Clostridioides difficile Whole-genome Sequencing Differentiates Relapse With the Same Strain From Reinfection With a New Strain

Abstract Background Current approaches in tracking Clostridioides difficile infection (CDI) and individualizing patient management are incompletely defined. Methods We recruited 468 subjects with CDI at Mayo Clinic Rochester between May and December 2016 and performed whole-genome sequencing (WGS) on C. difficile isolates from 397. WGS was also performed on isolates from a subset of the subjects at the time of a recurrence of infection. The sequence data were analyzed by determining core genome multilocus sequence type (cgMLST), with isolates grouped by allelic differences and the predicted ribotype. Results There were no correlations between C. difficile isolates based either on cgMLST or ribotype groupings and CDI outcome. An epidemiologic assessment of hospitalized subjects harboring C. difficile isolates with ≤2 allelic differences, based on standard infection prevention and control assessment, revealed no evidence of person-to-person transmission. Interestingly, community-acquired CDI subjects in 40% of groups with ≤2 allelic differences resided within the same zip code. Among 18 subjects clinically classified as having recurrent CDI, WGS revealed 14 with initial and subsequent isolates differing by ≤2 allelic differences, suggesting a relapse of infection with the same initial strain, and 4 with isolates differing by >50 allelic differences, suggesting reinfection. Among the 5 subjects classified as having a reinfection based on the timing of recurrence, 3 had isolates with ≤2 allelic differences between them, suggesting a relapse, and 2 had isolates differing by >50 allelic differences, suggesting reinfection. Conclusions Our findings point to potential transmission of C. difficile in the community. WGS better differentiates relapse from reinfection than do definitions based on the timing of recurrence.

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Anin silicosurvey ofClostridioides difficileextrachromosomal elements

10.1101/651539 ◽

2019 ◽

Cited By ~ 1

Author(s):

Bastian Hornung ◽

Ed J. Kuijper ◽

Wiep Klaas Smits

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

In Silico ◽

Sequence Data ◽

Whole Genome ◽

Clostridioides Difficile ◽

Extrachromosomal Elements ◽

European Nucleotide Archive ◽

Healthcare Associated ◽

Systematic Identification

AbstractThe gram-positive enteropathogenClostridioides difficileis the major cause of healthcare associated diarrhoea and is also an important cause of community-acquired infectious diarrhoea. Considering the burden of the disease, many studies have employed whole genome sequencing to identify factors that contribute to virulence and pathogenesis. Though extrachromosomal elements such as plasmids are important for these processes in other bacteria, the few characterized plasmids ofC. difficilehave no relevant functions assigned and no systematic identification of plasmids has been carried out to date. Here, we perform anin silicoanalysis of publicly available sequence data, to show that ∼13% of allC. difficilestrains contain extrachromosomal elements, with 1-6 elements per strain. Our approach identifies known plasmids (e.g. pCD6, pCD630 and cloning plasmids) and 6 novel putative plasmid families. Our study shows that plasmids are abundant and may encode functions that are relevant forC. difficilephysiology. The newly identified plasmids may also form the basis for the construction of novel cloning plasmids forC. difficilethat are compatible with existing tools.RepositoriesThe assembled circular type plasmids have been deposited at the European Nucleotide Archive (ENA) under accession numbers ERZ940801 and ERZ940803-ERZ940808.

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Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A

Clinical Infectious Diseases ◽

10.1093/cid/ciz020 ◽

2019 ◽

Vol 69 (10) ◽

pp. 1649-1656 ◽

Cited By ~ 6

Author(s):

Sunando Roy ◽

John Hartley ◽

Helen Dunn ◽

Rachel Williams ◽

Charlotte A Williams ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Prevention And Control ◽

Influenza A ◽

Infection Prevention ◽

Team Work ◽

Infection Prevention And Control ◽

Whole Genome ◽

Street Hospital ◽

And Control

Abstract Background Influenza A virus causes annual epidemics in humans and is associated with significant morbidity and mortality. Haemagglutinin (HA) and neuraminidase (NA) gene sequencing have traditionally been used to identify the virus genotype, although their utility in detecting outbreak clusters is still unclear. The objective of this study was to determine the utility, if any, of whole-genome sequencing over HA/NA sequencing for infection prevention and control (IPC) in hospitals. Methods We obtained all clinical samples from influenza (H1N1)-positive patients at the Great Ormond Street Hospital between January and March 2016. Samples were sequenced using targeted enrichment on an Illumina MiSeq sequencer. Maximum likelihood trees were computed for both whole genomes and concatenated HA/NA sequences. Epidemiological data was taken from routine IPC team activity during the period. Results Complete genomes were obtained for 65/80 samples from 38 patients. Conventional IPC analysis recognized 1 outbreak, involving 3 children, and identified another potential cluster in the haemato-oncology ward. Whole-genome and HA/NA phylogeny both accurately identified the previously known outbreak cluster. However, HA/NA sequencing additionally identified unrelated strains as part of this outbreak cluster. A whole-genome analysis identified a further cluster of 2 infections that had been previously missed and refuted suspicions of transmission in the haemato-oncology wards. Conclusions Whole-genome sequencing is better at identifying outbreak clusters in a hospital setting than HA/NA sequencing. Whole-genome sequencing could provide a faster and more reliable method for outbreak monitoring and supplement routine IPC team work to allow the prevention of transmission.

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875. Pseudo-outbreak of Clostridioides (Clostridium) difficile amongst post-operative Oncology Patients

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.1064 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S475-S475

Author(s):

Daniel Kagedan ◽

Roderich Schwarz ◽

Jillianna Wasiura ◽

Nikolaos Almyroudis ◽

Robin Patel ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Healthcare Facility ◽

Whole Genome ◽

Research Support ◽

National Healthcare ◽

Clostridioides Difficile ◽

National Healthcare Safety Network ◽

Allelic Differences ◽

Inpatient Units

Abstract Background Clostridioides difficile infection rates are subject to infection prevention surveillance as a quality measure within the hospital setting. A large spike in Clostridioides difficile infections in post-operative patients, the majority of whom were gastrointestinal surgery (GIS) patients, was noted within a six month period (June through November 2019) at our comprehensive cancer center. These patients had been housed in one of two inpatient units and there was appropriate concern that this represented a C. difficile outbreak possibly related some type of infection control breach. Methods In an effort to query case relatedness, whole genome sequencing was performed using Illumina MiSeq instrumentation and chemistry with Illumina Nextera XT library chemistry. Assembly and core genome multilocus sequence typing analysis were performed with Ridom SeqSphere+ software. Cases were classified as community or hospital acquired based on the National Healthcare Safety Network (NHSN) definitions. Results There were 23 samples submitted for possible whole genome sequencing (WGS). 5 samples were unable to be grown therefore WGS was not completed; 16 were found to be unrelated (51 or more allelic differences); 2 of the 18 isolates were found to be possibly related (7 to 50 allelic differences). There were no isolates found to be definitively related (zero to 6 allelic differences). Conclusion Given the overwhelming unrelatedness of the isolates via whole genome sequencing, this increase of C. difficile cases, identified by routine surveillance within two inpatient units, was determined to be representative of a pseudo-outbreak rather than an outbreak. This study has implications on public health reporting. National Healthcare Safety Network definitions are used to identify healthcare facility-onset C. difficile infections (CDI). The majority of cases in this study met the definition of healthcare facility-onset, and thus were reported as such, despite being genetically unrelated. This raises the concern that a significant percentage of C. difficile infections may be currently misclassified as hospital-associated and this may have negative, unfair consequences for hospitals, such as implications on reimbursement. Disclosures Robin Patel, MD, Accelerate Diagnostics (Grant/Research Support)CD Diagnostics (Grant/Research Support)Contrafect (Grant/Research Support)Curetis (Consultant)GenMark Diagnostics (Consultant)Heraeus Medical (Consultant)Hutchison Biofilm Medical Solutions (Grant/Research Support)Merck (Grant/Research Support)Next Gen Diagnostics (Consultant)PathoQuest (Consultant)Qvella (Consultant)Samsung (Other Financial or Material Support, Dr. Patel has a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an anti-biofilm substance issued.)Selux Dx (Consultant)Shionogi (Grant/Research Support)Specific Technologies (Consultant)

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Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.681518 ◽

2021 ◽

Vol 11 ◽

Author(s):

Helena M. B. Seth-Smith ◽

Michael Biggel ◽

Tim Roloff ◽

Vladimira Hinic ◽

Thomas Bodmer ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sequence Data ◽

Molecular Diagnostic ◽

Whole Genome ◽

Clostridioides Difficile ◽

Challenges And Opportunities ◽

Long Read ◽

Illumina Sequence ◽

Pcr Ribotyping

Clostridioides difficile causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C. difficile.

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Whole genome sequencing evidences higher rates of relapse in Clostridioides difficile infection caused by PCR ribotype 106

10.1101/2021.03.23.436720 ◽

2021 ◽

Author(s):

Loreto Suárez-Bode ◽

Carla López-Causapé ◽

Antonio Oliver ◽

Ana Mena

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Resistance Mutations ◽

Single Nucleotide Variants ◽

Recurrence Rates ◽

Great Capacity ◽

Clostridioides Difficile ◽

Clostridioides Difficile Infection ◽

Different Strains

ABSTRACTIncreasing prevalence and widespread of Clostridioides difficile infection (CDI) caused by the epidemic DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or the higher resistance rates found in some strains. Previous studies have also attributed higher recurrence rates to RT106 as compared to others. This study describes the genetic analysis by whole genome sequencing (WGS) of primary and recurrent isolates of RT106 to determine if the higher rate of recurrence associated to RT106 is due to relapses, caused by the same strain, or reinfections, caused by different strains. The whole-genome sequences of ten primaries and fourteen recurrent RT106 isolates from ten patients were obtained to determine MLST profiles, resistance mutations and phylogenetic relatedness between the different isolates by comparative single nucleotide variants (SNV) analysis using the C. difficile DH/NAP11/106/ST-42 genome as reference (GenBank accession: GCA_002234355.1). All isolates were classified as ST42 and SNVs comparative analysis showed that those belonging to the same patient were isogenic (differed by ≤3 SNVs), with one exception (6 SNVs); while strains belonging to different patients were not (differing by 4 to 43 SNVs) with two exceptions of isogenic isolates from different patients, suggesting putative transmission events. Phylogenetic analysis suggested the presence of similar local epidemic lineages, except for one patient whose isolates clustered with different US isolates. All the isolates, except those clustering with the US lineage, were also associated to moxifloxacin resistant since all of them were resistant by agar diffusion (MIC >32) and contained the Thr82Ile mutation in gyrA. Our results evidence that recurrent Clostridioides difficile infections caused by RT06/ST42 are mainly due to relapses, caused by primary strains, showing the great capacity of RT106/ST42 to persist and cause recurrences as compared to other ribotypes.

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NovelblaKPC-carrying species identified in the hospital environment

10.1101/069856 ◽

2016 ◽

Author(s):

Hang T.T. Phan ◽

Zoie Aiken ◽

Oluwafemi Akinremi ◽

Julie Cawthorne ◽

Andrew Dodgson ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Prevention And Control ◽

Infection Prevention ◽

Diagnostic Methods ◽

Hospital Environment ◽

Infection Prevention And Control ◽

Clinical Implications ◽

Whole Genome ◽

And Control

AbstractblaKPC, encoding one of five dominant global carbapenemase families, is increasingly identified in environmental species difficult to characterize using routine diagnostic methods, with epidemiological and clinical implications. During environmental hospital infection prevention and control investigations (Manchester, UK) we used whole genome sequencing to confirm species identification for isolates infrequently associated withblaKPCand/or difficult to classify by MALDI-ToF. Four previously undescribedblaKPC-carrying species were identified from the hospital environment, including a putative, novelEnterobacterspecies.

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Utility of Real-Time Whole Genome Sequencing in Partner Notification and Control of Neisseria gonorrhoeae Infection

SSRN Electronic Journal ◽

10.2139/ssrn.3689601 ◽

2020 ◽

Author(s):

Ling Yuan Kong ◽

Janet Wilson ◽

Ines B. Moura ◽

Warren Fawley ◽

Laura Kelly ◽

...

Keyword(s):

Neisseria Gonorrhoeae ◽

Whole Genome Sequencing ◽

Real Time ◽

Genome Sequencing ◽

Partner Notification ◽

Whole Genome ◽

And Control

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Whole genome sequencing and the prevention and control of meticillin-resistant Staphylococcus aureus infection

Journal of Hospital Infection ◽

10.1016/j.jhin.2013.05.002 ◽

2013 ◽

Vol 85 (1) ◽

pp. 85-86 ◽

Cited By ~ 1

Author(s):

H. Humphreys ◽

D.C. Coleman

Keyword(s):

Staphylococcus Aureus ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Prevention And Control ◽

Whole Genome ◽

Aureus Infection ◽

And Control

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Genome Sequencing of Polydrug-, Multidrug-, and Extensively Drug-Resistant Mycobacterium tuberculosis Strains from South India

Microbiology Resource Announcements ◽

10.1128/mra.01388-18 ◽

2019 ◽

Vol 8 (12) ◽

Author(s):

Sivakumar Shanmugam ◽

Narender Kumar ◽

Dina Nair ◽

Mohan Natrajan ◽

Srikanth Prasad Tripathy ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

South India ◽

Sequence Data ◽

Whole Genome ◽

Drug Resistant ◽

Resistance Mutations ◽

Content Type ◽

Extensively Drug Resistant

The genomes of 16 clinical Mycobacterium tuberculosis isolates were subjected to whole-genome sequencing to identify mutations related to resistance to one or more anti-Mycobacterium drugs. The sequence data will help in understanding the genomic characteristics of M. tuberculosis isolates and their resistance mutations prevalent in South India.

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