A retrospective molecular epidemiological scenario of carbapenemase-producing Klebsiella pneumoniae clinical isolates in a Sicilian transplantation hospital shows a swift polyclonal divergence among sequence types, resistome and virulome

ABSTRACTThe global emergence ofKlebsiella pneumoniaecarbapenemase-producingK. pneumoniae(KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258K. pneumoniaein the setting of an outbreak mediated by an endemic plasmid. We describe the interplay ofblaKPCplasmids andK. pneumoniaestrains and their relationship to the location of acquisition in a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied to KPC-Kpclinical isolates collected from a single institution over 5 years following the introduction ofblaKPCin August 2007, as well as two plasmid transformants. KPC-Kpfrom 37 patients yielded 16 distinct sequence types (STs). Two novel conjugativeblaKPCplasmids (pKPC_UVA01 and pKPC_UVA02), carried by the hospital index case, accounted for the presence ofblaKPCin 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02 in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kpstrain, ST258, mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate the unexpected dispersal ofblaKPCto many non-ST258 lineages in a hospital through spread of at least two novelblaKPCplasmids. In contrast, ST258 KPC-Kpwas imported into the institution on numerous occasions, with otherblaKPCplasmid vectors and without sustained transmission. Instead, a newly recognized KPC-Kpstrain, ST941, became associated with both novelblaKPCplasmids and spread locally, making it a future candidate for clinical persistence and dissemination.

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Co-occurrence of Carbapenemase-encoding Genes Among Klebsiella pneumoniae Clinical Isolates: Positive Relationship of bla NDM and bla SIM with Imipenem Resistance

Jundishapur Journal of Microbiology ◽

10.5812/jjm.112486 ◽

2021 ◽

Vol 14 (2) ◽

Author(s):

Maryam Galehdar ◽

Maryam Ghane ◽

Laleh Babaeekhou

Keyword(s):

Klebsiella Pneumoniae ◽

Multilocus Sequence Typing ◽

Positive Relationship ◽

Clinical Isolates ◽

Microdilution Method ◽

Broth Microdilution Method ◽

Significant Public Health ◽

Overall Resistance ◽

Encoding Genes ◽

Sequence Types

Background: Carbapenem-resistant Klebsiella pneumoniae (CR-KP), known as a significant public health threat, is the most common causative agent of nosocomial and community-acquired infections. Objectives: This study aimed to evaluate resistance to carbapenems and determine the prevalence of carbapenemase genes and multilocus sequence typing (MLST) of K. pneumoniae clinical isolates. Methods: One-hundred K. pneumoniae isolates were evaluated. The minimum inhibitory concentrations (MIC) of imipenem and meropenem were assessed by the broth microdilution method. Multiplex-polymerase chain reaction (PCR) was applied to detect 11 carbapenemase-encoding genes belonging to different classes. The alleles and sequence types (ST) of three isolates were identified by MLST. Results: The MIC of carbapenems for the isolates ranged from 0.062 to 32 µg/mL. Overall, resistance rates to imipenem and meropenem were reported 11% and 34%, respectively. The bla IMP gene was the most abundant (78.4%), followed by bla OXA-48 (48.6%), bla GIM (27%), bla KPC (27%), bla SIM (21.6%), bla BIC (6.6%), bla NDM (16.2%), bla AIM (16.2%), bla VIM (16.2%), bla DIM (8.1%), and bla SPM (8.1%). The co-existence of carbapenemase genes was observed in 81.8% of the isolates. A positive relationship was found between the presence of bla NDM and bla SIM and resistance to imipenem. Multilocus sequence typing results showed three different sequence types, including ST14, ST5188, and ST1861. Conclusions: This study revealed a high prevalence of CR-KP isolates that suggests a high risk of horizontal gene transfer and potential to spread resistance among other strains. Since STs are reported for the first time in Iran, they can be considered as emerging strains.

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Multiplex Real-Time PCR for Detection of an Epidemic KPC-Producing Klebsiella pneumoniae ST258 Clone

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00316-12 ◽

2012 ◽

Vol 56 (6) ◽

pp. 3444-3447 ◽

Cited By ~ 37

Author(s):

Liang Chen ◽

Kalyan D. Chavda ◽

José R. Mediavilla ◽

Yanan Zhao ◽

Henry S. Fraimow ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Real Time ◽

Real Time Pcr ◽

Clinical Isolates ◽

Pcr Assay ◽

Content Type ◽

Carbapenem Resistant ◽

Sequence Types ◽

Single Reaction

ABSTRACTWe describe a multiplex real-time PCR assay capable of identifying both the epidemicKlebsiella pneumoniaeST258 clone andblaKPCcarbapenemase genes in a single reaction. The assay displayed excellent sensitivity (100%) and specificity (100%) for identification of ST258 clone andblaKPCin a collection of 75K. pneumoniaeisolates comprising 41 sequence types. Our results suggest that this assay is an effective tool for surveillance of this clone among carbapenem-resistantK. pneumoniaeclinical isolates.

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Genetic Characterisation of Colistin Resistant Klebsiella pneumoniae Clinical Isolates From North India

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.666030 ◽

2021 ◽

Vol 11 ◽

Author(s):

Sanjay Singh ◽

Ashutosh Pathak ◽

Mohibur Rahman ◽

Avinash Singh ◽

Soumyabrata Nag ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Virulence Genes ◽

Efflux Pumps ◽

Clinical Isolates ◽

North India ◽

Drug Resistant ◽

Colistin Resistance ◽

Genomic Plasticity ◽

Resistant Genes ◽

Sequence Types

BackgroundIncreasing use of colistin has led to the world-wide emergence of mobile colistin resistant gene (mcr). The present study aimed to identify and characterise mcr and other drug-resistant genes in colistin resistant Klebsiella pneumoniae clinical isolates.MethodsTwenty-two colistin resistant K. pneumoniae were analysed for mcr and other drug-resistant genes, efflux pumps, and virulence genes, and for their biofilm forming ability. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were performed for all mcr-1 positive isolates. S1-PFGE and Southern hybridisation were performed for localisation of mcr-1 and blaNDM.ResultsNineteen colistin resistant K. pneumoniae harboured mcr-1 and 3 had mgrB disruption. All isolates harboured blaOXA-48-type and ESBL genes; eight strains (five with mcr-1 and three with mgrB disruption) co-harboured blaNDM. Efflux pumps genes AcrAB and mdtK were detected in all 22 and tol-C in 21 isolates. Virulence-related genes entB and irp-1 were detected in all 22, mrkD in 20, and fimH-1 in 18 isolates; 11 isolates were strong biofilm producers. PFGE clustered mcr-1 positive isolates into eight groups based on ≥90% similarity; MLST revealed diverse sequence types, predominant being ST-15 (n = 4) and ST-16 (n = 4). Both mcr-1 and blaNDM were localised on plasmid and chromosome; mcr-1 was present on IncFII type and blaNDM on IncFIB and IncA/C type plasmids.ConclusionsColistin resistance in K. pneumoniae was predominantly mediated by mcr-1. Co-existence of colistin, carbapenem, and other drug-resistant genes along with efflux pumps indicates towards enormous genomic plasticity in K. pneumoniae with ability to emerge as super-spreader of drug-resistance.

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Contribution of β-Lactamases and Porin Proteins OmpK35 and OmpK36 to Carbapenem Resistance in Clinical Isolates of KPC-2-Producing Klebsiella pneumoniae

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02045-12 ◽

2013 ◽

Vol 58 (2) ◽

pp. 1214-1217 ◽

Cited By ~ 41

Author(s):

Ying Zhang ◽

Xiaofei Jiang ◽

Yanyan Wang ◽

Gang Li ◽

Yueru Tian ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Carbapenem Resistance ◽

Clinical Isolates ◽

Content Type ◽

Carbapenem Resistant ◽

Sds Page ◽

Porin Proteins ◽

A Minor ◽

Sequence Types ◽

M 14

ABSTRACTFifty-seven carbapenem-resistantKlebsiella pneumoniaeisolates belonging to ST11 (50 isolates), ST423 (5 isolates), and two other sequence types were studied. All were positive forblaKPC-2,blaTEM-1, andblaCTX-M-14. SDS-PAGE analysis of six representative isolates demonstrated varied porin expression. Nevertheless, whenblaKPC-2was deleted, carbapenem resistance was markedly reduced. Additionally, SHV-12, DHA-1, and/or VIM-1 appeared to contribute to accessory carbapenemase activity. In contrast, OmpK35 and/or OmpK36 deficiency seemed to serve only as a minor cooperative factor.

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