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Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, Lam MMC, Duchêne S, Jenney A, Holt KE. Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. PLoS Genet 2019; 15:e1008114. [PMID: 30986243 PMCID: PMC6483277 DOI: 10.1371/journal.pgen.1008114] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/25/2019] [Accepted: 03/29/2019] [Indexed: 11/19/2022] Open
Abstract
Klebsiella pneumoniae has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare-associated infections and drug susceptible community-acquired invasive infections. These pathotypes are generally associated with two distinct subsets of K. pneumoniae lineages or 'clones' that are distinguished by the presence of acquired resistance genes and several key virulence loci. Genomic evolutionary analyses of the most notorious MDR and invasive community-associated ('hypervirulent') clones indicate differences in terms of chromosomal recombination dynamics and capsule polysaccharide diversity, but it remains unclear if these differences represent generalised trends. Here we leverage a collection of >2200 K. pneumoniae genomes to identify 28 common clones (n ≥ 10 genomes each), and perform the first genomic evolutionary comparison. Eight MDR and 6 hypervirulent clones were identified on the basis of acquired resistance and virulence gene prevalence. Chromosomal recombination, surface polysaccharide locus diversity, pan-genome, plasmid and phage dynamics were characterised and compared. The data showed that MDR clones were highly diverse, with frequent chromosomal recombination generating extensive surface polysaccharide locus diversity. Additional pan-genome diversity was driven by frequent acquisition/loss of both plasmids and phage. In contrast, chromosomal recombination was rare in the hypervirulent clones, which also showed a significant reduction in pan-genome diversity, largely driven by a reduction in plasmid diversity. Hence the data indicate that hypervirulent clones may be subject to some sort of constraint for horizontal gene transfer that does not apply to the MDR clones. Our findings are relevant for understanding the risk of emergence of individual K. pneumoniae strains carrying both virulence and acquired resistance genes, which have been increasingly reported and cause highly virulent infections that are extremely difficult to treat. Specifically, our data indicate that MDR clones pose the greatest risk, because they are more likely to acquire virulence genes than hypervirulent clones are to acquire resistance genes.
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Affiliation(s)
- Kelly L. Wyres
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Ryan R. Wick
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Roni Froumine
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Alex Tokolyi
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Claire L. Gorrie
- Department of Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Margaret M. C. Lam
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Adam Jenney
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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202
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Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M. Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 2019; 13:e0007374. [PMID: 31026256 PMCID: PMC6513109 DOI: 10.1371/journal.pntd.0007374] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/13/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.
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Affiliation(s)
- Julien Guglielmini
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
| | - Pascale Bourhy
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Olivier Schiettekatte
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
- Université Paris Diderot, Ecole Doctorale BioSPC, Paris, France
| | - Farida Zinini
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Mathieu Picardeau
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
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203
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Xu M, Fu Y, Fang Y, Xu H, Kong H, Liu Y, Chen Y, Li L. High prevalence of KPC-2-producing hypervirulent Klebsiella pneumoniae causing meningitis in Eastern China. Infect Drug Resist 2019; 12:641-653. [PMID: 30936727 PMCID: PMC6430001 DOI: 10.2147/idr.s191892] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae has been the leading causative pathogen for adult bacterial meningitis in several Asian countries. The clinical and microbiological characteristics of K. pneumoniae meningitis in mainland China are still unknown. MATERIALS AND METHODS The clinical data of patients with K. pneumoniae meningitis from January 2011 to July 2017 in a tertiary hospital were retrospectively evaluated. The isolates were tested for antibiotic-resistance genes, virulence-associated genes, and molecular subtypes. Hyper-virulent K. pneumoniae (hvKP) was defined as the presence of pLVPK-like virulence plasmid. RESULTS During the study period, a total of 48 patients with meningitis caused by K. pneumoniae were identified, accounting for 21.2% (48/226) of Gram-negative bacilli meningitis. Of the 44 available isolates, 65.9% (29/44) were carbapenem resistant, and all except one har-bored bla KPC-2. K64 was the most common serotype (n=13), followed by K47 (n=11) and K1 (n=5). The pLVPK-related genetic loci were found in about half of isolates (iutA: 56.8%, iucA: 56.8%, rmpA2:50.0%, rmpA: 43.2%, and iroN: 40.9%). Twenty-two strains carrying pLVPK-derived virulence plasmid were defined as hvKP. Notably, the coexistence of bla KPC-2-encoding plasmid and the pLVPK-derived virulence plasmid was detected in 15 strains (34.1%, 15/44), suggesting K. pneumoniae carbapenemase-2 (KPC-2)-producing hvKP. The proportion of KPC-2-producing hvKP by year increased remarkably from 0% (2011) to 71.4% (2017). Of the 15 KPC-2-producing hvKP strains, 80.0% (12/15) were assigned to sequence type 11 and 2 strains (13.3%) belonged to clonal complex 23. Most of the patients infected with KPC-2-producing hvKP had preceding postneurosurgical state (93.3%, 14/15) and severe pneumonia (73.3%, 11/15). All the cases (100%, 15/15) had fatal outcome. CONCLUSION The high prevalence and mortality of K. pneumoniae, especially KPC-2-producing hvKP meningitis, in China should be of concern. The implementation of epidemiological surveillance and identification of an effective clinical treatment are paramount.
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Affiliation(s)
- Min Xu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yiqi Fu
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yunhui Fang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
| | - Haishen Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
| | - Yanchao Liu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yu Chen
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
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Timilsina S, Pereira-Martin JA, Minsavage GV, Iruegas-Bocardo F, Abrahamian P, Potnis N, Kolaczkowski B, Vallad GE, Goss EM, Jones JB. Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida. Front Microbiol 2019; 10:448. [PMID: 30930868 PMCID: PMC6425879 DOI: 10.3389/fmicb.2019.00448] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/20/2019] [Indexed: 11/23/2022] Open
Abstract
Prior to the identification of Xanthomonas perforans associated with bacterial spot of tomato in 1991, X. euvesicatoria was the only known species in Florida. Currently, X. perforans is the Xanthomonas sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant X. perforans genotype in Florida. We previously reported recombination of X. perforans strains with closely related Xanthomonas species as a potential driving factor for X. perforans evolution. However, the extent of recombination across the X. perforans genomes was unknown. We used a core genome multilocus sequence analysis approach to identify conserved genes and evaluated recombination-associated evolution of these genes in X. perforans. A total of 1,356 genes were determined to be "core" genes conserved among the 58 X. perforans genomes used in the study. Our approach identified three genetic groups of X. perforans in Florida based on the principal component analysis (PCA) using core genes. Nucleotide variation in 241 genes defined these groups, that are referred as Phylogenetic-group Defining (PgD) genes. Furthermore, alleles of many of these PgD genes showed 100% sequence identity with X. euvesicatoria, suggesting that variation likely has been introduced by recombination at multiple locations throughout the bacterial chromosome. Site-specific recombinase genes along with plasmid mobilization and phage associated genes were observed at different frequencies in the three phylogenetic groups and were associated with clusters of recombinant genes. Our analysis of core genes revealed the extent, source, and mechanisms of recombination events that shaped the current population and genomic structure of X. perforans in Florida.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | | | - Gerald V. Minsavage
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | | | - Peter Abrahamian
- Gulf Coast Research and Education Center, University of Florida, Gainesville, FL, United States
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, United States
| | - Bryan Kolaczkowski
- Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Gary E. Vallad
- Gulf Coast Research and Education Center, University of Florida, Gainesville, FL, United States
| | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
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205
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Wyres KL, Lam MMC, Holt KE. Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City. J Antimicrob Chemother 2019; 74:831-833. [PMID: 30508109 PMCID: PMC6376848 DOI: 10.1093/jac/dky472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Margaret M C Lam
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia.,London School of Hygiene and Tropical Medicine, London, UK
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206
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Zhang F, Mulati N, Wang Y, Li Y, Gong S, Karthik L, Sun W, Li Z. Biosynthesis in vitro of bacillamide intermediate-heterocyclic AlaCysthiazole by heterologous expression of nonribosomal peptide synthetase (NRPS). J Biotechnol 2019; 292:5-11. [DOI: 10.1016/j.jbiotec.2018.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/16/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023]
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207
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Molecular characterization of NDM-1-producing Klebsiella pneumoniae ST29, ST347, ST1224, and ST2558 causing sepsis in neonates in a tertiary care hospital of North-East India. INFECTION GENETICS AND EVOLUTION 2019; 69:166-175. [PMID: 30677535 DOI: 10.1016/j.meegid.2019.01.024] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 11/21/2022]
Abstract
Geographical differences can manifest in different spectra of microorganisms and patterns of antibiotic resistance. Considering this, Enterobacteriacae isolated from septicemic neonates from a tertiary care centre in Agartala, India were studied with focus on carbapenem resistance. Two hundred non-duplicate Enterobacteriaceae, of which 12 NDM-1-producing Klebsiella pneumoniae were recovered. Antibiotic susceptibility tests and detection of ESBLs and carbapenemases were performed for all Enterobacteriaceae. For NDM-1-producing isolates, plasmid-mediated quinolone resistance genes, addiction systems, genetic environment of blaNDM-1 and virulence genes was investigated by PCR. Bacterial clonal relatedness was established using REP-PCR, PFGE, and multi-locus sequence typing (MLST). Transferability of blaNDM-1 was tested by conjugation and transconjugants were characterized. K. pneumoniae was the primary organism causing sepsis in neonates. Resistance to different antimicrobials was high except for aminoglycosides and carbapenems. blaCTX-M was present in all isolates. All carbapenem-resistant isolates harboured blaNDM-1 as the only carbapenemase. blaCTX-M-15 and qnrS1 were detected in all NDM-1-producing isolates. Plasmid analysis of transconjugants revealed that blaNDM-1 along with blaCTX-M-15, qnrS1, qnrB1, aac(6')-Ib, aac(6')-Ib-cr and ccdAB or vagCD addiction systems were carried on large IncFIIK conjugative plasmids of varied sizes. blaNDM-1 was associated with ISAba125 or ISEc33 element at its 5'-end. In addition, isolates also harboured wabG, uge, fimH, mrkD, and entB virulence genes. The NDM-1-producing K. pneumoniae belonged to four distinct clones and were distributed in 4 STs (ST347, ST29, ST2558, and ST1224), of which ST347 was predominant. The association of blaNDM-1 with diverse STs in K. pneumoniae from neonates indicates the promiscuity of the gene and its widespread dissemination.
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208
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Türkel İ, Yıldırım T, Yazgan B, Bilgin M, Başbulut E. Relationship between antibiotic resistance, efflux pumps, and biofilm formation in extended-spectrum β-lactamase producing Klebsiella pneumoniae. J Chemother 2019; 30:354-363. [DOI: 10.1080/1120009x.2018.1521773] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- İbrahim Türkel
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Amasya, Turkey,
| | - Tuba Yıldırım
- Department of Biology, Faculty of Arts and Sciences, Amasya University, Amasya, Turkey,
- Central Research Laboratory, Amasya University, Amasya, Turkey,
| | - Burak Yazgan
- Central Research Laboratory, Amasya University, Amasya, Turkey,
- Department of Medical Sevices and Techniques, Amasya University Sabuncuoğlu Serefeddin Vocational Higher School of Health Services, Amasya, Turkey,
| | - Melek Bilgin
- Microbiology Laboratory, Education and Research Hospital, Samsun, Turkey
| | - Eşe Başbulut
- Microbiology Laboratory, Education and Research Hospital, Samsun, Turkey
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209
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Fu Y, Xu M, Liu Y, Li A, Zhou J. Virulence and genomic features of a bla CTX-M-3 and bla CTX-M-14 coharboring hypermucoviscous Klebsiella pneumoniae of serotype K2 and ST65. Infect Drug Resist 2019; 12:145-159. [PMID: 30655681 PMCID: PMC6322562 DOI: 10.2147/idr.s187289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Capsular serotype K2 Klebsiella pneumoniae of sequence type (ST) 65 has been recognized as a hypervirulent clone. Simultaneous presence of different blaCTX-M genes has never been reported in this clone. In the present study, the genetic characteristics and virulence phenotype of a CTX-M-3 and CTX-M-14 coproducing ST65 K. pneumoniae human isolate, KP_06, that caused an intracranial infection, are evaluated. Methods The potential virulence of KP_06 was assayed by in vitro and in vivo methods. The molecular biology and whole-genome sequencing technology were used to analyze the genomic features associated with the virulence of this strain. Results The KP_06 exhibited typical features of hypervirulent K. pneumoniae (hvKP), showing hypermucoviscosity phenotype and belonging to K2 and ST65. Apart from virulence genes linked to hvKP, including rmpA, rmpA2, and clb cluster and genes encoding siderophores, it was found to harbor a ~170 kb pLVPK-like virulence plasmid. In contrast to most hvKP, KP_06 was resistant to cephalosporins and the coexistence of blaCTX-M-3 and blaCTX-M-14 was detected. Further experiments demonstrated that this strain was classified as a nonbiofilm producer and serum sensitivity (grade 1) and killed only 30% of Galleria mellonella inoculated with 1×106 colony-forming unit of the specimen within 48 hours, suggesting relatively low virulence. Comparative genomic analysis of KP_06 with five K2 hypermucoviscous K. pneumoniae (HMKP) revealed seven unique orthologies with varied function in this strain. Intriguingly, the virulence genes identified in KP-06 were unexpectedly more diverse than those observed in five other K2 HMKP strains. Conclusion Our data support the notion that neither virulence-associated genes (clusters) nor the pLVPK-like virulence plasmid is sufficient for the hypervirulence of K. pneumoniae. Future studies aiming to explore the virulence of K. pneumoniae should take genome-based profile together with experimental work. The detailed mechanism involving in the impaired virulence of KP_06 remains to be further explored.
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Affiliation(s)
- Yiqi Fu
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
| | - Min Xu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanchao Liu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ang Li
- Department of Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
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Rodríguez-Medina N, Barrios-Camacho H, Duran-Bedolla J, Garza-Ramos U. Klebsiella variicola: an emerging pathogen in humans. Emerg Microbes Infect 2019; 8:973-988. [PMID: 31259664 PMCID: PMC6609320 DOI: 10.1080/22221751.2019.1634981] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/13/2019] [Accepted: 06/16/2019] [Indexed: 12/13/2022]
Abstract
The Klebsiella pneumoniae complex comprises seven K. pneumoniae-related species, including K. variicola. K. variicola is a versatile bacterium capable of colonizing different hosts such as plants, humans, insects and animals. Currently, K. variicola is gaining recognition as a cause of several human infections; nevertheless, its virulence profile is not fully characterized. The clinical significance of K. variicola infection is hidden by imprecise detection methods that underestimate its real prevalence; however, several methods have been developed to correctly identify this species. Recent studies of carbapenemase-producing and colistin-resistant strains demonstrate a potential reservoir of multidrug-resistant genes. This finding presents an imminent scenario for spreading antimicrobial resistant genes among close relatives and, more concerningly, in clinical and environmental settings. Since K. variicola was identified as a novel bacterial species, different research groups have contributed findings elucidating this pathogen; however, important details about its epidemiology, pathogenesis and ecology are still missing. This review highlights the most significant aspects of K. variicola, discussing its different phenotypes, mechanisms of resistance, and virulence traits, as well as the types of infections associated with this pathogen.
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Affiliation(s)
- Nadia Rodríguez-Medina
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
| | - Humberto Barrios-Camacho
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
| | - Josefina Duran-Bedolla
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
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Epidemiological investigation of an Acinetobacter baumannii outbreak using core genome multilocus sequence typing. J Glob Antimicrob Resist 2018; 17:245-249. [PMID: 30553929 DOI: 10.1016/j.jgar.2018.11.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious nosocomial pathogen that causes a variety of serious, often life-threatening, infections and outbreaks. This study aimed to investigate the molecular epidemiology of clinical CRAB isolates from an outbreak that occurred in the intensive care unit (ICU) of an Italian hospital. METHODS From December 2016 to April 2017, 13 CRAB isolates were collected from seven patients treated in the ICU at 'L. Spallanzani' Hospital (Rome, Italy). Typing was performed by repetitive extragenic palindromic PCR (rep-PCR) using a DiversiLab® system. Whole-genome sequencing (WGS) data were used for in silico analysis of traditional multilocus sequence typing (MLST) results, to identify resistance genes and for core genome MLST (cgMLST) analysis. Epidemiological data were obtained from hospital records. RESULTS All isolates showed a carbapenem-resistant profile and carried the blaOXA-23 carbapenemase gene. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group, whilst the cgMLST approach, which uses 2390 gene targets to characterise the gene-by-gene allelic profile, highlighted the presence of two cluster types. These results allowed us to identify two patients who were likely to be the source of two separate transmission chains. CONCLUSION These results show that WGS by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.
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Caneiras C, Lito L, Mayoralas-Alises S, Díaz-Lobato S, Melo-Cristino J, Duarte A. Virulence and resistance determinants of Klebsiella pneumoniae isolated from a Portuguese tertiary university hospital centre over a 31-year period. Enferm Infecc Microbiol Clin 2018; 37:387-393. [PMID: 30553621 DOI: 10.1016/j.eimc.2018.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/04/2018] [Accepted: 11/02/2018] [Indexed: 11/16/2022]
Abstract
INTRODUCTION The rapid and complex evolution of bacterial resistance mechanisms in Klebsiella pneumoniae producing extended-spectrum β-lactamases and carbapenemases in Klebsiella pneumoniae is one of the most significant threats to public health. However, questions and controversies regarding the interactions between resistance and virulence in multidrug-resistant K. pneumoniae isolates remain unclear. METHODS A retrospective cohort study was performed with 100 K. pneumoniae isolates recovered from a tertiary care university hospital centre in Lisbon over a 31-year period. Resistance and virulence determinants were screened using molecular methods (PCR, M13-PCR and MLST). RESULTS The predominant virulence profile (fimH, mrkDv1, khe) was shared by all isolates, indicative of an important role of type 1 and 3 fimbrial adhesins and haemolysin, regardless of the type of β-lactamase produced. However, accumulation of virulence factors was identified in KPC-3-producers, with a higher frequency (p<0.05) of capsular serotype K2 and iucC aerobactin when compared with non-KPC-3 β-lactamases or carbapenemases. Additionally, 9 different virulence profiles were found, indicating that the KPC-3 carbapenemase producers seem to adapt successfully to the host environment and maintain virulence via several pathways. CONCLUSION This study describes an overlapping of multidrug-resistance and virulence determinants in ST-14K2 KPC-3 K. pneumoniae clinical isolates that may impose an additional challenge in the treatment of infections caused by this pathogen.
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Affiliation(s)
- Cátia Caneiras
- Microbiology and Immunology Department, Interdisciplinary Research Centre Egas Moniz (CiiEM), Faculty of Pharmacy, University of Lisbon, 1649-003, Lisbon, Portugal; Institute of Environmental Health (ISAMB), Faculty of Medicine, University of Lisbon, 1649-028, Lisbon, Portugal.
| | - Luís Lito
- Laboratory of Microbiology, Centro Hospitalar Lisboa Norte, 1649-035, Lisbon, Portugal
| | - Sagrario Mayoralas-Alises
- Pneumological Department, Moncloa University Hospital, 28008, Madrid, Spain; European University, 28108, Alcobendas, Madrid, Spain
| | - Salvador Díaz-Lobato
- Pneumological Department, Ramón y Cajal University Hospital, Madrid, Spain; Institute Ramón y Cajal for Health Research (IRYCIS), Alcalá de Henares University, 28034, Madrid, Spain
| | - José Melo-Cristino
- Laboratory of Microbiology, Centro Hospitalar Lisboa Norte, 1649-035, Lisbon, Portugal; Institute of Microbiology, Faculty of Medicine, University of Lisbon, 1649-028, Lisbon, Portugal; Institute of Microbiology, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Aida Duarte
- Microbiology and Immunology Department, Interdisciplinary Research Centre Egas Moniz (CiiEM), Faculty of Pharmacy, University of Lisbon, 1649-003, Lisbon, Portugal
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213
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Rodrigues C, Passet V, Rakotondrasoa A, Brisse S. Identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola and Related Phylogroups by MALDI-TOF Mass Spectrometry. Front Microbiol 2018; 9:3000. [PMID: 30581423 PMCID: PMC6294014 DOI: 10.3389/fmicb.2018.03000] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae (phylogroup Kp1), one of the most problematic pathogens associated with antibiotic resistance worldwide, is phylogenetically closely related to K. quasipneumoniae [subsp. quasipneumoniae (Kp2) and subsp. similipneumoniae (Kp4)], K. variicola (Kp3) and two unnamed phylogroups (Kp5 and Kp6). Together, Kp1 to Kp6 make-up the K. pneumoniae complex. Currently, the phylogroups can be reliably identified only based on gene (or genome) sequencing. Misidentification using standard laboratory methods is common and consequently, the clinical significance of K. pneumoniae complex members is imprecisely defined. Here, we evaluated and validated the potential of MALDI-TOF mass spectrometry (MS) to discriminate K. pneumoniae complex members. We detected mass spectrometry biomarkers associated with the phylogroups, with a sensitivity and specificity ranging between 80-100% and 97-100%, respectively. Strains within phylogroups Kp1, Kp2, Kp4, and Kp5 each shared two specific peaks not observed in other phylogroups. Kp3 strains shared a peak that was only observed otherwise in Kp5. Finally, Kp6 had a diagnostic peak shared only with Kp1. Kp3 and Kp6 could therefore be identified by exclusion criteria (lacking Kp5 and Kp1-specific peaks, respectively). Further, ranked Pearson correlation clustering of spectra grouped strains according to their phylogroup. The model was tested and successfully validated using different culture media. These results demonstrate the potential of MALDI-TOF MS for precise identification of K. pneumoniae complex members. Incorporation of spectra of all K. pneumoniae complex members into reference MALDI-TOF spectra databases, in which they are currently lacking, is desirable. MALDI-TOF MS may thereby enable a better understanding of the epidemiology, ecology, and pathogenesis of members of the K. pneumoniae complex.
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Affiliation(s)
- Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Andriniaina Rakotondrasoa
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
- Institut Pasteur Madagascar, Madagascar, Africa
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
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214
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Peltier F, Choquet M, Decroix V, Adjidé CC, Castelain S, Guiheneuf R, Pluquet E. Characterization of a multidrug-resistant Klebsiella pneumoniae ST607-K25 clone responsible for a nosocomial outbreak in a neonatal intensive care unit. J Med Microbiol 2018; 68:67-76. [PMID: 30507374 DOI: 10.1099/jmm.0.000884] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Multidrug-resistant Klebsiella pneumoniae strains are regularly involved in hospital outbreaks. This study describes an ESBL-producing K. pneumoniae clone (ST607-K25) responsible for a nosocomial outbreak in a neonatal intensive care unit. METHODOLOGY Fourteen strains isolated from 13 patients were included. Antimicrobial susceptibility testing was performed by the agar diffusion method. A clonal link was first investigated by fingerprinting (ERIC-PCR and REP-PCR) then confirmed by MLST. Characterization was performed by molecular detection and identification of several drug resistance and virulence determinants. RESULTS All strains expressed the same antibiotype, combining ESBL production, fluoroquinolones and aminoglycoside resistance, except for one which remained susceptible to fluoroquinolones. Fingerprinting methods confirmed the clonal link and MLST identified a ST607 clone. Molecular investigations revealed: (I) genes encoding for two narrow-spectrum beta-lactamases (SHV-1 and TEM-1) and an ESBL (CTX-M-15); (II) absence of any chromosomal mutation in quinolone resistance-determining- regions (QRDR) of gyrA/gyrB and parC/parE genes; (III) genes encoding for three plasmid-mediated quinolone-resistance (PMQR) determinants: oqxAB (14/14), aac(6')-Ib-cr (14/14) and qnrB (13/14); (IV) production of a K25 capsule; and (V) carriage of three genes encoding for virulence factors: mrkD (type 3 fimbriae) (14/14), ybts (yersiniabactin) (12/14) and entB (enterobactin) (14/14). CONCLUSION We described a multidrug-resistant Kp ST607 clone responsible for a nosocomial outbreak in vulnerable and premature newborns. Molecular investigations allowed us to identify several resistance factors responsible for ESBL production (CTX-M-15) and quinolone resistance (three PMQR determinants). The detection of a gene (ybtS) belonging to the high-pathogenicity island yersiniabactin could partly explain its high colonization and diffusion potential.
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Affiliation(s)
- F Peltier
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - M Choquet
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - V Decroix
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - C C Adjidé
- 3Nosocomial Infection Department, Amiens-Picardie University Hospital, Amiens, France
| | - S Castelain
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - R Guiheneuf
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - E Pluquet
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
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Mohammad Ali Tabrizi A, Badmasti F, Shahcheraghi F, Azizi O. Outbreak of hypervirulent Klebsiella pneumoniae harbouring blaVIM-2 among mechanically-ventilated drug-poisoning patients with high mortality rate in Iran. J Glob Antimicrob Resist 2018; 15:93-98. [DOI: 10.1016/j.jgar.2018.06.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/23/2018] [Accepted: 06/28/2018] [Indexed: 12/23/2022] Open
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216
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Espinal P, Nucleo E, Caltagirone M, Mattioni Marchetti V, Fernandes MR, Biscaro V, Rigoli R, Carattoli A, Migliavacca R, Villa L. Genomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232. Clin Microbiol Infect 2018; 25:385.e1-385.e5. [PMID: 30472424 DOI: 10.1016/j.cmi.2018.11.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/22/2018] [Accepted: 11/03/2018] [Indexed: 10/27/2022]
Abstract
OBJECTIVES Genomic characterization of the internationally spread sequence type (ST) 16 carbapenem-resistant Klebsiella pneumoniae. METHODS The complete genomes of three carbapenem producing ST16 K. pneumoniae from Italian patients were analysed by single-nucleotide polymorphism-based phylogeny, core genome multilocus sequence typing, resistance, plasmid, and virulence content and compared with ten genomes of ST16 strains isolated in other countries. Plasmids carrying blaNDM-1 or blaOXA-232 carbapenemase genes were assembled and sequences were analysed. RESULTS The internationally spread ST16 K. pneumoniae clone showed variability in terms of distribution of NDM-1 and OXA-232 type carbapenemases. In some ST16 strains, up to six plasmids can be simultaneously present in the same cell, including ColE-like plasmids carrying blaOXA-232 and IncF plasmids carrying blaNDM-1. The differences observed in plasmid, resistance, and virulence content and core genome suggested that there is not a unique, highly conserved ST16 clone, but instead different variants of this lineage circulate worldwide. CONCLUSIONS The ST16 K. pneumoniae clone has spread worldwide and may become a high-risk clone.
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Affiliation(s)
- P Espinal
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; Servei de Microbiologia Hospital de la Santa Creu i Sant Pau, Institut d'Investigaciò Biomèdica Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - E Nucleo
- Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - M Caltagirone
- Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - V Mattioni Marchetti
- Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - M R Fernandes
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy; Faculty of Pharmaceutical Sciences, University of São Paulo, Brazil
| | - V Biscaro
- Microbiology Department, Treviso Hospital, Treviso, Italy
| | - R Rigoli
- Microbiology Department, Treviso Hospital, Treviso, Italy
| | - A Carattoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - R Migliavacca
- Clinical-Surgical, Diagnostic and Paediatric Sciences Department, Unit of Microbiology and Clinical Microbiology, University of Pavia, Pavia, Italy
| | - L Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Lam MMC, Wyres KL, Judd LM, Wick RR, Jenney A, Brisse S, Holt KE. Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome Med 2018; 10:77. [PMID: 30371343 PMCID: PMC6205773 DOI: 10.1186/s13073-018-0587-5] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/12/2018] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a recognised agent of multidrug-resistant (MDR) healthcare-associated infections; however, individual strains vary in their virulence potential due to the presence of mobile accessory genes. In particular, gene clusters encoding the biosynthesis of siderophores aerobactin (iuc) and salmochelin (iro) are associated with invasive disease and are common amongst hypervirulent K. pneumoniae clones that cause severe community-associated infections such as liver abscess and pneumonia. Concerningly, iuc has also been reported in MDR strains in the hospital setting, where it was associated with increased mortality, highlighting the need to understand, detect and track the mobility of these virulence loci in the K. pneumoniae population. METHODS Here, we examined the genetic diversity, distribution and mobilisation of iuc and iro loci amongst 2503 K. pneumoniae genomes using comparative genomics approaches and developed tools for tracking them via genomic surveillance. RESULTS Iro and iuc were detected at low prevalence (< 10%). Considerable genetic diversity was observed, resolving into five iro and six iuc lineages that show distinct patterns of mobilisation and dissemination in the K. pneumoniae population. The major burden of iuc and iro amongst the genomes analysed was due to two linked lineages (iuc1/iro1 74% and iuc2/iro2 14%), each carried by a distinct non-self-transmissible IncFIBK virulence plasmid type that we designate KpVP-1 and KpVP-2. These dominant types also carry hypermucoidy (rmpA) determinants and include all previously described virulence plasmids of K. pneumoniae. The other iuc and iro lineages were associated with diverse plasmids, including some carrying IncFII conjugative transfer regions and some imported from Escherichia coli; the exceptions were iro3 (mobilised by ICEKp1) and iuc4 (fixed in the chromosome of K. pneumoniae subspecies rhinoscleromatis). Iro/iuc mobile genetic elements (MGEs) appear to be stably maintained at high frequency within known hypervirulent strains (ST23, ST86, etc.) but were also detected at low prevalence in others such as MDR strain ST258. CONCLUSIONS Iuc and iro are mobilised in K. pneumoniae via a limited number of MGEs. This study provides a framework for identifying and tracking these important virulence loci, which will be important for genomic surveillance efforts including monitoring for the emergence of hypervirulent MDR K. pneumoniae strains.
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Affiliation(s)
- Margaret M C Lam
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Louise M Judd
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Adam Jenney
- Department of Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, Victoria, 3004, Australia
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, 75015, Paris, France
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
- London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
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Niu L, Zhao F, Chen J, Nong J, Wang C, Wang J, Gao N, Zhu X, Wu L, Hu S. Isothermal amplification and rapid detection of Klebsiella pneumoniae based on the multiple cross displacement amplification (MCDA) and gold nanoparticle lateral flow biosensor (LFB). PLoS One 2018; 13:e0204332. [PMID: 30273362 PMCID: PMC6166938 DOI: 10.1371/journal.pone.0204332] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/06/2018] [Indexed: 11/18/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a frequent pathogen causing nosocomial infections and outbreaks. We developed a multiple cross displacement amplification (MCDA) assay for the detection of K. pneumoniae, which can get the positive results within 40 minutes’ isothermal amplification. Gold-nanoparticle lateral flow biosensor (LFB) and colorimetric indicators were used for the rapid readouts of MCDA amplification. The detection limit of this assay was 100 fg per reaction at 65°C, which was confirmed to be the optimal amplification temperature according to the real time turbidimeters. For specificity, all of the 30 clinical-source K. pneumoniae strains were positive for the MCDA, and all of the non-K. pneumoniae strains belonging to 31 different species were negative for this MCDA assay. To evaluate the practical applicability of this method, we assessed its detection limit for K. pneumoniae strains in sputum samples (24 CFU per reaction), and DNA templates of 100 sputum samples further underwent the MCDA-LFB tests. All of the sputum samples being positive for K. pneumoniae (30/100) with the culture method were successfully identified with the MCDA assay, the detection power of which was higher than that of polymerase chain reaction (PCR) (25/100). Thus, the MCDA test for K. pneumoniae combined with the gold nanoparticle LFB as the results readout scheme, are simple, specific, and sensitive methods for the rapid diagnosis of K. pneumoniae in clinical samples.
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Affiliation(s)
- Lina Niu
- Department of Pathogen Biology, School of Basic Medicine and Lifescience, Hainan Medical University, Haikou, Hainan, China
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Fan Zhao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jinlong Chen
- Department of Pathogen Biology, School of Basic Medicine and Lifescience, Hainan Medical University, Haikou, Hainan, China
| | - Jinqing Nong
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Chunmei Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Jing Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Naishu Gao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Xiaoxue Zhu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Lei Wu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
| | - Shoukui Hu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, China
- * E-mail:
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219
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de Campos TA, Gonçalves LF, Magalhães KG, de Paulo Martins V, Pappas Júnior GJ, Peirano G, Pitout JDD, Gonçalves GB, Furlan JPR, Stehling EG, Pitondo-Silva A. A Fatal Bacteremia Caused by Hypermucousviscous KPC-2 Producing Extensively Drug-Resistant K64-ST11 Klebsiella pneumoniae in Brazil. Front Med (Lausanne) 2018; 5:265. [PMID: 30298131 PMCID: PMC6161680 DOI: 10.3389/fmed.2018.00265] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/31/2018] [Indexed: 01/09/2023] Open
Abstract
We report a fatal bacteremia caused by Klebsiella pneumoniae in a 60–70-year-old patient from Brazil. The genomic analysis of three isolates (from blood culture, nasal and anal swabs) showed that the bacteremia was caused by a KPC-2 producing extensively drug-resistant K64-ST11 hypermucousviscous K. pneumoniae (hmKP) harboring several virulence and antimicrobial resistance genes. Although the isolates did not present virulence markers associated with hypervirulent K. pneumoniae (hvKP), they showed invasion and toxicity to epithelial Hep-2 cells; resistance to cell microbicidal mechanisms; and blood and human serum survival, evidencing their pathogenic potential. This study highlights the risk of infection caused by hmKp strains not characterized as hvKP as well as the clinical implications and difficulty of treatment, especially in elderly or immunocompromised patients.
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Affiliation(s)
- Tatiana Amabile de Campos
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Brazil
| | - Laura Fernandes Gonçalves
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Brazil
| | - Kelly Grace Magalhães
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Brazil
| | - Vicente de Paulo Martins
- Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Brazil
| | | | - Gisele Peirano
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Johann D D Pitout
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Guilherme Bartolomeu Gonçalves
- Department of Clinical, Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - João Pedro Rueda Furlan
- Department of Clinical, Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical, Toxicological and Bromatological Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
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220
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The intrinsic resistome of Klebsiella pneumoniae. Int J Antimicrob Agents 2018; 53:29-33. [PMID: 30236960 DOI: 10.1016/j.ijantimicag.2018.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/24/2018] [Accepted: 09/09/2018] [Indexed: 01/26/2023]
Abstract
Molecular epidemiology studies aiming at understanding the acquisition of antimicrobial resistance by clinical isolates of Klebsiella pneumoniae are regularly published; however, information on the genes that contribute to its characteristic phenotype of resistance to antibiotics (intrinsic resistome) is scarce. To fill this gap, a K. pneumoniae transposon mutant library was screened and 171 mutants presenting changes in their susceptibility to antibiotics were selected, in which the transposon insertion site was determined in 75. Twenty-seven mutants for which insertion points had been previously identified were included in the analysis. A total of 102 mutants were selected for further studies. In 70 mutants the transposon was inserted in a gene with a known function, whilst in 19 the insertion occurred in genes encoding proteins with unknown functions and 13 insertions occurred in intergenic regions. Moreover, 87 of the insertions were localised in the chromosome, with 15 insertions located in the two plasmids carried by this strain. Whereas some of the mutated genes are already known to be involved in antimicrobial resistance (ampG, acrB, tolC), several of them are involved in regular processes of bacterial physiology, including K. pneumoniae virulence. Together with results published for other organisms, these results support that determinants involved in basic processes of bacterial physiology may contribute to antimicrobial resistance. These findings also indicate that, besides acquired resistance genes, plasmids may harbour other genes belonging to their backbone that can also be involved in resistance.
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221
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Silveira MC, Azevedo da Silva R, Faria da Mota F, Catanho M, Jardim R, R Guimarães AC, de Miranda AB. Systematic Identification and Classification of β-Lactamases Based on Sequence Similarity Criteria: β-Lactamase Annotation. Evol Bioinform Online 2018; 14:1176934318797351. [PMID: 30210232 PMCID: PMC6131288 DOI: 10.1177/1176934318797351] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/08/2018] [Indexed: 12/11/2022] Open
Abstract
β-lactamases, the enzymes responsible for resistance to β-lactam antibiotics, are
widespread among prokaryotic genera. However, current β-lactamase classification
schemes do not represent their present diversity. Here, we propose a workflow to
identify and classify β-lactamases. Initially, a set of curated sequences was
used as a model for the construction of profiles Hidden Markov Models (HMM),
specific for each β-lactamase class. An extensive, nonredundant set of
β-lactamase sequences was constructed from 7 different resistance proteins
databases to test the methodology. The profiles HMM were improved for their
specificity and sensitivity and then applied to fully assembled genomes. Five
hierarchical classification levels are described, and a new class of
β-lactamases with fused domains is proposed. Our profiles HMM provide a better
annotation of β-lactamases, with classes and subclasses defined by objective
criteria such as sequence similarity. This classification offers a solid base to
the elaboration of studies on the diversity, dispersion, prevalence, and
evolution of the different classes and subclasses of this critical enzymatic
activity.
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Affiliation(s)
- Melise Chaves Silveira
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Rangeline Azevedo da Silva
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Fábio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Marcos Catanho
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Rodrigo Jardim
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Ana Carolina R Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Antonio B de Miranda
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
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Shi Q, Lan P, Huang D, Hua X, Jiang Y, Zhou J, Yu Y. Diversity of virulence level phenotype of hypervirulent Klebsiella pneumoniae from different sequence type lineage. BMC Microbiol 2018; 18:94. [PMID: 30157774 PMCID: PMC6116568 DOI: 10.1186/s12866-018-1236-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/16/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Hypervirulent Klebsiella pneumoniae (hvKP) is emerging around the Asian-Pacific region and it is the major cause of the community-acquired pyogenic liver abscesses. Multidrug-resistant hypervirulent Klebsiella pneumoniae (MDR-hvKP) isolates were reported in France, China and Taiwan. However, the international-ally agreed definition for hvKP and the virulence level of hvKP are not clear. RESULTS In this study, 56 hvKP isolates were collected from March 2008 to June 2012 and investigated by string test, capsule serotyping, multilocus sequence typing (MLST), virulence gene detection and serum resistance assay. Among the 56 K. pneumoniae isolates, 64.3% had the hypermucoviscosity phenotype, meanwhile, 64.3% were the K1 serotype and 19.6% were the K2 serotype. Within the K1 serotype, 94.4% were ST23, and within the K2 serotype, ST65, ST86 and ST375 accounted for the same percentage 27.3%. The serum resistance showed statistically normal distribution. According to the 50% lethal dose of Galleria. mellonella infection model, hvKP isolates were divided into high virulence level group and moderate virulence level group. The ability of each method evaluating the virulence level of hvKP was assessed using the area under the receiver operating characteristic curve. CONCLUSIONS K1 ST23 K. pneumoniae was the most prevalent clone of the hvKP. However, K1 ST23 K. pneumoniae was the dominant clone in the moderate virulence level group. MLST was a relatively reliable evaluation method to discriminate the virulence level of hvKP in our study.
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Affiliation(s)
- Qiucheng Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Peng Lan
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Danyan Huang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China. .,Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China.
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223
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Khaertynov KS, Anokhin VA, Rizvanov AA, Davidyuk YN, Semyenova DR, Lubin SA, Skvortsova NN. Virulence Factors and Antibiotic Resistance of Klebsiella pneumoniae Strains Isolated From Neonates With Sepsis. Front Med (Lausanne) 2018; 5:225. [PMID: 30155466 PMCID: PMC6102385 DOI: 10.3389/fmed.2018.00225] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/24/2018] [Indexed: 01/02/2023] Open
Abstract
Introduction:Klebsiella pneumoniae is one of the most important infectious agents in neonates. There are “classic” and hypervirulent strains of K. pneumoniae. The “classic” non-virulent strain of K. pneumoniae, producing extended-spectrum beta-lactamases (ESBLs), is associated with nosocomial infections. Hypervirulent K. pneumoniae strains are associated with invasive infections in previously healthy adult people, and most of them exhibit antimicrobial susceptibility. The role of virulent strains of K. pneumoniae (including hv-KP) in neonatal infections is unknown. The aim of the study was the assessment of the impact of virulence factors and antibiotic resistance of K. pneumoniae strains on clinical features and outcomes of neonatal infection. Materials and Methods: Two groups of infants were enrolled. The first group consisted of 10 neonates with sepsis caused by K. pneumoniae. The second group consisted of 10 neonates with urinary tract infection (UTI) caused by K. pneumoniae. We investigated the susceptibility of K. pneumoniae isolates to antibiotics, the ability of the microorganism to produce ESBL, and virulence factors, including the rmpA gene, aerobactin, and colibactin genes. In neonates with sepsis, we investigated K. pneumoniae isolates, which was taken from the blood, in neonates with UTI—from the urine. Results: In neonates with sepsis testing of K. pneumoniae isolates for ESBL production was positive in 60% of cases, in neonates with UTI—in 40% of cases. All blood and urine ESBL producing K. pneumoniae isolates were resistant to ampicillins, including protected ones, and third-generation cephalosporins. At the same time, these isolates were sensitive to meropenem, amikacin, and ciprofloxacin. The rmpA gene was detected in four blood, and three urine K. pneumoniae isolates. In neonates with sepsis rmpA gene in two cases was detected in ESBL-producing K. pneumoniae isolates. They were infants with meningitis, and both cases were fatal. In the group of infants with UTI, the rmpA gene was detected only in K. pneumoniae isolates not producing ESBL. Aerobactin and colibactin genes were detected in two neonates with sepsis and in three neonates with UTI. In all cases, aerobactin and colibactin genes were detected only in rmpA-positive K. pneumoniae isolates. Out of three fatal outcomes, two cases were caused by hv-KP producing ESBL. Conclusion: The prevalence of virulent strains of K. pneumoniae among neonates with sepsis and other neonatal infection is higher than we think. The most severe forms of neonatal sepsis with an unfavorable outcome in our study were due to virulent strains of K. pneumoniae.
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Affiliation(s)
- Khalit S Khaertynov
- Department of Children Infectious Diseases, Kazan State Medical University, Kazan, Russia
| | - Vladimir A Anokhin
- Department of Children Infectious Diseases, Kazan State Medical University, Kazan, Russia
| | - Albert A Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yuriy N Davidyuk
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Dina R Semyenova
- Department of Children Infectious Diseases, Kazan State Medical University, Kazan, Russia
| | - Sergey A Lubin
- The Neonatal Intensive Care Unit, City Children's Clinical Hospital N1, Kazan, Russia
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224
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Capsular type K54, clonal group 29 and virulence plasmids: an analysis of K54 and non-K54 closely related isolates of Klebsiella pneumoniae. Epidemiol Infect 2018; 146:1813-1823. [DOI: 10.1017/s0950268818001826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
AbstractCapsular type K54 of Klebsiella pneumoniae is associated with hypervirulence and we sought to discover the basis for this among isolates submitted to the UK reference laboratory between 2012 and 2017. Isolates were typed by variable number tandem repeat analysis, and capsular type and virulence elements sought by PCR. The most prevalent type found (15/31 isolates) corresponded to clonal group (CG) 29 and included five representatives carrying rmpA, rmpA2 (regulators of mucoid phenotype), iutA and iroD (from the aerobactin and salmochelin siderophore clusters) associated with virulence plasmids. These included isolate KpvK54, recovered from pus. The remaining isolates did not carry a virulence plasmid. We also noted 11 further related isolates, including NCTC 9159, not of capsular type K54, but nevertheless sometimes associated with sepsis and abscesses. Whole-genome sequencing showed that KpvK54 carried a large virulence plasmid and an ICEKp3-like structure carrying the yersiniabactin cluster, absent in NCTC 9159. Comparative chromosomal analysis with an additional four genomes showed that KpvK54 shared further genes with K1-ST23 hypervirulent isolates, and with LS358, a K54-ST29 isolate from liver abscess puncture fluid. While CG29 isolates displayed varying degrees of virulence, some, especially those with the virulence plasmid (all K54), were clearly associated with hypervirulence.
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225
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Moura Q, Esposito F, Fernandes MR, Espinoza-Muñoz M, Souza TA, Santos SR, Cerdeira L, Cassettari V, Lincopan N. Genome sequence analysis of a hypermucoviscous/hypervirulent and MDR CTX-M-15/K19/ST29 Klebsiella pneumoniae isolated from human infection. Pathog Dis 2018; 75:4705889. [PMID: 29228178 DOI: 10.1093/femspd/ftx121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/28/2017] [Indexed: 11/13/2022] Open
Abstract
The emergence of hypervirulent Klebsiella pneumoniae (hvKP) with multidrug resistance (MDR) profile is a worrisome public health issue. We report the first draft genome sequence of a hypermucoviscous (positive string test) and MDR K. pneumoniae serotype K19, belonging to ST29, isolated from human infection. This strain harboured multiple antimicrobial resistance genes, including blaCTX-M-15, besides yersiniabactin and type 3 fimbriae virulence genes. In vivo experiments carried out with the Galleria mellonella infection model revealed that K. pneumoniae K19/ST29 killed 100% of the larvae at 24 h post-infection, in a similar way to the known hypermucoviscous hvKP K1/ST23 lineage.
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Affiliation(s)
- Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Miriam R Fernandes
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Maria Espinoza-Muñoz
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Tiago A Souza
- Genome Investigation and Analysis Laboratory (GENIAL), Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Silvia R Santos
- Laboratory of Clinical Analysis, Hospital Universitário, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Valéria Cassettari
- Hospital Infection Control Committee, Hospital Universitário, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, CEP 05508-000, Brazil.,Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, CEP 05508-000, Brazil
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226
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Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O, Kibiki GS, Aarestrup FM. Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. Eur J Clin Microbiol Infect Dis 2018; 37:1901-1914. [PMID: 30030694 DOI: 10.1007/s10096-018-3324-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/09/2018] [Indexed: 11/30/2022]
Abstract
This study aimed to use whole-genome sequencing to determine virulence and antimicrobial resistance genes in K. pneumoniae isolated from patients in a tertiary care hospital in Kilimanjaro. K. pneumoniae isolates from patients attending Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced and analysed locally. Sequence analysis was done for identification of virulence and AMR genes. Plasmid and multi-locus sequence typing and capsular or capsular (K) typing were performed and phylogeny was done to ascertain K. pneumoniae relatedness. Stata 13 (College Station, TX, 77845, USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and sequence-predicted resistance. A total of 16 (47.1%) sequence types (STs) and 10 (29.4%) K types were identified in 30 (88.2%) and 17 (50.0%) of all analysed isolates, respectively. K. pneumoniae ST17 were 6 (17.6%). The commonest determinants were blaCTX-M-15 in 16 (47.1%) isolates, blaSHV in 30 (88.2%), blaOXA-1 in 8 (23.5%) and blaTEM-1 in 18 (52.9%) isolates. Resistance genes for aminoglycosides were detected in 21 (61.8%) isolates, fluoroquinolones in 13 (38.2%) and quinolones 34 (100%). Ceftazidime and ceftriaxone showed the strongest agreement between phenotype- and sequence-based resistance results: 93.8%, kappa = 0.87 and p = 0.0002. Yersiniabactin determinant was detected in 12 (35.3%) of K. pneumoniae. The proportion of AMR and virulence determinants detected in K. pneumoniae is alarming. WGS-based diagnostic approach has showed promising potentials in clinical microbiology, hospital outbreak source tracing virulence and AMR detection at KCMC.
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Affiliation(s)
- Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania. .,Kilimanjaro Christian Medical University College, Moshi, Tanzania.
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Marco van Zwetselaar
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.,Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Ole Lund
- Centre for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Gibson S Kibiki
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,East African Health Research Commission, Bujumbura, Burundi
| | - Frank M Aarestrup
- DTU-Food, Centre for Genomic Epidemiology, Technical University of Denmark, Lyngby, Denmark
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227
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Esposito EP, Cervoni M, Bernardo M, Crivaro V, Cuccurullo S, Imperi F, Zarrilli R. Molecular Epidemiology and Virulence Profiles of Colistin-Resistant Klebsiella pneumoniae Blood Isolates From the Hospital Agency "Ospedale dei Colli," Naples, Italy. Front Microbiol 2018; 9:1463. [PMID: 30061868 PMCID: PMC6054975 DOI: 10.3389/fmicb.2018.01463] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Resistance to colistin is increasingly reported in Klebsiella pneumoniae clinical isolates. The aim of this study was to analyze the molecular epidemiology and virulence profiles of 25 colistin-resistant K. pneumoniae blood isolates from the Hospital Agency “Ospedale dei Colli,” Naples, Italy, during 2015 and 2016. Colistin MIC values of isolates ranged from 4 to 256 mg/L. The inactivation of the mgrB gene, encoding a negative regulator of the PhoQ/PhoP signaling system, was the most frequent mechanism of colistin resistance found in 22 out of 25 isolates. Of these, 10 isolates assigned to ST512 and PFGE types A and A4 showed identical frameshift mutation and premature termination of mgrB gene; 4 isolates assigned to ST258 and PFGE types A1 showed non-sense, frameshift mutation, and premature termination; 3 and 1 isolates assigned to ST258 and PFGE A2 and ST512 and PFGE A3, respectively, had insertional inactivation of mgrB gene due to IS5-like mobile element; 2 isolates assigned to ST101 and 1 to ST392 had missense mutations in the mgrB gene, 1 isolate assigned to ST45 showed insertional inactivation of mgrB gene due to IS903-like mobile element. phoQ missense mutations were found in 2 isolates assigned to ST629 and ST101, respectively, which also showed a missense mutation in pmrA gene. The mcr-1-2-3-4 genes were not detected in any isolate. Colistin-resistant K. pneumoniae isolates showed variable virulence profiles in Galleria mellonella infection assays, with the infectivity of two isolates assigned to ST45 and ST629 being significantly higher than that of all other strains (P < 0.001). Interestingly, colistin MIC values proved to make a significant contribution at predicting lethal doses values (LD50 and LD90) of studied isolates in G. mellonella. Our data show that MgrB inactivation is a common mechanism of colistin resistance among K. pneumoniae in our clinical setting. The presence of identical mutations/insertions in isolates of the same ST and PFGE profile suggests the occurrence of clonal expansion and cross-transmission. Although virulence profiles differ among isolates irrespective of their genotypes, our results suggest that high colistin MIC could predict lower infectivity capability of the isolates.
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Affiliation(s)
- Eliana P Esposito
- Department of Public Health, University of Naples "Federico II,", Naples, Italy
| | - Matteo Cervoni
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy.,Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Mariano Bernardo
- Azienda Ospedaliera di Rilievo Nazionale (AORN) dei Colli, V. Monaldi Hospital, Naples, Italy
| | - Valeria Crivaro
- Azienda Ospedaliera di Rilievo Nazionale (AORN) dei Colli, V. Monaldi Hospital, Naples, Italy
| | - Susanna Cuccurullo
- Azienda Ospedaliera di Rilievo Nazionale (AORN) dei Colli, V. Monaldi Hospital, Naples, Italy
| | - Francesco Imperi
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy.,Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples "Federico II,", Naples, Italy.,Centro di Ingegneria Genetica (CEINGE) Biotecnologie Avanzate, Naples, Italy
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228
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Lam MMC, Wyres KL, Duchêne S, Wick RR, Judd LM, Gan YH, Hoh CH, Archuleta S, Molton JS, Kalimuddin S, Koh TH, Passet V, Brisse S, Holt KE. Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nat Commun 2018; 9:2703. [PMID: 30006589 PMCID: PMC6045662 DOI: 10.1038/s41467-018-05114-7] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/31/2018] [Indexed: 01/14/2023] Open
Abstract
Severe liver abscess infections caused by hypervirulent clonal-group CG23 Klebsiella pneumoniae have been increasingly reported since the mid-1980s. Strains typically possess several virulence factors including an integrative, conjugative element ICEKp encoding the siderophore yersiniabactin and genotoxin colibactin. Here we investigate CG23's evolutionary history, showing several deep-branching sublineages associated with distinct ICEKp acquisitions. Over 80% of liver abscess isolates belong to sublineage CG23-I, which emerged in ~1928 following acquisition of ICEKp10 (encoding yersiniabactin and colibactin), and then disseminated globally within the human population. CG23-I's distinguishing feature is the colibactin synthesis locus, which reportedly promotes gut colonisation and metastatic infection in murine models. These data show circulation of CG23 K. pneumoniae decades before the liver abscess epidemic was first recognised, and provide a framework for future epidemiological and experimental studies of hypervirulent K. pneumoniae. To support such studies we present an open access, completely sequenced CG23-I human liver abscess isolate, SGH10.
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Affiliation(s)
- Margaret M C Lam
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Sebastian Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Louise M Judd
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yunn-Hwen Gan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Chu-Han Hoh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Sophia Archuleta
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - James S Molton
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Shirin Kalimuddin
- Department of Infectious Diseases, Singapore General Hospital, Singapore, 169608, Singapore
| | - Tse Hsien Koh
- Department of Microbiology, Singapore General Hospital, Singapore, 169608, Singapore
| | - Virginie Passet
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, 75015, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, 75015, Paris, France
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
- The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom.
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229
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Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM, Jenney AWJ, Brisse S, Holt KE. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microb Genom 2018; 4. [PMID: 29985125 PMCID: PMC6202445 DOI: 10.1099/mgen.0.000196] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mobile genetic elements (MGEs) that frequently transfer within and between bacterial species play a critical role in bacterial evolution, and often carry key accessory genes that associate with a bacteria’s ability to cause disease. MGEs carrying antimicrobial resistance (AMR) and/or virulence determinants are common in the opportunistic pathogen Klebsiella pneumoniae, which is a leading cause of highly drug-resistant infections in hospitals. Well-characterised virulence determinants in K. pneumoniae include the polyketide synthesis loci ybt and clb (also known as pks), encoding the iron-scavenging siderophore yersiniabactin and genotoxin colibactin, respectively. These loci are located within an MGE called ICEKp, which is the most common virulence-associated MGE of K. pneumoniae, providing a mechanism for these virulence factors to spread within the population. Here we apply population genomics to investigate the prevalence, evolution and mobility of ybt and clb in K. pneumoniae populations through comparative analysis of 2498 whole-genome sequences. The ybt locus was detected in 40 % of K. pneumoniae genomes, particularly amongst those associated with invasive infections. We identified 17 distinct ybt lineages and 3 clb lineages, each associated with one of 14 different structural variants of ICEKp. Comparison with the wider population of the family Enterobacteriaceae revealed occasional ICEKp acquisition by other members. The clb locus was present in 14 % of all K. pneumoniae and 38.4 % of ybt+ genomes. Hundreds of independent ICEKp integration events were detected affecting hundreds of phylogenetically distinct K. pneumoniae lineages, including at least 19 in the globally-disseminated carbapenem-resistant clone CG258. A novel plasmid-encoded form of ybt was also identified, representing a new mechanism for ybt dispersal in K. pneumoniae populations. These data indicate that MGEs carrying ybt and clb circulate freely in the K. pneumoniae population, including among multidrug-resistant strains, and should be considered a target for genomic surveillance along with AMR determinants.
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Affiliation(s)
- Margaret M C Lam
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Ryan R Wick
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Kelly L Wyres
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Claire L Gorrie
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Louise M Judd
- 1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Adam W J Jenney
- 2Department Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Sylvain Brisse
- 3Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathryn E Holt
- 4London School of Hygiene and Tropical Medicine, London, UK.,1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
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230
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Rafat C, Messika J, Barnaud G, Dufour N, Magdoud F, Billard-Pomarès T, Gaudry S, Dreyfuss D, Branger C, Decré D, Ricard JD. Hypervirulent Klebsiella pneumoniae, a 5-year study in a French ICU. J Med Microbiol 2018; 67:1083-1089. [PMID: 29972348 DOI: 10.1099/jmm.0.000788] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a leading cause of severe community-acquired pneumonia, liver abscess and disseminated infection in the Far East. Data regarding the incidence, clinical features and microbiological characteristics related to hvKp infections in the Western world are scarce. METHODOLOGY The incidence, clinical features and microbiological characteristics of hvKp infections were investigated through a 5-year survey conducted in a single French intensive care unit. K. pneumoniae strains were screened for hypermucoviscosity based on a string test. Multilocus sequence typing and multiplex PCR analysis targeting virulence genes were performed on string test-positive strains. RESULTS Over a 53-month period, a total of 59 infections due to K. pneumoniae were identified including 26 community-onset infections. Twelve hvKp infections were documented, accounting for 46.1 % of community-acquired K. pneumoniae. Community-acquired pneumonia (n=6), aspiration pneumonia (n=4) and liver abscess (n=2) represented initial sites and mode of infection. Compared to non-hvKp infections, patients with hvKp infections displayed higher rates of multi-organ failure (83.3 % vs 35.7 %; P=0.04), but mortality rates were not different (50 % vs 35 %; P=0.71). Strains K1/ST23 (n=5) and K2/ST86 (n=5) predominated. All hvKp strains displayed wild-type susceptibility. CONCLUSION hvKp represent a potentially underestimated cause of fatal infections in the Western world.
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Affiliation(s)
- Cédric Rafat
- 2Urgences Néphrologiques et Transplantation Rénale, Groupe hospitalier des Hôpitaux Universitaires de l'Est Parisien, Hôpital Tenon, Assistance Publique-Hôpitaux de Paris, Paris, France
- 1Service de Réanimation Médico-Chirurgicale, Hôpital Louis Mourier Assistance Publique-Hôpitaux de Paris, Colombes, France
| | - Jonathan Messika
- 1Service de Réanimation Médico-Chirurgicale, Hôpital Louis Mourier Assistance Publique-Hôpitaux de Paris, Colombes, France
- 3INSERM, IAME, UMR 1137, F-75018 Paris, France
- 4Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Guilène Barnaud
- 5Service de Microbiologie, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes, France
| | - Nicolas Dufour
- 1Service de Réanimation Médico-Chirurgicale, Hôpital Louis Mourier Assistance Publique-Hôpitaux de Paris, Colombes, France
- 6Service de Réanimation médico-chirurgicale, Centre Hospitalier René Dubos, F-95300 Pontoise, France
| | - Fatma Magdoud
- 5Service de Microbiologie, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes, France
| | - Typhaine Billard-Pomarès
- 3INSERM, IAME, UMR 1137, F-75018 Paris, France
- 4Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- 5Service de Microbiologie, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes, France
| | - Stéphane Gaudry
- 1Service de Réanimation Médico-Chirurgicale, Hôpital Louis Mourier Assistance Publique-Hôpitaux de Paris, Colombes, France
- 7Univ Paris Diderot, Sorbonne Paris Cité, ECEVE, UMRS 1123, F-75010 Paris, France
- 8INSERM, ECEVE, U1123, CIC-EC 1425, F-75010 Paris, France
| | - Didier Dreyfuss
- 1Service de Réanimation Médico-Chirurgicale, Hôpital Louis Mourier Assistance Publique-Hôpitaux de Paris, Colombes, France
- 3INSERM, IAME, UMR 1137, F-75018 Paris, France
- 4Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
| | - Catherine Branger
- 3INSERM, IAME, UMR 1137, F-75018 Paris, France
- 4Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
- 5Service de Microbiologie, Hôpital Louis Mourier, Assistance Publique-Hôpitaux de Paris, Colombes, France
| | - Dominique Decré
- 9Sorbonne Université, Paris 06, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), Team E13 (Bacteriology), Paris, France
- 10AP-HP, Microbiology, St-Antoine Hospital, Paris, France
| | - Jean-Damien Ricard
- 1Service de Réanimation Médico-Chirurgicale, Hôpital Louis Mourier Assistance Publique-Hôpitaux de Paris, Colombes, France
- 3INSERM, IAME, UMR 1137, F-75018 Paris, France
- 4Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France
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231
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Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE. Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital. Clin Infect Dis 2018; 67:161-170. [PMID: 29340588 PMCID: PMC6030810 DOI: 10.1093/cid/ciy027] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background Klebsiella pneumoniae is a leading cause of extended-spectrum β-lactamase (ESBL)-producing hospital-associated infections, for which elderly patients are at increased risk. Methods We conducted a 1-year prospective cohort study, in which a third of patients admitted to 2 geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory. Colonizing and clinical isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing. Results K. pneumoniae throat carriage prevalence was 4.1%, rectal carriage 10.8%, and ESBL carriage 1.7%, and the incidence of K. pneumoniae infection was 1.2%. The isolates were diverse, and most patients were colonized or infected with a unique phylogenetic lineage, with no evidence of transmission in the wards. ESBL strains carried blaCTX-M-15 and belonged to clones associated with hospital-acquired ESBL infections in other countries (sequence type [ST] 29, ST323, and ST340). One also carried the carbapenemase blaIMP-26. Genomic and epidemiological data provided evidence that ESBL strains were acquired in the referring hospital. Nanopore sequencing also identified strain-to-strain transmission of a blaCTX-M-15 FIBK/FIIK plasmid in the referring hospital. Conclusions The data suggest the major source of K. pneumoniae was the patient's own gut microbiome, but ESBL strains were acquired in the referring hospital. This highlights the importance of the wider hospital network to understanding K. pneumoniae risk and infection prevention. Rectal screening for ESBL organisms on admission to geriatric wards could help inform patient management and infection control in such facilities.
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Affiliation(s)
- Claire L Gorrie
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mirjana Mirceta
- Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Louise M Judd
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom, Melbourne, Victoria, Australia
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kerrie M Watson
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Peter C Hunter
- Aged Care, Caulfield Hospital, Alfred Health, Melbourne, Victoria, Australia
| | | | - Denis W Spelman
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Adam W J Jenney
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Victoria, Australia
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232
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Zautner AE, Bunk B, Pfeifer Y, Spröer C, Reichard U, Eiffert H, Scheithauer S, Groß U, Overmann J, Bohne W. Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing. J Antimicrob Chemother 2018; 72:2737-2744. [PMID: 29091199 DOI: 10.1093/jac/dkx216] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/07/2017] [Indexed: 01/26/2023] Open
Abstract
Objectives Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for healthcare facilities worldwide. A continuous monitoring of ST distribution and its association with resistance and virulence genes is required for early detection of successful K. pneumoniae lineages. In this study, we used WGS to characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the University Medical Center Göttingen, Germany, between March 2013 and August 2014. Methods Closed genomes for 16 isolates of carbapenemase-producing K. pneumoniae were generated by single molecule real-time technology using the PacBio RSII platform. Results Eight of the 16 isolates showed identical XbaI macrorestriction patterns and shared the same MLST, ST147. The eight ST147 isolates differed by only 1-25 SNPs of their core genome, indicating a clonal origin. Most of the eight ST147 isolates carried four plasmids with sizes of 246.8, 96.1, 63.6 and 61.0 kb and a novel linear plasmid prophage, named pKO2, of 54.6 kb. The blaOXA-48 gene was located on a 63.6 kb IncL plasmid and is part of composite transposon Tn1999.2. The ST147 isolates expressed the yersinabactin system as a major virulence factor. The comparative whole-genome analysis revealed several rearrangements of mobile genetic elements and losses of chromosomal and plasmidic regions in the ST147 isolates. Conclusions Single molecule real-time sequencing allowed monitoring of the genetic and epigenetic microevolution of MDR OXA-48-producing K. pneumoniae and revealed in addition to SNPs, complex rearrangements of genetic elements.
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Affiliation(s)
- Andreas E Zautner
- Institute for Medical Microbiology, University Medical Center, Göttingen, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Yvonne Pfeifer
- Robert Koch Institute, FG13 Nosocomial Infections and Antibiotic Resistance, Wernigerode, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Utz Reichard
- Infection Control and Infectious Diseases, University Medical Center, Göttingen, Germany
| | - Helmut Eiffert
- Institute for Medical Microbiology, University Medical Center, Göttingen, Germany
| | - Simone Scheithauer
- Infection Control and Infectious Diseases, University Medical Center, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology, University Medical Center, Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany and German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Wolfgang Bohne
- Institute for Medical Microbiology, University Medical Center, Göttingen, Germany
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233
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Lin YT, Cheng YH, Juan CH, Wu PF, Huang YW, Chou SH, Yang TC, Wang FD. High mortality among patients infected with hypervirulent antimicrobial-resistant capsular type K1 Klebsiella pneumoniae strains in Taiwan. Int J Antimicrob Agents 2018; 52:251-257. [PMID: 29906566 DOI: 10.1016/j.ijantimicag.2018.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 05/23/2018] [Accepted: 06/02/2018] [Indexed: 01/08/2023]
Abstract
Capsular type K1 Klebsiella pneumoniae, highly virulent strains which are common in Asian countries, can cause pyogenic infections. These hypervirulent strains are usually susceptible to most antimicrobials, except for ampicillin. Little is known regarding the clinical and molecular characteristics of antimicrobial-resistant K1 K. pneumoniae strains. This retrospective study evaluated patients infected with capsular type K1 K. pneumoniae strains in a Taiwanese medical centre between April 2013 and March 2016. Antimicrobial-resistant strains were defined based on non-susceptibility to antimicrobial agents except ampicillin. We compared the clinical outcome of patients infected with and without antimicrobial-resistant strains. The in vivo virulence, genetic relatedness, and resistance mechanisms of these hypervirulent antimicrobial-resistant strains were also investigated. A total of 182 capsular type K1 K. pneumoniae strains were identified, including 18 antimicrobial-resistant strains. The 28-day mortality rate among the 18 cases caused by antimicrobial-resistant strains was significantly higher than that among 164 cases caused by antimicrobial-sensitive strains (50% vs. 10.4%, P < 0.001). Infection with antimicrobial-resistant strain independently increased the 28-day mortality risk. Most antimicrobial-resistant strains were not clonally related, and they exhibited high in vivo virulence in a mouse lethality experiment. The major resistance mechanisms involved the presence of β-lactamases and the overexpression of efflux pumps. In conclusion, hypervirulent antimicrobial-resistant capsular type K1 K. pneumoniae strains can predispose to a fatal outcome. These strains may represent an emerging threat to public health in Taiwan.
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Affiliation(s)
- Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; Institute of Emergency and Critical Care Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Yi-Hsiang Cheng
- Institute of Emergency and Critical Care Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Han Juan
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ping-Feng Wu
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Wei Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Sheng-Hua Chou
- Institute of Emergency and Critical Care Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Tsuey-Ching Yang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Fu-Der Wang
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan; School of Medicine, National Yang-Ming University, Taipei, Taiwan
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Roulston KJ, Bharucha T, Turton JF, Hopkins KL, Mack DJF. A case of NDM-carbapenemase-producing hypervirulent Klebsiella pneumoniae sequence type 23 from the UK. JMM Case Rep 2018; 5:e005130. [PMID: 30425831 PMCID: PMC6230755 DOI: 10.1099/jmmcr.0.005130] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/07/2017] [Indexed: 12/30/2022] Open
Abstract
Introduction Hypervirulent capsular type K1 Klebsiella pneumoniae strains of clonal complex 23 (CC23) are associated with severe community-acquired pyogenic liver abscesses, often complicated by metastatic infections and significant mortality. The majority of hypervirulent strains reported are susceptible to most antibiotics except ampicillin. To the best of our knowledge, this is the first case of New Delhi metallo-β-lactamase (blaNDM)-producing hypervirulent K. pneumoniae from the UK. Case presentation We present a case of pyogenic liver abscess in a 63-year-old female of Bangladeshi origin, with a recent diagnosis of pancreatic cancer. The patient was treated with piperacillin/tazobactam and blood cultures grew a fully susceptible Escherichia coli. Despite antimicrobial therapy and drainage of the abscess, the patient continued to deteriorate and died on day seven of admission. The fluid drained from the liver abscess grew a fully susceptible E. coli and a multi-drug-resistant K. pneumoniae. Two weeks prior to admission, a rectal screening swab grew a metallo-β-lactamase-producing K. pneumoniae. Molecular characterization revealed that both the K. pneumoniae isolates belonged to the hypervirulent K1 cluster of CC23, sequence type 23. The isolate from the rectal screen was positive for the blaNDM metallo-β-lactamase gene. Conclusion The emergence of carbapenemase-producing hypervirulent K. pneumoniae strains presents a new and significant threat to global public health. Management of these infections will be extremely challenging due to the limited treatment options available and they are likely to be associated with an even greater mortality.
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Affiliation(s)
- Kerry J Roulston
- Department of Microbiology, Royal Free London NHS Foundation Trust, Royal Free Site, Pond Street, London NW3 2QG, UK.,Centre for Clinical Microbiology, University College London, London, UK
| | - Tehmina Bharucha
- Department of Microbiology, Royal Free London NHS Foundation Trust, Royal Free Site, Pond Street, London NW3 2QG, UK
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Katie L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Damien J F Mack
- Department of Microbiology, Royal Free London NHS Foundation Trust, Royal Free Site, Pond Street, London NW3 2QG, UK.,Centre for Clinical Microbiology, University College London, London, UK
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235
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Zaman TU, Alrodayyan M, Albladi M, Aldrees M, Siddique MI, Aljohani S, Balkhy HH. Clonal diversity and genetic profiling of antibiotic resistance among multidrug/carbapenem-resistant Klebsiella pneumoniae isolates from a tertiary care hospital in Saudi Arabia. BMC Infect Dis 2018; 18:205. [PMID: 29724185 PMCID: PMC5934806 DOI: 10.1186/s12879-018-3114-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/25/2018] [Indexed: 11/10/2022] Open
Abstract
Background The nexus between resistance determinants, plasmid type, and clonality appears to play a crucial role in the dissemination and survival of carbapenem-resistant Klebsiella pneumoniae (CRKP). The incidence of infections involving CRKP in Saudi Arabia is increasing and there is a need for detailed molecular profiling of this pathogen for CRKP surveillance and control. Methods The resistance determinants of 71 non-redundant CRKP isolates were investigated by polymerase chain reaction (PCR) and sequencing. Plasmid typing was performed using PCR-based replicon typing and the clonality of isolates was determined by multilocus sequence typing. Capsular polysaccharide synthesis genes and other virulence factors were examined using multiplex PCR. Diversity was calculated using DIVEIN, clonal relationship was determined using eBURST, and phylogenetic analysis was performed using SplitsTree4. Results A polyclonal OXA-48 gene alone was the most common carbapenemase detected in 48/71 (67.6%) isolates followed by NDM-1 alone in 9/71 (12.7%) isolates. Coproduction of OXA-48 and NDM-1 was observed in 6/71 (8.5%) isolates. Both carbapenemase genes could be transferred into an Escherichia coli recipient. CTX-M-15 was the most abundant extended-spectrum β-lactamase gene detected in 47/71 (66.2%) isolates, whereas clone-specific CTX-M-14 (ST-199 and -709) was found in 15/71 (21%) isolates. Sixty-seven of 71 isolates were positive for one or more plasmid replicons. The replicons detected were: IncFII; IncFIIK; IncFIA; IncFIB; L/M; IncI1; and IncN. FIIK and L/M were predominant, with 69 and 67% positivity, respectively. All isolates were negative for the magA (K1), rmpA, and K2 genes and presented a non-hypermucoviscous phenotype. Conclusion A polyclonal CRKP reservoir of sequence types (STs)-37, − 199, and − 152 was observed and ST-152 appeared to be a “frequent carrier” of the NDM-1 gene. ST-199, a singleton not previously reported, showed a sequence diversity suggestive of positive selection. A significant association was evident between resistance determinants and the clonal types of K. pneumoniae: all ST-152 isolates were positive for NDM-1 but negative for OXA-48; ST-199 isolates were positive for OXA-48 but negative for NDM-1; and ST-709 and -199 isolates were positive for CTX-M-14. The incidence of certain clonal types in large numbers predicts an outbreak-like situation and warrants stringent surveillance and infection control. Electronic supplementary material The online version of this article (10.1186/s12879-018-3114-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taher Uz Zaman
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia.
| | - Maha Alrodayyan
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Maha Albladi
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Aldrees
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia.,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia
| | | | - Sameera Aljohani
- King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia.,Microbiology Section- King Abdul-Aziz Medical City, Riyadh, Kingdom of Saudi Arabia
| | - Hanan H Balkhy
- Infectious Diseases Section, King Abdullah International Medical Research Center National Guard Health Affairs, P.O. Box 22490, Mail Code 1515, Riyadh, 11426, Kingdom of Saudi Arabia. .,King Saud Bin Abdul-Aziz University of Health Sciences, Riyadh, Kingdom of Saudi Arabia. .,Infection Prevention and Control Prevention, King Abdul-Aziz Medical City, National Guard Health Affairs, P.O. Box 22490, Riyadh-11426, Riyadh, Kingdom of Saudi Arabia.
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236
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Hennequin C, Ravet V, Robin F. Plasmids carrying DHA-1 β-lactamases. Eur J Clin Microbiol Infect Dis 2018; 37:1197-1209. [PMID: 29663096 DOI: 10.1007/s10096-018-3231-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/12/2018] [Indexed: 01/22/2023]
Abstract
The aim of this review is to provide an update on the plasmids mediating DHA-1 cephalosporinase in Klebsiella pneumoniae. These plasmids have been mainly found in this bacterium but not only. The first was isolated from Salmonella sp. in France in the early 1990s. They are currently reported worldwide. BlaDHA-1 beta-lactamase gene is usually co-expressed with many other antibiotic resistance genes such as extended-spectrum β-lactamases (blaCTX-M-, bla SHV -types), oxacillinases (blaOXA-1, blaOXA-30), penicillinases (bla TEM -type), carbapenemases (bla OXA48 , blaKPC-2), aminoglycosides (aacA, aadA, armA), fluoroquinolones (qnrB4, aac6'-1b-cr), and sulfonamide (sul1) resistance genes. Plasmids carrying DHA-1 cephalosporinase have different sizes (22 to 313 kb), belong to diverse groups of incompatibility (R, L/M, FII(k), FIB, A/C2, HI2, HIB), and are self-transferable or not. The multidrug resistance region consists of a mosaic structure composed of resistance genes, insertion sequences, composite transposon, and integrons.
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Affiliation(s)
- Claire Hennequin
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France. .,Laboratoire de Bactériologie, CHU Clermont-Ferrand, 58, rue Montalembert, 63003, Clermont-Ferrand, France.
| | - Viviane Ravet
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, Clermont-Ferrand, France
| | - Frédéric Robin
- Laboratoire de Bactériologie, CHU Clermont-Ferrand, 58, rue Montalembert, 63003, Clermont-Ferrand, France.,Université Clermont Auvergne, UMR INSERM 1071, USC INRA2018, Clermont-Ferrand, France.,Laboratoire associé Résistance des Entérobactéries BLSE/Céphalosporinases, Centre National de Référence Résistance aux Antibiotiques, Clermont-Ferrand, France
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237
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Zhang X, Wang L, Li R, Hou P, Zhang Y, Fang M, Hu B. Presence and characterization of Klebsiella pneumoniae
from the intestinal tract of diarrhoea patients. Lett Appl Microbiol 2018. [DOI: 10.1111/lam.12877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- X. Zhang
- Tai'an Center for Disease Control and Prevention; Tai'an Shandong Province China
| | - L. Wang
- Laiwu Center for Disease Control and Prevention; Laiwu Shandong Province China
| | - R. Li
- Shandong Center for Disease Control and Prevention; Jinan Shandong Province China
| | - P. Hou
- Tai'an Center for Disease Control and Prevention; Tai'an Shandong Province China
| | - Y. Zhang
- Shandong Center for Disease Control and Prevention; Jinan Shandong Province China
| | - M. Fang
- Shandong Center for Disease Control and Prevention; Jinan Shandong Province China
| | - B. Hu
- Shandong Center for Disease Control and Prevention; Jinan Shandong Province China
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238
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Schürch A, Arredondo-Alonso S, Willems R, Goering R. Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches. Clin Microbiol Infect 2018; 24:350-354. [DOI: 10.1016/j.cmi.2017.12.016] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/21/2017] [Accepted: 12/22/2017] [Indexed: 11/30/2022]
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239
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Bokaeian M, Shahraki Zahedani S, Delarampoor A, Atashgah M, Dahmarde B. Evaluation of Antibiotic Resistance Patterns of Clinical Klebsiella pneumoniae Isolates from Educational Hospitals in Zahedan, Iran. MEDICAL LABORATORY JOURNAL 2018. [DOI: 10.29252/mlj.12.3.41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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240
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Harada S, Ishii Y, Saga T, Aoki K, Tateda K. Molecular epidemiology of Klebsiella pneumoniae K1 and K2 isolates in Japan. Diagn Microbiol Infect Dis 2018; 91:354-359. [PMID: 29678299 DOI: 10.1016/j.diagmicrobio.2018.03.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/03/2018] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
Abstract
Although severe infections caused by hypervirulent Klebsiella pneumoniae isolates, such as K1 isolates belonging to sequence type (ST) 23, have been a significant problem in Asian countries, epidemiology of these isolates in Japan remains unclear. We performed a nationwide molecular epidemiological study of K. pneumoniae K1 and K2 isolates in Japan. Of the 259K. pneumoniae isolates collected, 14 and 16 isolates were identified as capsular genotypes K1 and K2, respectively. All K1 isolates were ST23 or its closely related clones and showed high genetic similarity by pulsed-field gel electrophoresis (PFGE) and the DiversiLab system (DL). K2 isolates, belonging to ST14, ST25, ST65, ST86, and ST110, were more genetically diverse than K1 isolates. Isolates belonging to a specific ST showed identical virulence gene profiles with a few exceptions. PFGE and DL results using K1 and K2 isolates were generally in agreement.
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Affiliation(s)
- Sohei Harada
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, 143-8540, Tokyo, Japan; Department of Infectious Diseases, Cancer Institute Hospital, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku 135-8550, Tokyo, Japan.
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, 143-8540, Tokyo, Japan
| | - Tomoo Saga
- Central Laboratory Division, Akita University Hospital 1-1-1 Hondo, Akita 010-8543, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, 143-8540, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, 143-8540, Tokyo, Japan
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241
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Surgers L, Boyd A, Girard PM, Arlet G, Decré D. ESBL-Producing Strain of Hypervirulent Klebsiella pneumoniae K2, France. Emerg Infect Dis 2018; 22:1687-8. [PMID: 27532217 PMCID: PMC4994372 DOI: 10.3201/eid2209.160681] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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242
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Corbella M, Caltagirone M, Gaiarsa S, Mariani B, Sassera D, Bitar I, Muzzi A, Migliavacca R, Scudeller L, Stronati M, Cambieri P. Characterization of an Outbreak of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae in a Neonatal Intensive Care Unit in Italy. Microb Drug Resist 2018; 24:1128-1136. [PMID: 29368992 DOI: 10.1089/mdr.2017.0270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Here we report an outbreak of extended spectrum β-lactamase-producing Klebsiella pneumoniae that occurred in a neonatal intensive care unit in Northern Italy and involved 97 patients. Progressively tightened sets of containment measures were implemented but the epidemic event was stopped only 9 months later. The final, effective, containment strategy consisted of the application of strict geographic cohorting of colonized infants and their nursing staff, the suspension of any new admission and a rigorous daily sterilization protocol for all surfaces and fomites in the ward. A posteriori characterization of the outbreak strain was performed using both traditional microbiology and molecular biology techniques, and whole genome sequencing, allowing to compare outbreak isolates with other strains collected in the previous two years. The results allowed to determine that the outbreak strain had been circulating inside the ward since the year before. Genomic characterization revealed that the strain carried a wide array of virulence and antibiotic resistance determinants, including gene blaTEM-206, which had never been reported in a clinical isolate of K. pneumoniae before. The presence of such a high number of determinants for antibiotic resistance imposes significant therapeutic limitations on the treatment of infections, thus, further epidemiological investigations are needed to evaluate the prevalence of the newly described variant.
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Affiliation(s)
- Marta Corbella
- 1 U.O.C. Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy .,2 Servizio Biometria ed Epidemiologia Clinica, Direzione Scientifica, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy
| | - Mariasofia Caltagirone
- 3 Dipartimento di Scienze Clinico-Chirurgiche Diagnostiche e Pediatriche, Unità di Microbiologia e Microbiologia Clinica, Università di Pavia , Pavia, Italy
| | - Stefano Gaiarsa
- 1 U.O.C. Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy .,4 Dipartimento di Bioscienze, Università degli Studi di Milano , Milano, Italy
| | - Bianca Mariani
- 1 U.O.C. Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy
| | - Davide Sassera
- 5 Dipartimento di Biologia e Biotecnologie "L. Spallanzani," Università degli Studi di Pavia , Pavia, Italy
| | - Ibrahim Bitar
- 3 Dipartimento di Scienze Clinico-Chirurgiche Diagnostiche e Pediatriche, Unità di Microbiologia e Microbiologia Clinica, Università di Pavia , Pavia, Italy
| | - Alba Muzzi
- 6 U.O.C. Direzione Medica di Presidio, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy
| | - Roberta Migliavacca
- 3 Dipartimento di Scienze Clinico-Chirurgiche Diagnostiche e Pediatriche, Unità di Microbiologia e Microbiologia Clinica, Università di Pavia , Pavia, Italy
| | - Luigia Scudeller
- 2 Servizio Biometria ed Epidemiologia Clinica, Direzione Scientifica, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy
| | - Mauro Stronati
- 7 U.O.C. Neonatologia e Terapia Intensiva Neonatale, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy
| | - Patrizia Cambieri
- 1 U.O.C. Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo , Pavia, Italy
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243
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Martin RM, Bachman MA. Colonization, Infection, and the Accessory Genome of Klebsiella pneumoniae. Front Cell Infect Microbiol 2018; 8:4. [PMID: 29404282 PMCID: PMC5786545 DOI: 10.3389/fcimb.2018.00004] [Citation(s) in RCA: 474] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative pathogen that has a large accessory genome of plasmids and chromosomal gene loci. This accessory genome divides K. pneumoniae strains into opportunistic, hypervirulent, and multidrug-resistant groups and separates K. pneumoniae from two closely related species, Klebsiella variicola and Klebsiella quasipneumoniae. Some strains of K. pneumoniae act as opportunistic pathogens, infecting critically ill and immunocompromised patients. These K. pneumoniae are a common cause of health-care associated infections including pneumonia, urinary tract infections (UTIs), and bloodstream infections. K. variicola and K. quasipneumoniae are often clinically indistinguishable from opportunistic K. pneumoniae. Other strains of K. pneumoniae are hypervirulent, infecting healthy people in community settings and causing severe infections including pyogenic liver abscess, endophthalmitis, and meningitis. A third group of K. pneumoniae encode carbapenemases, making them highly antibiotic-resistant. These strains act as opportunists but are exceedingly difficult to treat. All of these groups of K. pneumoniae and related species can colonize the gastrointestinal tract, and the accessory genome may determine if a colonizing strain remains asymptomatic or progresses to cause disease. This review will explore the associations between colonization and infection with opportunistic, antibiotic-resistant, and hypervirulent K. pneumoniae strains and the role of the accessory genome in distinguishing these groups and related species. As K. pneumoniae infections become progressively more difficult to treat in the face of antibiotic resistance and hypervirulent strains, an increased understanding of the epidemiology and pathogenesis of these bacteria is vital.
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Affiliation(s)
| | - Michael A. Bachman
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
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244
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Kan B, Zhou H, Du P, Zhang W, Lu X, Qin T, Xu J. Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the trace. Front Med 2018; 12:23-33. [PMID: 29318441 DOI: 10.1007/s11684-017-0607-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/24/2017] [Indexed: 12/11/2022]
Abstract
Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention.We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.
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Affiliation(s)
- Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
| | - Haijian Zhou
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Wen Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Tian Qin
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, 310003, China.
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245
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Nordberg V, Jonsson K, Giske CG, Iversen A, Aspevall O, Jonsson B, Camporeale A, Norman M, Navér L. Neonatal intestinal colonization with extended-spectrum β-lactamase-producing Enterobacteriaceae-a 5-year follow-up study. Clin Microbiol Infect 2018; 24:1004-1009. [PMID: 29326011 DOI: 10.1016/j.cmi.2017.12.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 12/14/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022]
Abstract
OBJECTIVES To analyse Klebsiella pneumoniae (KP) isolates from an outbreak of extended-spectrum β-lactamase (ESBL)-producing KP and Escherichia coli (EC) among infants admitted to neonatal intensive care units and to determine the duration of the intestinal colonization. METHODS We performed a prospective cohort study of intestinal ESBL-KP/ESBL-EC colonized neonates after a 5-month outbreak in two neonatal intensive care units. Whole genome sequencing, multilocus sequence typing, core genome multilocus sequence typing, pulsed-field electrophoresis and PCR for blaCTX-M were performed on the first isolates. Stool cultures were performed every second month after discharge until 2 years after discharge and at 5 years of age. The last positive samples were analysed with pulsed-field gel electrophoresis and PCR for blaCTX-M. The intestinal relative dominance of ESBL-producing Enterobacteriaceae was determined. RESULTS Thirteen of 17 patients colonized with ESBL-KP/ESBL-EC survived. Isolates from 16 of 17 patients were available for analysis and featured the same strain type of ESBL-KP: sequence type 101. The strain had capsule type K29 and harboured blaCTX-M-15. The virulence genes irp1, irp2, iutA, kfu and mrk were detected in all isolates. The median length of colonization was 12.5 months (range, 5-68 months). After 2 years, two of 13 patients were carriers of ESBL-KP and one of 13 of ESBL-EC. At 5 years of age, one neonate was colonized with ESBL-EC. No infant experienced an ESBL-KP/EC-infection during follow-up. CONCLUSIONS Two years after discharge, almost one fourth of the study participants were ESBL/KP-EC carriers. ESBL-KP sequence type 101 persisted in two of 13 children for 23 to 26 months. One patient was colonized with ESBL-EC at age 5 years.
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Affiliation(s)
- V Nordberg
- Department of Neonatal Medicine, Karolinska University Hospital, Sweden; Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Paediatrics, Karolinska Institutet, Sweden.
| | - K Jonsson
- Department of Neonatal Medicine, Karolinska University Hospital, Sweden
| | - C G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Sweden
| | - A Iversen
- Department of Clinical Microbiology, Karolinska University Hospital, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Sweden
| | - O Aspevall
- The Public Health Agency of Sweden, Stockholm, Sweden
| | - B Jonsson
- Department of Neonatal Medicine, Karolinska University Hospital, Sweden; Department of Women's and Children's Health, Karolinska Institutet, Sweden
| | - A Camporeale
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Sweden
| | - M Norman
- Department of Neonatal Medicine, Karolinska University Hospital, Sweden; Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Paediatrics, Karolinska Institutet, Sweden
| | - L Navér
- Department of Neonatal Medicine, Karolinska University Hospital, Sweden; Department of Clinical Science, Intervention and Technology (CLINTEC), Division of Paediatrics, Karolinska Institutet, Sweden
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246
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Cubero M, Grau I, Tubau F, Pallarés R, Domínguez MÁ, Liñares J, Ardanuy C. Molecular Epidemiology of Klebsiella pneumoniae Strains Causing Bloodstream Infections in Adults. Microb Drug Resist 2017; 24:949-957. [PMID: 29227744 DOI: 10.1089/mdr.2017.0107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Molecular epidemiology of Klebsiella pneumoniae bacteremic strains allows for a better understanding of preventive and therapeutic strategies. Clinical and microbiological characteristics of 348 K. pneumoniae bacteremia cases (2007-2009) were retrospectively characterized by multilocus sequence typing and extended-spectrum beta-lactamases (ESBL) production. Overall, 223 (64.08%) cases were nosocomial (NA), 58 (16.67%) healthcare associated, and 67 (19.25%) community acquired. The main infection origins were urinary tract (16.6%, 50.0%, and 43.3%), biliary tract (10.8%, 24.2%, and 31.3%), and catheter-related infection (39.9%, 5.2%, and 0%). The 30-day mortality rate was around 20%. The rates of resistance were around 45% the highest being among NA cases, and ESBL production was detected in 7.2% of cases. A total of 161 different sequence types were grouped into 13 clonal sets by e-burst analysis. No relationship could be established between clonal sets and the origin of infection or the healthcare-related settings. The high genetic variability among the isolates suggests their intrapatient endogenous origin.
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Affiliation(s)
- Meritxell Cubero
- 1 Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL) , University of Barcelona, Barcelona, Spain .,2 Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain
| | - Imma Grau
- 2 Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain .,3 Infectious Diseases Department, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona , Barcelona, Spain
| | - Fe Tubau
- 1 Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL) , University of Barcelona, Barcelona, Spain .,2 Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain
| | - Román Pallarés
- 2 Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain .,3 Infectious Diseases Department, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), University of Barcelona , Barcelona, Spain
| | - M Ángeles Domínguez
- 1 Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL) , University of Barcelona, Barcelona, Spain .,4 Spanish Network for Research in Infectious Diseases (REIPI RD06/0008) , Barcelona, Spain
| | - Josefina Liñares
- 1 Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL) , University of Barcelona, Barcelona, Spain .,2 Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain
| | - Carmen Ardanuy
- 1 Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge (IDIBELL) , University of Barcelona, Barcelona, Spain .,2 Research Network for Respiratory Diseases (CIBERES), Instituto de Salud Carlos III (ISCIII) , Madrid, Spain
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247
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Garcia-Garcera M, Touchon M, Brisse S, Rocha EPC. Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter. Environ Microbiol 2017; 19:5010-5024. [PMID: 28967182 PMCID: PMC5767740 DOI: 10.1111/1462-2920.13949] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 09/08/2017] [Accepted: 09/26/2017] [Indexed: 01/22/2023]
Abstract
Most bacteria have poorly characterized environmental reservoirs and unknown closely related species. This hampers the study of bacterial evolutionary ecology because both the environment and the genetic background of ancestral lineages are unknown. We combined metagenomics, comparative genomics and phylogenomics to overcome this limitation, to identify novel taxa and to propose environments where they can be isolated. We applied this method to characterize the ecological distribution of known and novel lineages of Acinetobacter spp. We observed two major environmental transitions at deep phylogenetic levels, splitting the genus into three ecologically differentiated clades. One of these has rapidly shifted towards host‐association by acquiring genes involved in bacteria‐eukaryote interactions. We show that environmental perturbations affect species distribution in predictable ways: bovines have very diverse communities of Acinetobacter, unless they were administered antibiotics, in which case they show highly uniform communities of Acinetobacter spp. that resemble those of humans. Our results uncover the diversity of bacterial lineages, overpassing the limitations of classical cultivation methods and highlight the role of the environment in shaping their evolution.
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Affiliation(s)
- Marc Garcia-Garcera
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris 75015, France.,CNRS, UMR3525, Unité de Génétique des Genomes, 25-28 rue Dr. Roux, Paris 75015, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris 75015, France.,CNRS, UMR3525, Unité de Génétique des Genomes, 25-28 rue Dr. Roux, Paris 75015, France
| | - Sylvain Brisse
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris 75015, France.,CNRS, UMR3525, Unité de Génétique des Genomes, 25-28 rue Dr. Roux, Paris 75015, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 25-28 rue Dr Roux, Paris 75015, France.,CNRS, UMR3525, Unité de Génétique des Genomes, 25-28 rue Dr. Roux, Paris 75015, France
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248
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Lee CR, Lee JH, Park KS, Jeon JH, Kim YB, Cha CJ, Jeong BC, Lee SH. Antimicrobial Resistance of Hypervirulent Klebsiella pneumoniae: Epidemiology, Hypervirulence-Associated Determinants, and Resistance Mechanisms. Front Cell Infect Microbiol 2017; 7:483. [PMID: 29209595 PMCID: PMC5702448 DOI: 10.3389/fcimb.2017.00483] [Citation(s) in RCA: 283] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/09/2017] [Indexed: 01/09/2023] Open
Abstract
Klebsiella pneumoniae is one of the most clinically relevant species in immunocompromised individuals responsible for community-acquired and nosocomial infections, including pneumonias, urinary tract infections, bacteremias, and liver abscesses. Since the mid-1980s, hypervirulent K. pneumoniae, generally associated with the hypermucoviscosity phenotype, has emerged as a clinically significant pathogen responsible for serious disseminated infections, such as pyogenic liver abscesses, osteomyelitis, and endophthalmitis, in a generally younger and healthier population. Hypervirulent K. pneumoniae infections were primarily found in East Asia and now are increasingly being reported worldwide. Although most hypervirulent K. pneumoniae isolates are antibiotic-susceptible, some isolates with combined virulence and resistance, such as the carbapenem-resistant hypervirulent K. pneumoniae isolates, are increasingly being detected. The combination of multidrug resistance and enhanced virulence has the potential to cause the next clinical crisis. To better understand the basic biology of hypervirulent K. pneumoniae, this review will provide a summarization and discussion focused on epidemiology, hypervirulence-associated factors, and antibiotic resistance mechanisms of such hypervirulent strains. Epidemiological analysis of recent clinical isolates in China warns the global dissemination of hypervirulent K. pneumoniae strains with extensive antibiotic resistance in the near future. Therefore, an immediate response to recognize the global dissemination of this hypervirulent strain with resistance determinants is an urgent priority.
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Affiliation(s)
- Chang-Ro Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Jung Hun Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Kwang Seung Park
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Jeong Ho Jeon
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Young Bae Kim
- Biotechnology Program, North Shore Community College, Danvers, MA, United States
| | - Chang-Jun Cha
- Department of Systems Biotechnology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, South Korea
| | - Byeong Chul Jeong
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
| | - Sang Hee Lee
- National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, Yongin, South Korea
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249
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Ogrodzki P, Cheung CS, Saad M, Dahmani K, Coxill R, Liang H, Forsythe SJ. Rapid in situ imaging and whole genome sequencing of biofilm in neonatal feeding tubes: A clinical proof of concept. Sci Rep 2017; 7:15948. [PMID: 29162873 PMCID: PMC5698484 DOI: 10.1038/s41598-017-15769-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 11/01/2017] [Indexed: 11/10/2022] Open
Abstract
The bacterial flora of nasogastric feeding tubes and faecal samples were analysed for a low-birth weight (725 g) neonate EGA 25 weeks in intensive care. Samples were collected at age 6 and 8 weeks of life. Optical coherence tomography (OCT) was used to visualise bacterial biofilms inside the nasogastric feeding tubes. The biofilm was heterogeneously distributed along the tube lumen wall, and had a depth of up to 500 µm. The bacterial biofilm and faecal samples included Enterococcus faecalis and Enterobacter hormaechei. Representative strains, recovered from both feeding tubes and faecal samples, were whole genome sequenced using Illumina, Mi-Seq, which revealed indistinguishable strains, each with less than 28 SNP differences, of E. faecalis and E. hormaechei. The E. faecalis strains were from two sequence types (ST191 and ST211) and encoded for a number of traits related to biofilm formation (BopD), adherence (Epb pili), virulence (cps loci, gelatinase, SprE) and antibiotic resistances (IsaA, tetM). The E. hormaechei were all ST106, and encoded for blaACT-15 β–lactamase and fosfomycin resistance (fosA). This proof of concept study demonstrates that bacterial flora within the neonatal feeding tubes may influence the bacterial colonisation of the intestinal tract and can be visualised non-destructively using OCT.
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Affiliation(s)
- Pauline Ogrodzki
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Chi Shing Cheung
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Mohamed Saad
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Khaled Dahmani
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Rebecca Coxill
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Haida Liang
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
| | - Stephen J Forsythe
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
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250
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Samuelsen Ø, Overballe-Petersen S, Bjørnholt JV, Brisse S, Doumith M, Woodford N, Hopkins KL, Aasnæs B, Haldorsen B, Sundsfjord A. Molecular and epidemiological characterization of carbapenemase-producing Enterobacteriaceae in Norway, 2007 to 2014. PLoS One 2017; 12:e0187832. [PMID: 29141051 PMCID: PMC5687771 DOI: 10.1371/journal.pone.0187832] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/26/2017] [Indexed: 12/25/2022] Open
Abstract
The prevalence of carbapenemase-producing Enterobacteriaceae (CPE) is increasing worldwide. Here we present associated patient data and molecular, epidemiological and phenotypic characteristics of all CPE isolates in Norway from 2007 to 2014 confirmed at the Norwegian National Advisory Unit on Detection of Antimicrobial Resistance. All confirmed CPE isolates were characterized pheno- and genotypically, including by whole genome sequencing (WGS). Patient data were reviewed retrospectively. In total 59 CPE isolates were identified from 53 patients. Urine was the dominant clinical sample source (37%) and only 15% of the isolates were obtained from faecal screening. The majority of cases (62%) were directly associated with travel or hospitalization abroad, but both intra-hospital transmission and one inter-hospital outbreak were observed. The number of CPE cases/year was low (2–14 cases/year), but an increasing trend was observed. Klebsiella spp. (n = 38) and E. coli (n = 14) were the dominant species and blaKPC (n = 20), blaNDM (n = 19), blaOXA-48-like (n = 12) and blaVIM (n = 7) were the dominant carbapenemase gene families. The CPE isolates were genetically diverse except for K. pneumoniae where clonal group 258 associated with blaKPC dominated. All isolates were multidrug-resistant and a significant proportion (21%) were resistant to colistin. Interestingly, all blaOXA-48-like, and a large proportion of blaNDM-positive Klebsiella spp. (89%) and E. coli (83%) isolates were susceptible in vitro to mecillinam. Thus, mecillinam could have a role in the treatment of uncomplicated urinary tract infections caused by OXA-48- or NDM-producing E. coli or K. pneumoniae. In conclusion, the impact of CPE in Norway is still limited and mainly associated with travel abroad, reflected in the diversity of clones and carbapenemase genes.
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Affiliation(s)
- Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Søren Overballe-Petersen
- Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Katie L. Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, United Kingdom
| | - Bettina Aasnæs
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Bjørg Haldorsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
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