Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014

Abstract

BackgroundBy using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014.MethodsWe selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches. Relevant information was extracted from NGS data (antibiotic resistance determinants, wzi gene/cps type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on K. pneumoniae.ResultsNGS-based analyses revealed a preferred prevalence of KPC-2-producing ST258 and KPC-3-producing ST512 isolates. OXA-48, being the most prevalent carbapenemase type in Germany, was associated with various K. pneumoniae strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of blaOXA-48 via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European K. pneumoniae isolates. ST23 being the most frequent MLST type in Asia was found only once in Germany. This latter isolate contained an almost complete set of virulence genes and a K1 capsule suggesting occurrence of a hypervirulent ST23 strain producing OXA-48 in Germany.ConclusionsOur study results suggest prevalence of “classical” K. pneumonaie strain types associated with widely distributed carbapenemase genes such as ST258/KPC-2 or ST512/KPC-3 also in Germany. The finding of a supposed hypervirulent and OXA-48-producing ST23 K. pneumoniae isolates outside Asia is highly worrisome and requires intense molecular surveillance.Electronic supplementary materialThe online version of this article (10.1186/s13756-018-0352-y) contains supplementary material, which is available to authorized users.

Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania

“…It is interesting to note that in our study, of the two isolates containing bla OXA-162 , one has also harboured bla OXA-1 . Also, similar to the German and Hungarian studies, bla OXA-162 is co-expressed in both isolates with the bla CTX-M-15 [29,38]. In contrast with other reports where bla OXA-162 was found in clinical isolates, in this study we have identified it in WWTP samples (both influent and effluent).…”

“…The most frequent carbapenemases genes (e.g. bla OXA-48, bla KPC-2, bla NDM-1 and bla OXA-162 ) found in the majority of the influent, effluent and clinical isolates are those reported as prevalent both in Romania and in other geographical areas [29]. Previous studies performed in Romania on carbapenem-non-susceptible Klebsiella pneumoniae clinical isolates have shown that bla OXA-48 was by far the most predominant genotype, followed by bla NDM-1 and bla KPC-2 [30,31,32].…”

NDM Metallo-β-Lactamases and Their Bacterial Producers in Health Care Settings

“…Although bla NDM has been found on bacterial chromosomes (82)(83)(84), the vast majority of carriage occurs on plasmids, which play a vital role in dissemination. bla NDM has been reported to be carried on plasmids with a variety of replicon types (33,82,(85)(86)(87)(88)(89)(90)(91)(92)(93)(94)(95)(96)(97)(98)(99)(100)(101)(102)(103)(104). There are a total of 355 bla NDM -carrying plasmids with complete sequences available in GenBank (accessed on 8 January 2018) (see Data Set S2 in the supplemental material).…”

A roadmap to mammalian oral microbiome evolution with dental calculus

“…To survey global AMR potential, we blasted the contamination-filtered reads against the Comprehensive Antibiotic Resistance Database (CARD) 45 and assigned the top match for each read to its respective gene family under the Antibiotic Resistance Ontology (ARO). To identify AMR genes encoded by A. baumannii and K. pneumoniae, which were both present in our studied host species ( Figure S7), we extracted reads that mapped to these bacterial genomes with bwa 46,47 . We confirmed that reads from both bacterial species exhibited characteristic deamination patterns consistent with historical DNA damage ( Figure 5B-C) and subsequently processed these reads in CARD, as above.…”

“…The Illumina sequencing control phage PhiX was spiked into our sequencing runs and has previously been reported to have been erroneously integrated into many microbial genomes 23,67 . Reads were therefore mapped to PhiX (accession: GCA_000819615.1) with bwa mem v0.7.17 46,47 and the unmapped reads retained with SAMTools v1.9 68 and BEDTools v2.21.0 69 . To remove reads originating from the host organism and human contamination, we mapped all reads in a sample to a combined reference consisting of the human genome 70 (RefSeq accession: GCF_000001405.38) and the respective host genome (GCF_000151905.2 (Gorilla gorilla gorilla) 71 , GCF_003584765.1 (U. arctos horribilis) 72 and GCA_004026565.1 (Rangifer tarandus)) with bwa mem.…”