Hospital outbreak due to Clostridium difficile ribotype 018 (RT018) in Southern Germany

Бергер, Фабиан; Gfrörer, Sabine; Becker, Sören L.; Baldan, Rossella; Cirillo, Daniela María; Frentrup, Martinique; Steglich, Matthias; Engling, Pit; Nübel, Ulrich; Mellmann, Alexander; Bischoff, Markus; Гартнер, Барбара; Müller, Lutz von

doi:10.1016/j.ijmm.2019.03.001

Cited by 17 publications

(19 citation statements)

References 28 publications

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“…These included 176 isolates from four patients with recurring CDI ( C. difficile infection), 63 isolates from four transmission chains in multiple hospitals [14, 19, 26], and a comprehensive sample of 1158 isolates collected over several years in four hospitals in Oxfordshire, UK [13]. A strong linear relationship (R 2 , 0.71–0.93) was found in all three analyses between the pairwise differences in cgMLST alleles and non-recombinant SNPs (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Indeed, some of the outbreaks investigated here did consist of more than one HC2 cluster (). For example, nine isolates from a recently reported ribotype 018 (RT018) outbreak in Germany [26] encompassed four related HC2 clusters, and outbreaks with RT027 and RT106 in a hospital in Spain [14] were each affiliated with two or three HC2 clusters ().…”

Section: Resultsmentioning

confidence: 99%

“…Neighbour-joining trees based on cgMLST showing the phylogenetic relationships among C. difficile isolates from previously published CDI outbreaks as indicated [14, 19, 26]. Nodes are coloured by HC2.…”

Section: Resultsmentioning

confidence: 99%

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A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

Frentrup¹,

Zhou

Steglich

et al. 2020

Microbial Genomics

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Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled C. difficile genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of C. difficile at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (P<10−4) or single wards (P=0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with k-mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled C. difficile genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile .

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

Frentrup¹,

Zhou

Steglich

et al. 2020

Microbial Genomics

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“…Moreover, recent data from South-Eastern Europe captured an outbreak of ribotype 176 CDIs in a Croatian hospital in 2015 (Rupnik et al, 2016). In Slovakia, ongoing CDI surveillance, including ribotyping of C. difficile isolates, is needed in order to monitor further the development of CDI epidemiology and the possible emergence of newly recognized epidemic ribotypes such as ribotype 018 in France and Italy (Berger et al, 2019, Gateau et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

The emergence of Clostridium difficile ribotypes 027 and 176 with a predominance of the Clostridium difficile ribotype 001 recognized in Slovakia following the European standardized Clostridium difficile infection surveillance of 2016

Nováková

Štefkovičová

Kopilec

et al. 2020

International Journal of Infectious Diseases

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HighlightsBetween October and December 2016, 36 Slovak hospitals performed Clostridium difficile infection (CDI) surveillance.The overall mean CDI incidence was 2.8 (95% confidence interval 1.9–3.9) cases per 10 000 patient-days.The most prevalent ribotypes were 001 (n = 46, 59.0%) and 176 (n = 23, 29.5%).Almost all isolates showed reduced susceptibility to moxifloxacin (n = 73, 93.6%).A reduced susceptibility to metronidazole was observed in 13 primary fresh isolates.

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“…The MLVA and WGS fingerprinting methods exhibit similarly high discriminatory power for C. difficile, although they target different parts of the genome [2,7]; when compared in CDI outbreak/clusters settings, 95% concordance was observed [7]. For instance, through a combination of PCR ribotyping, MLVA and WGS, an outbreak and cross-national transmission of ribotype 018 was identified by in Germany [9].…”

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confidence: 99%

A two-step approach for the investigation of a Clostridium difficile outbreak by molecular methods

Krutova

Wilcox

Kuijper

2019

Clinical Microbiology and Infection

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Hospital outbreak due to Clostridium difficile ribotype 018 (RT018) in Southern Germany

Cited by 17 publications

References 28 publications

A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

The emergence of Clostridium difficile ribotypes 027 and 176 with a predominance of the Clostridium difficile ribotype 001 recognized in Slovakia following the European standardized Clostridium difficile infection surveillance of 2016

A two-step approach for the investigation of a Clostridium difficile outbreak by molecular methods

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