Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario

Becker, Laura; Fuchs, Stephan; Pfeifer, Yvonne; Semmler, Torsten; Eckmanns, Tim; Korr, Gerit; Sissolak, Dagmar; Friedrichs, Michael; Zill, Edith; Tung, Mei-Lin; Dohle, Christian; Kaase, Martin; Gatermann, Sören; Rüssmann, Holger; Steglich, Matthias; Haller, Sebastian; Werner, Guido

doi:10.3389/fmicb.2018.00322

Cited by 40 publications

(35 citation statements)

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“…Since no stable task templates are available for Morganella morganii, phylogenetic relationships were reconstructed on the level of single nucleotide polymorphisms (SNPs). A reference sequence was selected by using refRank (Becker et al, 2018a) with a set of 11 complete M. morganii genome sequences available at RefSeq (Park et al, 2006). Subsequently, trimmed paired-end reads were aligned to Morganella morganii subsp.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

“…morganii KT (NC_020418) using our in-house pipeline batchMap 5 as previously described (Halbedel et al, 2018). Alignment of consensus sequences were reduced to variant positions using SNPFilter v3.2.3 with default parameters (Becker et al, 2018a) and then used to calculate distance matrices and minimum spanning trees (Geneious v11.1.5).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

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IS26-Mediated Transfer of blaNDM–1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital

et al. 2019

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One of the most demanding challenges in infection control is the worldwide dissemination of multidrug-resistant (MDR) bacteria in clinical settings. Especially the increasing prevalence of carbapenemase producing Gram-negative pathogens poses an urgent threat to public health, as these enzymes confer resistance to almost all β-lactam antibiotics including carbapenems. In this study, we report a prolonged nosocomial outbreak of various NDM-1-producing Enterobacterales species due to clonal spread and cross-species exchange of plasmids and possibly transposons. Between July 2015 and September 2017, a total of 51 carbapenemase-positive isolates were collected from 38 patients and three environmental sources in a single German hospital. Combining molecular typing methods and whole genome sequencing, the metallo-β-lactamase gene bla NDM-1 was found to be present in 35 isolates of which seven additionally carried the carbapenemase gene bla KPC-2. Core genome MLST (cgMLST) revealed different clusters of closely related isolates of Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Morganella morganii or Enterobacter cloacae indicating clonal spread. The detailed reconstruction of the plasmid sequences revealed that in all outbreak-associated isolates bla NDM-1 was located on similar composite transposons, which were also very similar to Tn125 previously described for Acinetobacter baumannii. In contrast to Tn125, these structures were flanked by IS26 elements, which could facilitate horizontal gene transfer. Moreover, the identical plasmid was found to be shared by E. coli and M. morganii isolates. Our results highlight the importance of detailed genome-based analyses for complex nosocomial outbreaks, allowing the identification of causal genetic determinants and providing insights into potential mechanisms involved in the dissemination of antibiotic resistances between different bacterial species.

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Section: Phylogenetic Analysismentioning

confidence: 99%

Section: Phylogenetic Analysismentioning

confidence: 99%

IS26-Mediated Transfer of blaNDM–1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital

et al. 2019

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“…The outbreak of multidrug-resistant bacteria is a serious public health problem, and nosocomial outbreaks caused by ESBL-producing K. pneumoniae have been reported worldwide. [6][7][8][9][10][11] ESBL-producing K. pneumoniae is the most frequently implicated pathogen causing outbreaks in neonatal intensive care units (NICUs), with mortality rates up to 31% among infected infants. 12 Traditional molecular typing methods, such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST), can define the outbreak strains well, but cannot reveal the transmission routes between strains.…”

Section: Introductionmentioning

confidence: 99%

<p>Genomic Epidemiology of an Outbreak of <em>Klebsiella pneumoniae</em> ST471 Producing Extended-Spectrum β-Lactamases in a Neonatal Intensive Care Unit</p>

Wang¹,

Luo²,

Du³

et al. 2020

IDR

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Purpose: Klebsiella pneumoniae producing extended-spectrum β-lactamases (ESBLs) causes nosocomial infections worldwide. The present study aimed to determine the molecular subtyping characteristics and antibiotic resistance mechanisms of ESBL-producing K. pneumoniae strains collected during an outbreak. Moreover, we attempted to reveal the fine transmission route of the strains within this outbreak using whole-genome sequencing (WGS). Methods: Collecting cases and strain information were carried out. Outbreak-related strains were identified using pulsed-field gel electrophoresis (PFGE). The antibiotic susceptibility, drug-resistant genes, and molecular subtype characteristics of ESBL-producing K. pneumoniae were analyzed. The fine transmission route of the strains within this outbreak was revealed using WGS and minimum core genome (MCG) sequence typing. Results: In mid-January, 2015, five cases of neonatal pneumonia caused by ESBLproducing K. pneumoniae were observed in the neonatal intensive care unit (NICU) of the Affiliated Hospital of Chifeng University, China. Eight ESBL-producing K. pneumoniae were isolated from these five cases, and two additional strains from another two cases were identified using PFGE. All ten isolates harbored bla CTX-M-15 , bla TEM-1 , bla SHV-108 , and bla OXA-1 genes, and belonged to the sequence type 471 (ST471) clone. A putative transmission map was constructed via comprehensive consideration of genomic and epidemiological information. WGS identified the initial case and the "superspreader". The genomic epidemiological investigation revealed that the outbreak was caused by the introduction of the bacteria one month before the first case appeared. Conclusion: As far as we know, this is the first report to describe the characteristics of an ST471 ESBL-producing K. pneumoniae outbreak. The data showed that epidemiological inferences could be greatly improved by interpretation in the context of WGS and that K. pneumoniae strains isolated from the same outbreak contain sufficient genomic differences to refine epidemiological linkages on the basis of genetic lineage. These findings suggested that integration of genomic and epidemiological data can help us to have a clearer understanding of when and how outbreaks occur, so as to better control nosocomial transmission.

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“…Together with two novel phylogroups (Kp5 and Kp6) described recently (5), these taxa constitute the K. pneumoniae complex. Although K. pneumoniae is numerically the major cause of human infections among members of the complex, the involvement of the other members of the complex in human infections is gaining recognition (4, 8–12). However, the unsuitability of traditional clinical microbiology methods to distinguish species within the complex leads to high rates of misidentifications (most often as K. pneumoniae ) that are masking the true clinical significance of each phylogroup and their potential epidemiological specificities (8, 9, 12, 13).…”

Section: Introductionmentioning

confidence: 99%

Identification of Klebsiella pneumoniae complex members using MALDI-TOF mass spectrometry

Rodrigues¹,

Passet²,

Brisse³

2018

Preprint

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29Klebsiella pneumoniae (phylogroup Kp1), one of the most problematic pathogens associated 30 with antibiotic resistance worldwide, is phylogenetically closely related to K. quasipneumoniae 31 [subsp. quasipneumoniae (Kp2) and subsp. similipneumoniae (Kp4)], K. variicola (Kp3) and two 32 unnamed phylogroups (Kp5 and Kp6). Together, Kp1 to Kp6 make-up the K. pneumoniae complex. 33Currently, the phylogroups can be reliably identified only by gene sequencing. Misidentification using 34 standard methods is common and the clinical significance of K. pneumoniae complex members is 35 therefore imprecisely defined. Here, we evaluated the potential of MALDI-TOF mass spectrometry to 36 discriminate K. pneumoniae complex members. We report for the first time the existence of mass 37 spectrometry biomarkers associated with the phylogroups, with a sensitivity and specificity ranging 38 between 80-100% and 97-100%, respectively. Strains within phylogroups Kp1, Kp2, Kp4 and Kp5 39 each shared two specific peaks not observed in other phylogroups. Kp3 strains shared a peak that was 40 only observed otherwise in Kp5. Finally, Kp6 had a diagnostic peak shared only with Kp1. Kp3 and 41Kp6 could therefore be identified by exclusion criteria (lacking Kp5 and Kp1-specific peaks, 42 respectively). Further, ranked Pearson correlation clustering of spectra grouped strains according to 43 their phylogroup. These results call for incorporation of spectra of all K. pneumoniae complex 44 members into reference MALDI-TOF spectra databases, in which they are currently lacking. This 45 advance may allow for simple and precise identification of K. pneumoniae and closely related species, 46 opening the way to a better understanding of their epidemiology, ecology and pathogenesis. 47 *

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Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario

Cited by 40 publications

References 77 publications

IS26-Mediated Transfer of blaNDM–1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital

IS26-Mediated Transfer of blaNDM–1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital

<p>Genomic Epidemiology of an Outbreak of <em>Klebsiella pneumoniae</em> ST471 Producing Extended-Spectrum β-Lactamases in a Neonatal Intensive Care Unit</p>

Identification of Klebsiella pneumoniae complex members using MALDI-TOF mass spectrometry

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