Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing

Jia, Hao; Du, Pengcheng; Yang, Hui; Zhang, Yuanyuan; Wang, Jing; Zhang, Wen; Gui-ling, Han; Han, Ning; Zhi-yuan, Yao; Wang, Haiyin; Zhang, Jing; Wang, Zhen; Qingming, Ding; Qiang, Yujun; Barbut, Frédéric; Gao, George F.; Cao, Yongtong; Cheng, Ying; Chen, Chen

doi:10.1186/s12864-016-2708-0

Cited by 37 publications

(34 citation statements)

References 36 publications

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“…A convenient alternative to SNP-based genotyping is offered by the commercial software SeqSphere, which implements a 85 core genome multilocus sequence typing scheme (cgMLST) for the analysis of genomic diversity in C. difficile 18 and other organisms. Indeed, cgMLST 18 confirmed the prior conclusion from genomic SNP analyses 19 that a common clone of C. difficile had been isolated over two successive years at a hospital in China. However, we are not aware of a quantitative comparison of the sensitivity of both methods.…”

Section: Introductionsupporting

confidence: 75%

“…Multiple bacterial strains from local outbreaks of C. difficile disease in hospitals in Oxfordshire and China differ by very few SNPs 13,15,19 . The published data indicates a 95% probability that the genomes of pairs of strains from a transmission chain differ by two non-recombinant SNPs, or less 13 .…”

Section: Suitability Of Cgmlst For Epidemiological Analyses Of Transmmentioning

confidence: 99%

“…(B) Intra-outbreak diversity. Pairwise genomic distances among isolates from four previously reported CDI outbreaks, including an outbreak protracting over two years in a hospital in China (number of isolates, n, 12)19 , an outbreak involving two hospitals in Southern Germany (n = 9) 28 , and two 635 transmission chains with ribotypes 027 (n=22) and 106/500 (n=20) in a hospital in Madrid, Spain 14 . (C) Regional diversity.…”

mentioning

confidence: 99%

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Global genomic population structure of Clostridioides difficile

Frentrup¹,

Zhou

Steglich

et al. 2019

Preprint

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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 50 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 EnteroBase, a publicly accessible database (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome 55 multilocus sequence typing (cgMLST). We demonstrate that the identification of highly related genomes is 89% consistent between cgMLST and single-nucleotide polymorphisms. EnteroBase currently contains 13,515 quality-controlled genomes which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. Hierarchical clustering can be used to identify populations of C. difficile at 60 all epidemiological levels, from recent transmission chains through to pandemic and endemic strains, and is largely compatible with prior ribotyping. Hierarchical clustering thus enables comparisons to earlier surveillance data and will facilitate communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile. 65 toxin variant Clostridium difficile PCR ribotype 017 reveals the evolution of two

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Section: Introductionsupporting

confidence: 75%

Section: Suitability Of Cgmlst For Epidemiological Analyses Of Transmmentioning

confidence: 99%

mentioning

confidence: 99%

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Global genomic population structure of Clostridioides difficile

Frentrup¹,

Zhou

Steglich

et al. 2019

Preprint

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“…For C. difficile, initial studies also confirmed the general applicability of WGS-based typing (9,15,16). Nevertheless, the broad use of WGS-based typing of C. difficile is still hampered by the lack of standardized nomenclature (17); this has already been established for other pathogens (18)(19)(20)(21) and would facilitate interlaboratory exchange of data.…”

mentioning

confidence: 85%

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile

et al. 2018

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, recently renamed , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for Initially, we determined the breadth of the population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping ( = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange.

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“…Moreover, in consideration of the complex personnel mobility in medical institutions, the majority of CDI is hospital-acquired, and nosocomial transmission of C. difficile contributes greatly to the spread of different genotypes. Recently, whole genome sequencing (WGS) identified the dissemination and spread of C. difficile ribotype 027 (RT027) and sequence type 081 (ST081) in two Chinese hospitals [8,9]. Therefore, a better understanding of regional epidemiology is helpful to guide priorities for the management of hospital-acquired Clostridium difficile infection (HA-CDI).…”

Section: Introductionmentioning

confidence: 99%

Characteristics of Clostridium difficile isolates and the burden of hospital-acquired Clostridium difficile infection in a tertiary teaching hospital in Chongqing, Southwest China

Dai

TianXiang²,

Yan

et al. 2020

BMC Infect Dis

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Background: Clostridium difficile infection (CDI), especially hospital-acquired Clostridium difficile infection (HA-CDI), continues to be a public health problem and has aroused great concern worldwide for years. This study aimed to elucidate the clinical and epidemiological features of HA-CDI and the characteristics of C.difficile isolates in Chongqing, Southwest China.Methods: A case-control study was performed to identify the clinical incidence and risk factors of HA-CDI. C. difficile isolates were characterised by polymerase chain reaction (PCR) ribotyping, multilocus sequence typing (MLST), toxin gene detection and antimicrobial susceptibility testing.Results: Of the 175 suspicious patients, a total of 122 patients with antibiotic-associated diarrhea (AAD) were included in the study; among them, 38 had HA-CDI. The incidence of AAD and HA-CDI was 0.58 and 0.18 per 1000 patient admissions, respectively. Chronic renal disease and cephalosporin use were independent risk factors for HA-CDI. Fifty-five strains were assigned into 16 sequence types (STs) and 15 ribotypes (RTs). ST2/RT449 (8, 14.5%) was the predominant genotype. Of the 38 toxigenic isolates, A + B + CDT-isolates accounted for most (34, 89.5%) and 1 A + B + CDT+ isolate emerged. No isolate was resistant to vancomycin, metronidazole or tigecycline, with A-B-CDTbeing more resistant than A + B + CDT-.Conclusions: Different genotypes of C. difficile strains were witnessed in Chongqing, which hinted at the necessary surveillance of HA-CDI. Adequate awareness of patients at high risk of HA-CDI acquisition is advocated and cautious adoption of cephalosporins should be highlighted.

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Nosocomial transmission of Clostridium difficile ribotype 027 in a Chinese hospital, 2012–2014, traced by whole genome sequencing

Cited by 37 publications

References 36 publications

Global genomic population structure of Clostridioides difficile

Global genomic population structure of Clostridioides difficile

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile

Characteristics of Clostridium difficile isolates and the burden of hospital-acquired Clostridium difficile infection in a tertiary teaching hospital in Chongqing, Southwest China

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