthier
- Bactériologie-Hygiène Unit, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France.,EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases' Paris-Sud University, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Associate French National Reference Centre for Antimicrobial Resistance 'Carbapenem-Resistant Enterobacteriaceae', Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Bactériologie-Hygiène Unit, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France.,EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases' Paris-Sud University, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Associate French National Reference Centre for Antimicrobial Resistance 'Carbapenem-Resistant Enterobacteriaceae', Le Kremlin-Bicêtre, France
| | - Agnès B Jousset
- Bactériologie-Hygiène Unit, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France.,EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases' Paris-Sud University, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Associate French National Reference Centre for Antimicrobial Resistance 'Carbapenem-Resistant Enterobacteriaceae', Le Kremlin-Bicêtre, France
| | - Liliana Mihaila
- Bactériologie-Hygiène Unit, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France
| | - Nicolas Golse
- Department of Surgery, Paul Brousse Hospital, APHP Centre Hépato-Biliaire, Villejuif, France
| | - Thierry Naas
- Bactériologie-Hygiène Unit, Bicêtre Hospital, APHP, Le Kremlin-Bicêtre, France.,EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases' Paris-Sud University, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Associate French National Reference Centre for Antimicrobial Resistance 'Carbapenem-Resistant Enterobacteriaceae', Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- EA7361 'Structure, Dynamic, Function and Expression of Broad Spectrum β-Lactamases' Paris-Sud University, LabEx LERMIT, Le Kremlin-Bicêtre, France.,Associate French National Reference Centre for Antimicrobial Resistance 'Carbapenem-Resistant Enterobacteriaceae', Le Kremlin-Bicêtre, France
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Soria-Segarra C, González-Bustos P, López-Cerero L, Fernández-Cuenca F, Rojo-Martín MD, Fernández-Sierra MA, Gutiérrez-Fernández J. Tracking KPC-3-producing ST-258 Klebsiella pneumoniae outbreak in a third-level hospital in Granada (Andalusia, Spain) by risk factors and molecular characteristics. Mol Biol Rep 2019; 47:1089-1097. [PMID: 31792747 DOI: 10.1007/s11033-019-05203-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/21/2019] [Indexed: 12/26/2022]
Abstract
The objective of this study was to determine clinical-epidemiological characteristics of the patients and the genetic characteristics of carbapenemase KPC-3-producing Klebsiella pneumoniae isolates belonging to sequence type ST258. The eligible study population was all patients with isolates detected between October 2015 and March 2017. Clinical-epidemiological and microbiological data were gathered on risk factors associated with infection by this clone. Antimicrobial susceptibility was determined using MicroScan system and diffusion in agar. Genes encoding carbapenemases were detected using PCR and Sanger sequencing. The sequence type was assigned by MLST, and the genetic relationship among clinical isolates was determined by pulsed field electrophoresis and by analysis of the genetic environment. The study included 23 individuals with isolates of KPC-3/ST258; the mean age was 77 year, and mean stay pre-isolation was 32 days; 81% received empirical antimicrobial treatment. Isolates were only susceptible to gentamicin (CIM ≤ 2 mg/L), tigecycline (CIM ≤ 1 mg/L), and colistin (CIM ≤ 2 mg/L). The isolates belonged to ST258, with five pulse types or subgroups. All isolates showed amplification of KPC, which was identified as KPC-3 variant. Gene blaKPC-3 was flanked by insertion sequences Kpn6 and Kpn7 within Tn4401 transposon isoform a. We report, for the first time in Spain, an 18-month outbreak by KPC-3-producing ST258 K. pneumoniae. Its acquisition was associated with a history of antimicrobial therapy, with three treatment options, and with high mortality. The detection of different pulse types is attributable to different introductions of the clone in our setting, supporting the need for multi-resistant isolate surveillance studies.
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Affiliation(s)
- Carmen Soria-Segarra
- Department of Internal Medicine, School of Medicine, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador.,Program in Clinical Medicine and Public Health, University of Granada-Instituto de Investigación Biosanitaria ibs.Granada, Granada, Spain
| | - Pablo González-Bustos
- Department of Internal Medicine, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria ibs.Granada, Granada, Spain
| | - Lorena López-Cerero
- Department of Microbiology and Infectious Diseases. Laboratorio de Tipado Molecular de Andalucía, Programa PIRASOA, Hospital Virgen Macarena, Seville, Spain
| | - Felipe Fernández-Cuenca
- Department of Microbiology and Infectious Diseases. Laboratorio de Tipado Molecular de Andalucía, Programa PIRASOA, Hospital Virgen Macarena, Seville, Spain
| | - María Dolores Rojo-Martín
- Department of Microbiology, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria - ibs.Granada, Avenida de las Fuerzas Armadas, 2, 18014, Granada, Spain
| | - María Amelia Fernández-Sierra
- Department of Preventive Medicine, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria - ibs.Granada, Granada, Spain
| | - José Gutiérrez-Fernández
- Department of Microbiology, Hospital Universitario Virgen de las Nieves-Instituto de Investigación Biosanitaria - ibs.Granada, Avenida de las Fuerzas Armadas, 2, 18014, Granada, Spain. .,Department of Microbiology, School of Medicine, University of Granada-Instituto de Investigación Biosanitaria - ibs.Granada, Granada, Spain.
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14
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Multidrug-Resistant Bacteria and Alternative Methods to Control Them: An Overview. Microb Drug Resist 2019; 25:890-908. [DOI: 10.1089/mdr.2018.0319] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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15
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Machulska M, Baraniak A, Żak I, Bojarska K, Żabicka D, Sowa-Sierant I, Hryniewicz W, Gniadkowski M. KPC-2-producing Klebsiella pneumoniae ST11 in a Children's Hospital in Poland. Pol J Microbiol 2019; 66:401-404. [PMID: 29319505 DOI: 10.5604/01.3001.0010.4884] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Four Klebsiella pneumoniae isolates from children hospitalized over 10 months in an intensive care unit in a children's teaching hospital in Poland were analyzed. All of the isolates belonged to a single pulsotype and sequence type (ST) 11, and produced the KPC-2 carbapenemase and extended-spectrum β-lactamase (ESBL) CTX-M-15. They were resistant to a variety of antimicrobials, and their β-lactam resistance patterns were typical for KPC producers. This is one of few cases of identification of KPC (or carbapenemase)-producing K. pneumoniae in a pediatric center in Poland.
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Affiliation(s)
- Monika Machulska
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Anna Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Iwona Żak
- Department of Clinical Microbiology, Children's University Hospital, Kraków, Poland
| | - Katarzyna Bojarska
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - Iwona Sowa-Sierant
- Department of Clinical Microbiology, Children's University Hospital, Kraków, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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16
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Gharout-Sait A, Touati A, Ahmim M, Brasme L, Guillard T, Agsous A, de Champs C. Occurrence of Carbapenemase-Producing Klebsiella pneumoniae in Bat Guano. Microb Drug Resist 2019; 25:1057-1062. [PMID: 31021173 DOI: 10.1089/mdr.2018.0471] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The aim of this study was to screen for the presence of carbapenemase-producing Enterobacteriaceae (CPE) isolates from bat guano in Bejaia, Algeria. Guano samples (n = 110) were collected in Aokas's cave, Bejaia, Algeria, between March and May 2016. Samples were plated on MacConkey agar supplemented with ertapenem (0.5 mg/L) and vancomycin (32 mg/L). The isolates were identified and antimicrobial susceptibility was determined using disk diffusion method. Carbapenemase, extended spectrum β-lactamases, plasmid-mediated AmpC, and plasmid-mediated quinolone resistance genes were studied using PCR and sequencing. Clonal relatedness was studied using multilocus sequence typing (MLST). Two CPE isolates were identified as Klebsiella pneumoniae. PCR and sequencing identified the blaOXA-48 in one K. pneumoniae strain (CS34) and blaKPC-3 in the other strain (CS63). K. pneumoniae CS63 was found to carry blaTEM-1 and aac(6')-Ib genes. The MLST showed that K. pneumoniae CS63 was assigned to ST512, whereas K. pneumoniae CS34 belonged to ST1878. This is the first description of CPE from bats' guano.
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Affiliation(s)
- Alima Gharout-Sait
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Mourad Ahmim
- Laboratoire d'Ecologie et d'Environnement, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Lucien Brasme
- Laboratoire de Bactériologie, Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert DEBRE, Avenue du Général Koenig, Reims, France.,Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims Champagne-Ardenne, Reims, France
| | - Thomas Guillard
- Laboratoire de Bactériologie, Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert DEBRE, Avenue du Général Koenig, Reims, France.,Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims Champagne-Ardenne, Reims, France
| | - Amir Agsous
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Christophe de Champs
- Laboratoire de Bactériologie, Virologie-Hygiène Hospitalière, CHU Reims, Hôpital Robert DEBRE, Avenue du Général Koenig, Reims, France.,Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims Champagne-Ardenne, Reims, France
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17
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Izdebski R, Baraniak A, Zabicka D, Machulska M, Urbanowicz P, Fiett J, Literacka E, Bojarska K, Kozinska A, Zieniuk B, Hryniewicz W, Gniadkowski M. Enterobacteriaceae producing OXA-48-like carbapenemases in Poland, 2013-January 2017. J Antimicrob Chemother 2019; 73:620-625. [PMID: 29237086 DOI: 10.1093/jac/dkx457] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/06/2017] [Indexed: 11/14/2022] Open
Abstract
Objectives To analyse OXA-48 (OXA-48/181)-type carbapenemase-producing Enterobacteriaceae reported in Poland from 2013 until January 2017. Methods Bacterial isolates were typed by PFGE and MLST. Genes coding for OXA-48/181 types and other β-lactamases were amplified and sequenced. Mobile elements with blaOXA-48/181-like genes were PCR mapped. blaOXA-48/181-carrying plasmids were characterized by nuclease S1-hybridization profiling, transfer assays and PCR-based replicon typing, while the chromosomal location of the genes was confirmed by the I-CeuI analysis. Results Fifty-four isolates from 52 patients in 20 hospitals (14 cities) were included, in 14 cases having probable foreign origins indicated. The organisms were genetically diverse and represented numerous pandemic clones, including Klebsiella pneumoniae ST395 (n = 23), ST11, ST15 and ST101, Escherichia coli ST38, ST410 and ST648, and Enterobacter cloacae complex ST78. These produced OXA-48 (n = 49), OXA-181 (n = 4) or OXA-232 (n = 1). One of five K. pneumoniae ST395 pulsotypes caused a multicentre outbreak with 18 cases, which significantly contributed to the total number of patients. Depending on the variant, the blaOXA-48/181-like genes were parts of the Tn1999-, Tn2013- or Tn2016-like transposons, with blaOXA-48 found in an ISEcp1-associated module (Tn2016-like) for the first time. Three genotypes, including E. coli ST38, had chromosomal blaOXA-48 genes, while others carried transmissible IncL (∼60 kb; blaOXA-48; n = 30), IncM (∼80-95 kb; blaOXA-48; n = 4), IncX3 (∼50 kb; blaOXA-181; n = 4) or non-typeable (∼90-160 kb; blaOXA-48 or blaOXA-232) plasmids. Conclusions Even though OXA-48/181 producers seem to occur infrequently in Poland, their epidemiology has been marked by various phenomena, namely multiple imports, several limited transmissions plus one larger clonal outbreak, and possible plasmid transfers.
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Affiliation(s)
- R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - D Zabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725 Warsaw, Poland
| | - M Machulska
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - J Fiett
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
| | - E Literacka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725 Warsaw, Poland
| | - K Bojarska
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725 Warsaw, Poland
| | - A Kozinska
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725 Warsaw, Poland
| | - B Zieniuk
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725 Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725 Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland
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18
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Markovska R, Stoeva T, Boyanova L, Stankova P, Schneider I, Keuleyan E, Mihova K, Murdjeva M, Sredkova M, Lesseva M, Nedelcheva G, Petrova A, Ivanova D, Lazarova G, Kaneva R, Mitov I. Multicentre investigation of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in Bulgarian hospitals - Interregional spread of ST11 NDM-1-producing K. pneumoniae. INFECTION GENETICS AND EVOLUTION 2019; 69:61-67. [PMID: 30654179 DOI: 10.1016/j.meegid.2019.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 01/11/2019] [Indexed: 11/24/2022]
Abstract
AIM The aim of this study was to investigate the mechanisms of beta-lactam-resistance and the clonal relatedness of carbapenem-nonsusceptible Klebsiella pneumoniae and Escherichia coli isolates, collected consecutively in eight centers in five Bulgarian cities from November 2014 to March 2018. Carbapenemase-producing enterobacteria were detected in all but one centers. Overall, 104 K. pneumoniae and one E. coli were analysed. MATERIALS AND METHODS Antimicrobial susceptibility and beta-lactamases were analysed. Conjugation experiments, plasmid fingerprinting and replicon typing, as well as MLST and ERIC-PCR were carried out. RESULTS KPC-2 (51%) and NDM-1 (47%) were the main carbapenemases identified. KPC-2 producing K. pneumoniae were classified into 10 MLST-types. The four dominating MLST-types ST29, ST15, ST336 and ST902 comprised 79% of the KPC-2 producers. All but one of the NDM-1 producing isolates belonged to the MLST-type ST11 and were found in seven centers. Furthermore, single K. pneumoniae isolates producing VIM-1 (ST147) and OXA-48 (ST15) were identified. In addition to the carbapenemases, the ESBLs CTX-M-15, CTX-M-3, and SHV-12 as well as AmpC enzyme CMY-4 were found. The FIIAs-replicon-type was found in all KPC-2 producers while the A/C-replicons dominated in NDM-1 producing isolates. The single NDM-1 producing E. coli was determined as MLST-Type ST10 (Warwick scheme). CONCLUSION The interregional clonal expansion of NDM-1 producing ST11 K. pneumoniae and the dissemination of blaKPC-2 carrying plasmids were responsible for the spread of carbapenemase-producing K. pneumoniae in Bulgaria. Our findings highlight the urgency to prevent dissemination of these highly transmissible and dangerous lineages.
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Affiliation(s)
- Rumyana Markovska
- Medical University of Sofia, Medical Faculty, Department of Medical Microbiology, Bulgaria.
| | - Temenuga Stoeva
- Medical University of Varna, Department of Microbiology and Virology, University Multiprofile Hospital for Active Treatment (UMHAT), St Marina, Varna, Bulgaria
| | - Lyudmila Boyanova
- Medical University of Sofia, Medical Faculty, Department of Medical Microbiology, Bulgaria
| | - Petya Stankova
- Medical University of Sofia, Medical Faculty, Department of Medical Microbiology, Bulgaria
| | | | - Emma Keuleyan
- Department of Clinical Microbiology, Medical Institute - Ministry of the Interior, Sofia, Bulgaria
| | - Kalina Mihova
- Molecular Medicine Center, Medical University of Sofia, Sofia, Bulgaria
| | - Marianna Murdjeva
- Medical University of Plovdiv, Department of Microbiology and Immunology, UMHAT, "St George", Plovdiv, Bulgaria
| | - Mariya Sredkova
- Medical University of Pleven, Department of Microbiology and Virology, UMHAT "Georgi Stranski", Pleven, Bulgaria
| | | | - Gergana Nedelcheva
- Medical University of Varna, Department of Microbiology and Virology, University Multiprofile Hospital for Active Treatment (UMHAT), St Marina, Varna, Bulgaria
| | - Atanaska Petrova
- Medical University of Plovdiv, Department of Microbiology and Immunology, UMHAT, "St George", Plovdiv, Bulgaria
| | - Dobrinka Ivanova
- Second Multiprofile Hospital for Active Treatment, Sofia, Bulgaria
| | - Grozdanka Lazarova
- UMHAT "Prof. dr St Kirkovich" Stara Zagora, Thracian University, Stara Zagora, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Medical University of Sofia, Sofia, Bulgaria
| | - Ivan Mitov
- Medical University of Sofia, Medical Faculty, Department of Medical Microbiology, Bulgaria
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Shankar C, Kumar M, Baskaran A, Paul MM, Ponmudi N, Santhanam S, Michael JS, Veeraraghavan B. Molecular Characterisation for Clonality and Transmission Dynamics of an Outbreak of Klebsiella pneumoniae amongst Neonates in a Tertiary Care Centre in South India. Indian J Med Microbiol 2018; 36:54-60. [DOI: 10.4103/ijmm.ijmm_17_426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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