Local outbreak of Clostridioides difficile PCR-Ribotype 018 investigated by multi locus variable number tandem repeat analysis, whole genome multi locus sequence typing and core genome single nucleotide polymorphism typing

Gateau, Cécile; Deboscker, Stéphanie; Couturier, Jeanne; Vogel, Thomas; Schmitt, Élise; Müller, J.; Ménard, Céline; Turcan, Béatrice; Zaidi, Rabab Syed; Youssouf, Anlyata; Lavigne, Thierry; Barbut, Frédéric

doi:10.1016/j.anaerobe.2019.102087

Cited by 22 publications

(11 citation statements)

References 33 publications

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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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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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“…Interpretation of DNA banding patterns, generated by PCR ribotyping, has previously been shown to be problematic [ 42 ], verified by data from our study. WGS is more suitable for outbreak investigation due to its objective data interpretation also shown by others [ 31 ].…”

Section: Discussionmentioning

confidence: 93%

“…Outbreaks caused by other RTs e.g. 017 and 018 have also been reported [ 4 , 24 , 27 , 30 , 31 ]. Common to all these outbreak strains is multidrug resistance, e.g.…”

Section: Discussionmentioning

confidence: 99%

Characterization of a Clostridioides difficile outbreak caused by PCR ribotype 046, associated with increased mortality

Magnusson

Mernelius

Bengnér

et al. 2022

Emerging Microbes & Infections

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This study describes a large nosocomial outbreak of Clostridioides difficile infections (CDI) dominated by ribotype (RT) 046 in a Swedish hospital. The present study aimed to examine the pathogenicity of this RT, explore epidemiological links by whole genome sequencing (WGS), and evaluate different interventions implemented to stop the outbreak. Clinical isolates ( n = 366) collected during and after the outbreak were ribotyped and 246 isolates were subjected to WGS. Medical records of patients infected with the seven most common RTs were evaluated. RT046 was spread effectively throughout the hospital and was the most common among the 44 different RTs found (114/366 isolates). Infection with RT046 was associated with higher mortality compared to other strains (20.2% to 7.8%), although there were no differences in concomitant disease, age or antibiotic treatment. To control the outbreak, several measures were successfully implemented.

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“…The first commercial platform is SeqSphere+ software [Ridom GmbH, Germany] comprising of a scheme (the cgMLST.org Nomenclature Server) using up to 2147 core genes and 1357 accessory genes out of 3756 genes present in strain 630 (14). The second is BioNumerics [bioMérieux, France] with the cgMLST/wgMLST scheme developed by Applied-Maths, comprising 1999 core genes and 6713 accessory genes and several other genes associated with virulence, antimicrobial resistance and others from different C. difficile strains (15).…”

Section: Introductionmentioning

confidence: 99%

“…Several studies have been published on the application of cgMLST (14), (11), (15), (16). Most studies show that cgMLST is backward compatible with CE-PCR ribotyping but only a restricted number of different ribotypes were analysed and outbreaks were not included.…”

Section: Introductionmentioning

confidence: 99%

Performance of Core Genome Multilocus Sequence Typing Compared to Capillary-Electrophoresis PCR Ribotyping and SNP Analysis ofClostridioides difficile

Baktash

Corver

Harmanus

et al. 2021

Preprint

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Clostridioides difficile is the most common cause of antibiotic-associated gastrointestinal infections. Capillary-electrophoresis (CE)-PCR ribotyping is currently the gold standard for C. difficile typing but lacks discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better, but backward compatibility with CE-PCR ribotyping must be assessed. Using a well-characterized collection of diverse strains (N=630; 100 unique ribotypes [RTs]), we aimed to investigate PCR ribotyping prediction from core genome multilocus sequence typing (cgMLST). Additionally, we compared the discriminatory power of cgMLST (SeqSphere & EnteroBase) and whole genome MLST (wgMLST) (EnteroBase) with single nucleotide polymorphism (SNP) analysis). A unique cgMLST profile (>6 allele differences) was observed in 82/100 ribotypes, indicating sufficient backward compatibility. Intra-RT allele difference varied per ribotype and MLST clade. Application of cg/wgMLST and SNP analysis in two outbreak settings with ribotypes RT078 and RT181 (known with a low intra-ribotype allele difference) showed no distinction between outbreak- and non-outbreak strains, in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize and offers higher discrimination. However, in some ribotype complexes adjusted cut-off thresholds and epidemiological data are necessary to recognize outbreaks. We propose to decrease the current threshold of 6 to 3 alleles to better identify outbreaks.

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Local outbreak of Clostridioides difficile PCR-Ribotype 018 investigated by multi locus variable number tandem repeat analysis, whole genome multi locus sequence typing and core genome single nucleotide polymorphism typing

Cited by 22 publications

References 33 publications

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

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

Characterization of a Clostridioides difficile outbreak caused by PCR ribotype 046, associated with increased mortality

Performance of Core Genome Multilocus Sequence Typing Compared to Capillary-Electrophoresis PCR Ribotyping and SNP Analysis ofClostridioides difficile

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