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Shaidullina ER, Schwabe M, Rohde T, Shapovalova VV, Dyachkova MS, Matsvay AD, Savochkina YA, Shelenkov AA, Mikhaylova YV, Sydow K, Lebreton F, Idelevich EA, Heiden SE, Becker K, Kozlov RS, Shipulin GA, Akimkin VG, Lalk M, Guenther S, Zautner AE, Bohnert JA, Mardanova AM, Bouganim R, Marchaim D, Hoff KJ, Schaufler K, Edelstein MV. Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395. Genome Med 2023; 15:9. [PMID: 36782220 PMCID: PMC9926764 DOI: 10.1186/s13073-023-01159-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage. METHODS We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features. RESULTS Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of "hybrid" resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype. CONCLUSIONS To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.
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Affiliation(s)
- Elvira R Shaidullina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - Michael Schwabe
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Rohde
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Valeria V Shapovalova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Marina S Dyachkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Alina D Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | - Yuliya A Savochkina
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Katharina Sydow
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - François Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, USA
| | - Evgeny A Idelevich
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan E Heiden
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Roman S Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - German A Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, Moscow, Russia
| | | | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Sebastian Guenther
- Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Andreas E Zautner
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
| | - Jürgen A Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ayslu M Mardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ruth Bouganim
- Department of Internal Medicine A, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel
| | - Dror Marchaim
- Infection Control Unit, Shamir (Assaf Harofeh) Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany.
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Mikhail V Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
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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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Alekseeva AE, Brusnigina NF, Gordinskaya NA, Makhova MA, Kolesnikova EA. Molecular genetic characteristics of resistome and virulome of carbapenem-resistant Klebsiella pneumoniae clinical strains. Klin Lab Diagn 2022; 67:186-192. [PMID: 35320636 DOI: 10.51620/0869-2084-2022-67-3-186-192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The characteristics of resistome and virulome structure of four carbapenem-resistant Klebsiella pneumoniae clinical strains are present in the work. Two strains belonged to the sequence-type ST395, one strain - ST2262, one strain - to the new sequence-type 5816. The genes of fimbriae, enterobactin, beta-lactamase SHV type, resistance to fosfomycin fosA and transport of fluoroquinolones oqxAB in all Klebsiella strains chromosome structure were identified. The determinants of yersineobactin and aerobactin are enriched the virulome of ST395 NNKP315 and NNKP343 strains. The aerobactin genes are located on IncHI1B plasmids (IncHI1B/FIB) which highly homologous to the virulence pLVPK and pK2044 plasmids. IncR, IncL, IncQ plasmids carrying blaOXA-48, blaCTX-M-15, blaOXA-1, blaTEM-1, qnrS1, tetA, sul1, dfrA1, aac(6 ')-Ib-cr, catA1, catB3 etc. were identified in these strains. As a result of in silico analysis, an assumption about the localization of the blaOXA-48 in the structure of the IncHI1B plasmid of NNKP315 strain was made. This plasmid also contains the aminoglycosidases genes inserted into a class 1 integron In822. The mutations were found in the porin proteins OmpK35, OmpK36 and OmpK37 genes, which increases the carbapenem resistance. The virulome of NNKP16 (ST2262) strain additionally includes of the iron utilization system kfuABC chromosomal genes, and the virulome of NNKP15 (ST5816) strain contains of the capsular polysaccharide kvgAS and microcin E492 genes. Additional determinants of resistance were not identified in the resistome structure of K. pneumoniae NNKP16 and only the blaCTX-M-15 gene was found in the NNKP15 strain. The absence of acquired resistance genes seems to be due to the presence of the type I-E CRISPR-Cas system. Multiple drug resistance of the studied strains is associated with mutations identified in the gene structure of porin proteins OmpK36 and OmpK37, as well as the activity of efflux systems. It was showed the stop codon formation in the nucleotide sequence of the regulatory gene ramR to both strains, which can potentially provide overexpression of AcrAB efflux proteins.
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Affiliation(s)
- A E Alekseeva
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - N F Brusnigina
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - N A Gordinskaya
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - M A Makhova
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - E A Kolesnikova
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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