1
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Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L, Negus D. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36156193 DOI: 10.1099/mic.0.001247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
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Affiliation(s)
| | - Preetha Shibu
- Life Sciences, University of Westminster, London, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | | | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
| | - David Negus
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
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2
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Cuénod A, Wüthrich D, Seth-Smith HMB, Ott C, Gehringer C, Foucault F, Mouchet R, Kassim A, Revathi G, Vogt DR, von Felten S, Bassetti S, Tschudin-Sutter S, Hettich T, Schlotterbeck G, Homberger C, Casanova C, Moran-Gilad J, Sagi O, Rodríguez-Sánchez B, Müller F, Aerni M, Gaia V, van Dessel H, Kampinga GA, Müller C, Daubenberger C, Pflüger V, Egli A. Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study. Genome Med 2021; 13:150. [PMID: 34517886 PMCID: PMC8438989 DOI: 10.1186/s13073-021-00960-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently been described, yet their clinical impact and antibiotic resistance profiles are largely unknown. We aimed to explore Klebsiella group- and species-specific clinical impact, antimicrobial resistance (AMR) and virulence. METHODS We analysed whole-genome sequence data of a diverse selection of Klebsiella spp. isolates and identified resistance and virulence factors. Using the genomes of 3594 Klebsiella isolates, we predicted the masses of 56 ribosomal subunit proteins and identified species-specific marker masses. We then re-analysed over 22,000 Matrix-Assisted Laser Desorption Ionization - Time Of Flight (MALDI-TOF) mass spectra routinely acquired at eight healthcare institutions in four countries looking for these species-specific markers. Analyses of clinical and microbiological endpoints from a subset of 957 patients with infections from Klebsiella species were performed using generalized linear mixed-effects models. RESULTS Our comparative genomic analysis shows group- and species-specific trends in accessory genome composition. With the identified species-specific marker masses, eight Klebsiella species can be distinguished using MALDI-TOF MS. We identified K. pneumoniae (71.2%; n = 12,523), K. quasipneumoniae (3.3%; n = 575), K. variicola (9.8%; n = 1717), "K. quasivariicola" (0.3%; n = 52), K. oxytoca (8.2%; n = 1445), K. michiganensis (4.8%; n = 836), K. grimontii (2.4%; n = 425) and K. huaxensis (0.1%; n = 12). Isolates belonging to the K. oxytoca group, which includes the species K. oxytoca, K. michiganensis and K. grimontii, were less often resistant to 4th-generation cephalosporins than isolates of the K. pneumoniae group, which includes the species K. pneumoniae, K. quasipneumoniae, K. variicola and "K. quasivariicola" (odds ratio = 0.17, p < 0.001, 95% confidence interval [0.09,0.28]). Within the K. pneumoniae group, isolates identified as K. pneumoniae were more often resistant to 4th-generation cephalosporins than K. variicola isolates (odds ratio = 2.61, p = 0.003, 95% confidence interval [1.38,5.06]). K. oxytoca group isolates were found to be more likely associated with invasive infection to primary sterile sites than K. pneumoniae group isolates (odds ratio = 2.39, p = 0.0044, 95% confidence interval [1.05,5.53]). CONCLUSIONS Currently misdiagnosed Klebsiella spp. can be distinguished using a ribosomal marker-based approach for MALDI-TOF MS. Klebsiella groups and species differed in AMR profiles, and in their association with invasive infection, highlighting the importance for species identification to enable effective treatment options.
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Affiliation(s)
- Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland.
| | - Daniel Wüthrich
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Chantal Ott
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Christian Gehringer
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | | | | | - Ali Kassim
- Aga Khan University Hospital, Nairobi, Kenya
| | | | - Deborah R Vogt
- Department of Clinical Research, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Stefanie von Felten
- Department of Clinical Research, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Stefano Bassetti
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Timm Hettich
- Division of Instrumental Analytics, School of Applied Sciences (FHNW), Muttenz, Switzerland
| | - Götz Schlotterbeck
- Division of Instrumental Analytics, School of Applied Sciences (FHNW), Muttenz, Switzerland
| | - Christina Homberger
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jacob Moran-Gilad
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Soroka University Medical Center, Beer Sheva, Israel
| | - Orli Sagi
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Soroka University Medical Center, Beer Sheva, Israel
| | - Belén Rodríguez-Sánchez
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | | | - Valeria Gaia
- Servizio di microbiologia EOLAB, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Helke van Dessel
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Greetje A Kampinga
- Department of Medical Microbiology & Infection prevention, University of Groningen, Groningen, the Netherlands
- University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | | | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Department of Sciences, University of Basel, Basel, Switzerland
| | | | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland.
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3
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Merla C, Rodrigues C, Passet V, Corbella M, Thorpe HA, Kallonen TVS, Zong Z, Marone P, Bandi C, Sassera D, Corander J, Feil EJ, Brisse S. Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov. Front Microbiol 2019; 10:2360. [PMID: 31708881 PMCID: PMC6824210 DOI: 10.3389/fmicb.2019.02360] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 09/27/2019] [Indexed: 02/05/2023] Open
Abstract
Klebsiella oxytoca causes opportunistic human infections and post-antibiotic haemorrhagic diarrhea. This Enterobacteriaceae species is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4 and Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from, Klebsiella michiganensis (Ko1), K. oxytoca (Ko2), K. huaxiensis (Ko8), and K. grimontii (Ko6). The average nucleotide identity (ANI) of Ko3 and Ko4 were 90.7% with K. huaxiensis and 95.5% with K. grimontii, respectively. In addition, three strains of K. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human feces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4, and Ko8 from the other K. oxytoca species. Based on these results, we propose the names Klebsiella spallanzanii for the Ko3 phylogroup, with SPARK_775_C1T (CIP 111695T and DSM 109531T) as type strain, and Klebsiella pasteurii for Ko4, with SPARK_836_C1T (CIP 111696T and DSM 109530T) as type strain. Strains of K. spallanzanii were isolated from human urine, cow feces, and farm surfaces, while strains of K. pasteurii were found in fecal carriage from humans, cows, and turtles.
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Affiliation(s)
- Cristina Merla
- Fondazione IRCCS Policlinico San Matteo, Unità Operativa Complessa Microbiologia e Virologia, Pavia, Italy.,Scuola di Specializzazione in Microbiologia e Virologia, Università degli Studi di Pavia, Pavia, Italy
| | - Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Marta Corbella
- Fondazione IRCCS Policlinico San Matteo, Unità Operativa Complessa Microbiologia e Virologia, Pavia, Italy
| | - Harry A Thorpe
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Teemu V S Kallonen
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom.,Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Piero Marone
- Fondazione IRCCS Policlinico San Matteo, Unità Operativa Complessa Microbiologia e Virologia, Pavia, Italy
| | - Claudio Bandi
- Department of Biosciences, University of Milan, Milan, Italy.,Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Davide Sassera
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Jukka Corander
- Infection Genomics, Wellcome Sanger Institute, Cambridge, United Kingdom.,Department of Biostatistics, University of Oslo, Oslo, Norway.,Department of Mathematics and Statistics, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
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4
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Passet V, Brisse S. Description of Klebsiella grimontii sp. nov. Int J Syst Evol Microbiol 2018; 68:377-381. [DOI: 10.1099/ijsem.0.002517] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Virginie Passet
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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5
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Unusual carbapenem resistant but ceftriaxone and cefepime susceptible Klebsiella oxytoca isolated from a blood culture: Case report and whole-genome sequencing investigation. IDCases 2017; 11:9-11. [PMID: 29204354 PMCID: PMC5709312 DOI: 10.1016/j.idcr.2017.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 01/13/2023] Open
Abstract
A carbapenem resistant but ceftriaxone and cefepime susceptible Klebsiella oxytoca was isolated from the blood of a patient with polymicrobial bacteremia after 2 weeks of ertapenem treatment. Whole-genome sequencing identified no carbapenemase gene nor plasmid, but only blaOXY-2-8 gene with a mutation in the promoter that's been reported to increase its expression. Two other specific carbapenem resistance mechanisms including mutated porin genes and the AcrAB-TolC efflux system genes were also identified. Clinicians need to be aware of such unusual antibiogram and should not assume carbapenems are always broader spectrum antibiotics than expanded-spectrum cephalosporins.
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6
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Characterization of Piperacillin/Tazobactam-Resistant Klebsiella oxytoca Recovered from a Nosocomial Outbreak. PLoS One 2015; 10:e0142366. [PMID: 26539828 PMCID: PMC4634934 DOI: 10.1371/journal.pone.0142366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/21/2015] [Indexed: 11/19/2022] Open
Abstract
We characterized 12 clinical isolates of Klebsiella oxytoca with the extended-spectrum β-lactamase (ESBL) phenotype (high minimum inhibitory concentration [MIC] values of ceftriaxone) recovered over 9 months at a university hospital in Japan. To determine the clonality of the isolates, we used pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and PCR analyses to detect blaRBI, which encodes the β-lactamase RbiA, OXY-2-4 with overproduce-type promoter. Moreover, we performed the isoelectric focusing (IEF) of β-lactamases, and the determination of the MICs of β-lactams including piperacillin/tazobactam for 12 clinical isolates and E. coli HB101 with pKOB23, which contains blaRBI, by the agar dilution method. Finally, we performed the initial screening and phenotypic confirmatory tests for ESBLs. Each of the 12 clinical isolates had an identical PFGE pulsotype and MLST sequence type (ST9). All 12 clinical isolates harbored identical blaRBI. The IEF revealed that the clinical isolate produced only one β-lactamase. E. coli HB101 (pKOB23) and all 12 isolates demonstrated equally resistance to piperacillin/tazobactam (MICs, >128 μg/ml). The phenotypic confirmatory test after the initial screening test for ESBLs can discriminate β-lactamase RbiA-producing K. oxytoca from β-lactamase CTX-M-producing K. oxytoca. Twelve clinical isolates of K. oxytoca, which were recovered from an outbreak at one university hospital, had identical genotypes and produced β-lactamase RbiA that conferred resistance to piperacillin/tazobactam. In order to detect K. oxytoca isolates that produce RbiA to promote research concerning β-lactamase RbiA-producing K. oxytoca, the phenotypic confirmatory test after the initial screening test for ESBLs would be useful.
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7
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Izdebski R, Fiett J, Urbanowicz P, Baraniak A, Derde LPG, Bonten MJM, Carmeli Y, Goossens H, Hryniewicz W, Brun-Buisson C, Brisse S, Gniadkowski M. Phylogenetic lineages, clones and β-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins. J Antimicrob Chemother 2015; 70:3230-7. [PMID: 26318191 DOI: 10.1093/jac/dkv273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/10/2015] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES The objective of this study was to examine Klebsiella oxytoca clonal and phylogenetic diversity, based on an international collection of carriage isolates non-susceptible to expanded-spectrum cephalosporins (ESCs). METHODS The study material comprised 68 rectal carriage K. oxytoca isolates non-susceptible to ESCs recovered in 2008-11 from patients in 14 hospitals across Europe and Israel. ESC resistance was tested phenotypically; genes encoding ESBLs, AmpC cephalosporinases and carbapenemases were amplified and sequenced. The isolates were typed by PFGE and MLST, followed by sequencing of blaOXY genes. RESULTS MLST and PFGE distinguished 34 STs and 47 pulsotypes among the isolates, respectively. Six STs were split into several pulsotypes each. Five STs were more prevalent (n = 2-9) and occurred in several countries each, including ST2, ST9 and ST141, which belong to a growing international clonal complex (CC), CC2. Four phylogenetic lineages were distinguished, each with another type of chromosomal OXY-type β-lactamase. Three of these, with OXY-1/-5, OXY-2 types and OXY-4, corresponded to previously described phylogroups KoI, KoII and KoIV, respectively. A single isolate from Israel represented a distinct lineage with a newly defined OXY-7 type. The phylogroups showed interesting differences in mechanisms of ESC resistance; KoI strains rarely overexpressed the OXY enzymes but commonly produced ESBLs, whereas KoII strains often were OXY hyperproducers and carried ESBLs much less frequently. AmpCs (DHA-1) and carbapenemases (VIM-1) occurred sporadically. CONCLUSIONS The study confirmed the high genetic diversity of the collection of K. oxytoca ESC-non-susceptible isolates, composed of phylogroups with distinct types of OXY-type β-lactamases, and revealed some STs of broad geographical distribution.
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Affiliation(s)
- R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - J Fiett
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - L P G Derde
- Department of Medical Microbiology and Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M J M Bonten
- Department of Medical Microbiology and Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Y Carmeli
- Division of Epidemiology and Preventive Medicine, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - H Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - W Hryniewicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - C Brun-Buisson
- Service de reanimation médicale, INSERM, U957 & Université Paris-Est, Créteil, France
| | - S Brisse
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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Younes A, Hamouda A, Amyes S. First Report of a Novel Extended-Spectrum Beta-Lactamase KOXY-2 ProducingKlebsiella oxytocathat Hydrolyses Cefotaxime and Ceftazidime. J Chemother 2013; 23:127-30. [DOI: 10.1179/joc.2011.23.3.127] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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9
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Liang YH, Gao R, Su XD. Structural insights into the broadened substrate profile of the extended-spectrum β-lactamase OXY-1-1 fromKlebsiella oxytoca. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1460-7. [DOI: 10.1107/s090744491203466x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 08/03/2012] [Indexed: 11/10/2022]
Abstract
Klebsiella oxytocais a pathogen that causes serious infections in hospital patients. It shows resistance to many clinically used β-lactam antibiotics by producing chromosomally encoded OXY-family β-lactamases. Here, the crystal structure of an OXY-family β-lactamase, OXY-1-1, determined at 1.93 Å resolution is reported. The structure shows that the OXY-1-1 β-lactamase has a typical class A β-lactamase fold and exhibits greater similarity to CTX-M-type β-lactamases than to TEM-family or SHV-family β-lactamases. It is also shown that the enzyme provides more space around the active cavity for theR1andR2substituents of β-lactam antibiotics. The half-positive/half-negative distribution of surface electrostatic potential in the substrate-binding pocket indicates the preferred properties of substrates or inhibitors of the enzyme. The results reported here provide a structural basis for the broadened substrate profile of the OXY-family β-lactamases.
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10
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[Enterobacteriaceae and beta-lactams : wild susceptibility patterns]. ACTA ACUST UNITED AC 2012; 60:112-26. [PMID: 22280847 DOI: 10.1016/j.patbio.2011.12.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 12/07/2011] [Indexed: 11/21/2022]
Abstract
Four susceptibility patterns of wild types of enterobacteria against old beta-lactams including aminopenicillins, carboxypenicillins and first-generation cephalosporins were individualized during the 1980s : susceptible, penicillinase low level, cephalosporinase and a combination of penicillinase and cephalosporinase. Such indirect detection of a mechanism of resistance allowed an interpretative reading for this class of antibiotics. At the present time, seven susceptibility patterns were proposed for this family of gram negative bacilli. Nevertheless, an analysis of results in terms of MICs and diameters of inhibition zone sizes of the main bacterial species of enterobacteria, mainly obtained from the databank of European Committee on Antimicrobial Susceptibility Testing (EUCAST), compared to that observed when overproducing strains were isolated in vivo and in vitro and to the type of beta-lactamase identified and their amino acid sequences conducted to a proposal of five susceptibility patterns. The fifth wild type individualized in several enterobacteria since 2005 is related to the synthesis of various chromosomal extended-spectrum beta-lactamases (ESBL) which hydrolyze many beta-lactams including oxyimino-cephalosporins such as ceftriaxone or cefotaxime. Their expression in a wild strain is characteristic and conducted to our interest for their role as progenitors of the transferable CTM-M types. Otherwise, a medical biologist must consider the possibility of selection of a mutant with a chromosomal overproduced beta-lactamase. But within the same beta-lactam susceptibility pattern such as for Klebsiella pneumoniae and K. oxytoca or Citrobacter amalonaticus, the spectrum of inactivation will be highly variable according to the type of enzyme overproduced. Finally, a nice synergy observed between clavulanic acid and cefotaxime or ceftriaxone or even aztreonam does not mean anytime a transferable ESBL. In some cases according to the result of enterobacterial identification, the epidemiological impact will be very low, because without multidrug resistance (MDR).
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11
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Stojowska K, Krawczyk B, Kałuzewski S, Kur J. Retrospective analysis of the genetic diversity of Klebsiella oxytoca isolated in Poland over a 50-year period. Eur J Clin Microbiol Infect Dis 2009; 28:1263-6. [PMID: 19562392 DOI: 10.1007/s10096-009-0768-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 06/01/2009] [Indexed: 12/25/2022]
Abstract
Population genetics analyses and determination of the phylogenetic relationships between strains have proven to be extremely useful approaches, enabling deeper insights into the epidemiological pattern of bacterial species. There is no longitudinal data describing the molecular epidemiology of Klebsiella oxytoca strains that are opportunistic pathogens responsible for an increasing number of multi-resistant infections in hospitals. The aim of the present study was to assess the genetic diversity of K. oxytoca strains over a 50-year period using internal transcribed spacer polymerase chain reaction (ITS-PCR) and PCR MP (ang. PCR melting profiles) genotyping methods on a large collection of strains isolated from the patients of several hospitals in Poland. The phylogenetic analysis based on ITS-PCR exhibited six distinct branches. Two main groups, KoX and KoY, with four and two sub-groups within KoX and KoY, respectively, have been identified. Typing by the PCR MP method showed a higher level of genetic diversity. However, all K. oxytoca strains were also divided into six genotype groups (KoA, KoB, KoC, KoD, KoE and KoF). In conclusion, we found that the ITS-PCR and PCR MP methods are useful for the phylogenetic delineation of genetic groups in K. oxytoca.
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Affiliation(s)
- K Stojowska
- Department of Microbiology, Gdańsk University of Technology, ul. G. Narutowicza 11/12, 80-233, Gdańsk, Poland
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Monstein HJ, Tärnberg M, Nilsson LE. Molecular identification of CTX-M and blaOXY/K1 beta-lactamase genes in Enterobacteriaceae by sequencing of universal M13-sequence tagged PCR-amplicons. BMC Infect Dis 2009; 9:7. [PMID: 19161622 PMCID: PMC2651175 DOI: 10.1186/1471-2334-9-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 01/22/2009] [Indexed: 11/10/2022] Open
Abstract
Background Plasmid encoded blaCTX-M enzymes represent an important sub-group of class A β-lactamases causing the ESBL phenotype which is increasingly found in Enterobacteriaceae including Klebsiella spp. Molecular typing of clinical ESBL-isolates has become more and more important for prevention of the dissemination of ESBL-producers among nosocomial environment. Methods Multiple displacement amplified DNA derived from 20 K. pneumoniae and 34 K. oxytoca clinical isolates with an ESBL-phenotype was used in a universal CTX-M PCR amplification assay. Identification and differentiation of blaCTX-M and blaOXY/K1 sequences was obtained by DNA sequencing of M13-sequence-tagged CTX-M PCR-amplicons using a M13-specific sequencing primer. Results Nine out of 20 K. pneumoniae clinical isolates had a blaCTX-M genotype. Interestingly, we found that the universal degenerated primers also amplified the chromosomally located K1-gene in all 34 K. oxytoca clinical isolates. Molecular identification and differentiation between blaCTX-M and blaOXY/K1-genes could only been achieved by sequencing of the PCR-amplicons. In silico analysis revealed that the universal degenerated CTX-M primer-pair used here might also amplify the chromosomally located blaOXY and K1-genes in Klebsiella spp. and K1-like genes in other Enterobacteriaceae. Conclusion The PCR-based molecular typing method described here enables a rapid and reliable molecular identification of blaCTX-M, and blaOXY/K1-genes. The principles used in this study could also be applied to any situation in which antimicrobial resistance genes would need to be sequenced.
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Affiliation(s)
- Hans-Jürg Monstein
- Clinical Microbiology-LMC, University Hospital S-581 85 Linköping, Sweden.
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Fevre C, Jbel M, Passet V, Weill FX, Grimont PAD, Brisse S. Six groups of the OXY beta-Lactamase evolved over millions of years in Klebsiella oxytoca. Antimicrob Agents Chemother 2005; 49:3453-62. [PMID: 16048960 PMCID: PMC1196214 DOI: 10.1128/aac.49.8.3453-3462.2005] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity and evolution of the class A OXY beta-lactamase from Klebsiella oxytoca were investigated and compared to housekeeping gene diversity. The entire bla(OXY) coding region was sequenced in 18 clinical isolates representative of the four K. oxytoca beta-lactamase gene groups bla(OXY-1) to bla(OXY-4) and of two new groups identified here, bla(OXY-5) (with four isolates with pI 7.2 and one with pI 7.7) and bla(OXY-6) (with four isolates with pI 7.75 and three with pI 8.1). Genes bla(OXY-5) and bla(OXY-6) showed 99.8% within-group nucleotide similarity but differed from each other by 4.2% and from bla(OXY-1), their closest relative, by 2.5% and 2.9%, respectively. Antimicrobial susceptibility to beta-lactams was similar among OXY groups. Nucleotide sequence diversity of the 16S rRNA (1,454 bp), rpoB (940 bp), gyrA (383 bp), and gapDH (573 bp) genes was in agreement with the beta-lactamase gene phylogeny. Strains with bla(OXY-1), bla(OXY-2), bla(OXY-3), bla(OXY-4), and bla(OXY-6) genes formed five phylogenetic groups, named KoI, KoII, KoIII, KoIV, and KoVI, respectively. Isolates harboring bla(OXY-5) appeared to represent an emerging lineage within KoI. We estimated that the bla(OXY) gene has been evolving within K. oxytoca for approximately 100 million years, using as calibration the 140-million-year estimation of the Escherichia coli-Salmonella enterica split. These results show that the bla(OXY) gene has diversified along K. oxytoca phylogenetic lines over long periods of time without concomitant evolution of the antimicrobial resistance phenotype.
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Affiliation(s)
- Cindy Fevre
- Unité Biodiversité des Bactéries Pathogènes Emergentes (U389 INSERM), Institut Pasteur, 25-28 rue du Dr Roux, 75724 Paris Cedex 15, France
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Decré D, Burghoffer B, Gautier V, Petit JC, Arlet G. Outbreak of multi-resistant Klebsiella oxytoca involving strains with extended-spectrum β-lactamases and strains with extended-spectrum activity of the chromosomal β-lactamase. J Antimicrob Chemother 2004; 54:881-8. [PMID: 15472005 DOI: 10.1093/jac/dkh440] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This study was conducted to analyse broad-spectrum cephalosporin-resistant Klebsiella oxytoca strains. METHODS The 57 isolates studied were recovered from clinical specimens (n=23) or from rectal swabs (n=34) during a 26-month period. Antibiotic susceptibility patterns were determined using standard agar diffusion and dilution methods including the synergy test between extended-spectrum cephalosporins and clavulanic acid. ERIC-2 PCR and pulsed-field gel electrophoresis (PFGE) methods were used to study the clonal relatedness of the strains. Plasmid-mediated and chromosomal beta-lactamases were characterized by mating and specific bla gene amplification and sequencing. RESULTS Four different antibiotic resistance patterns were identified whereas ERIC-2 PCR and PFGE revealed six main profiles. Extended-spectrum beta-lactamases (ESBLs) were found in 32 strains: TEM-7 (n=26), TEM-129 (n=1), TEM-3 (n=4), SHV-2 (n=1). The new TEM-type beta-lactamase, TEM-129, differed from TEM-7 by one mutation (Glu-104-->Lys). All TEM-7 or TEM-129 producers were genetically related. Twenty-five other strains with identical ERIC-2 PCR and PFGE profiles harboured a bla(OXY-2) gene different from the reference gene: 24 strains displayed one substitution (Ala-237-->Ser) in the KTG motif and one strain, highly resistant to ceftazidime, showed an additional substitution (Pro-167-->Ser). CONCLUSIONS The study demonstrated that the majority of strains (n=52) harbouring the OXY-2-type beta-lactamase corresponded to two clones. The first clone (n=27) corresponded to ESBL-producing strains. The second clone (n=25) displayed extended-spectrum activity of the chromosomal beta-lactamase.
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Affiliation(s)
- Dominique Decré
- UPRES n EA2392, Faculté de Médecine, UFR Saint-Antoine, Université Paris 6.
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Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother 2004. [PMID: 15215087 DOI: 10.1128/aac.48.7.2400-2408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We investigated the diversity of the chromosomal class A beta-lactamase gene in Klebsiella pneumoniae in order to study the evolution of the gene. A 789-bp portion was sequenced in a panel of 28 strains, representative of three phylogenetic groups, KpI, KpII, and KpIII, recently identified in K. pneumoniae and of different chromosomal beta-lactamase variants previously identified. Three groups of sequences were found, two of them corresponding to the families SHV (pI 7.6) and LEN (pI 7.1), respectively, and one, more heterogeneous, corresponding to a new family that we named OKP (for other K. pneumoniae beta-lactamase). Levels of susceptibility to ampicillin, cefuroxime, cefotaxime, ceftazidime, and aztreonam and inhibition by clavulanic acid were similar in the three groups. One new SHV variant, seven new LEN variants, and four OKP variants were identified. The OKP variants formed two subgroups based on nucleotide sequences, one with pIs of 7.8 and 8.1 and the other with pIs of 6.5 and 7.0. The nucleotide sequences of the housekeeping genes gyrA, coding for subunit A of gyrase, and mdh, coding for malate dehydrogenase, were also determined. Phylogenetic analysis of the three genes studied revealed parallel evolution, with the SHV, OKP, and LEN beta-lactamase families corresponding to the phylogenetic groups KpI, KpII, and KpIII, respectively. This correspondence was fully confirmed for 34 additional strains in PCR assays specific for the three beta-lactamase families. We estimated the time since divergence of the phylogenetic groups KpI and KpIII at between 6 and 28 million years, confirming the ancient presence of the beta-lactamase gene in the genome of K. pneumoniae.
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Haeggman S, Löfdahl S, Paauw A, Verhoef J, Brisse S. Diversity and evolution of the class A chromosomal beta-lactamase gene in Klebsiella pneumoniae. Antimicrob Agents Chemother 2004; 48:2400-8. [PMID: 15215087 PMCID: PMC434173 DOI: 10.1128/aac.48.7.2400-2408.2004] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the diversity of the chromosomal class A beta-lactamase gene in Klebsiella pneumoniae in order to study the evolution of the gene. A 789-bp portion was sequenced in a panel of 28 strains, representative of three phylogenetic groups, KpI, KpII, and KpIII, recently identified in K. pneumoniae and of different chromosomal beta-lactamase variants previously identified. Three groups of sequences were found, two of them corresponding to the families SHV (pI 7.6) and LEN (pI 7.1), respectively, and one, more heterogeneous, corresponding to a new family that we named OKP (for other K. pneumoniae beta-lactamase). Levels of susceptibility to ampicillin, cefuroxime, cefotaxime, ceftazidime, and aztreonam and inhibition by clavulanic acid were similar in the three groups. One new SHV variant, seven new LEN variants, and four OKP variants were identified. The OKP variants formed two subgroups based on nucleotide sequences, one with pIs of 7.8 and 8.1 and the other with pIs of 6.5 and 7.0. The nucleotide sequences of the housekeeping genes gyrA, coding for subunit A of gyrase, and mdh, coding for malate dehydrogenase, were also determined. Phylogenetic analysis of the three genes studied revealed parallel evolution, with the SHV, OKP, and LEN beta-lactamase families corresponding to the phylogenetic groups KpI, KpII, and KpIII, respectively. This correspondence was fully confirmed for 34 additional strains in PCR assays specific for the three beta-lactamase families. We estimated the time since divergence of the phylogenetic groups KpI and KpIII at between 6 and 28 million years, confirming the ancient presence of the beta-lactamase gene in the genome of K. pneumoniae.
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Affiliation(s)
- S Haeggman
- Swedish Institute for Infectious Disease Control, SE-171 82 Solna, Sweden
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