Genetically related clostridium difficile from water sources and human CDI cases revealed by whole-genome sequencing

Authors

Su Chen Lim, Edith Cowan University
Natasza M. R. Hain-Saunders, Edith Cowan University
Korakrit Imwattana
Papanin Putsathit, Edith Cowan UniversityFollow
Deirdre A. Collins, Edith Cowan UniversityFollow
Thomas V. Riley, Edith Cowan UniversityFollow

Document Type

Journal Article

Publication Title

Environmental Microbiology

Volume

24

Issue

3

First Page

1221

Last Page

1230

PubMed ID

34693624

Publisher

Wiley

School

School of Medical and Health Sciences

RAS ID

39862

Funders

Edith Cowan University

Grant Number

G1004458

Comments

Lim, S. C., Hain‐Saunders, N. M., Imwattana, K., Putsathit, P., Collins, D. A., & Riley, T. V. (2022). Genetically related Clostridium difficile from water sources and human CDI cases revealed by whole‐genome sequencing. Environmental Microbiology, 24(3), 1221-1230. https://doi.org/10.1111/1462-2920.15821

Abstract

Clostridium difficile isolates from the environment are closely related to those from humans, indicating a possible environmental transmission route for C. difficile infection (CDI). In this study, C. difficile was isolated from 47.3% (53/112) of lake/pond, 23.0% (14/61) of river, 20.0% (3/15) of estuary and 0.0% (0/89) of seawater samples. The most common toxigenic strain isolated was C. difficile PCR ribotype (RT) 014/020 (10.5%, 8/76). All water isolates were susceptible to fidaxomicin, metronidazole, rifaximin, amoxicillin/clavulanic acid, moxifloxacin and tetracycline. Resistance to vancomycin, clindamycin, erythromycin and meropenem was detected in 5.3% (4/76), 26.3% (20/76), 1.3% (1/76) and 6.6% (5/76) of isolates, respectively. High-resolution core-genome analysis was performed on RT 014/020 isolates of water origin and 26 clinical RT 014/020 isolates from the same year and geographical location. Notably, both human and water strains were intermixed across three sequence types (STs), 2, 13 and 49. Six closely related groups with ≤10 core-genome single nucleotide polymorphisms were identified, five of which comprised human and water strains. Overall, 19.2% (5/26) of human strains shared a recent genomic relationship with one or more water strains. This study supports the growing hypothesis that environmental contamination by C. difficile plays a role in CDI transmission.

DOI

10.1111/1462-2920.15821

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