TY - JOUR
T1 - A genomic survey of Clostridioides difficile isolates from hospitalized patients in Melbourne, Australia
AU - Larcombe, Sarah
AU - Williams, Galain C.
AU - Amy, Jacob
AU - Lim, Su Chen
AU - Riley, Thomas V.
AU - Muleta, Anthony
AU - Barugahare, Adele A.
AU - Powell, David R.
AU - Johanesen, Priscilla A.
AU - Cheng, Allen C.
AU - Peleg, Anton Y.
AU - Lyras, Dena
N1 - Funding Information:
Dena Lyras was supported by Future Fellowship FT120100779 (Australian Research Council). Jacob Amy was supported through a Monash Departmental Scholarship (Department of Microbiology, Monash University) and an Australian Government Research Training Program Scholarship. Department of Education and Training | Australian Research FT120100779 Dena Lyras Council (ARC)
Funding Information:
Dena Lyras was supported by Future Fellowship FT120100779 (Australian Research Council). Jacob Amy was supported through a Monash Departmental Scholarship (Department of Microbiology, Monash University) and an Australian Government Research Training Program Scholarship.
Publisher Copyright:
© Crown copyright 2023.
PY - 2023/12
Y1 - 2023/12
N2 - There has been a decrease in healthcare-associated Clostridioides difficile infection (CDI) in Australia, coupled with an increase in the genetic diversity of strains isolated in these settings, and an increase in community-associated cases. To explore this changing epidemiology, we studied the genetic relatedness of C. difficile isolated from patients at a major hospital in Melbourne, Australia. Whole-genome sequencing of C. difficile isolates from symptomatic (n = 61) and asymptomatic (n = 10) hospital patients was performed. Genomic comparisons were made using single-nucleotide polymorphism (SNP) analysis, ribotyping, and toxin, resistome, and mobilome profiling. C. difficle clade 1 strains were found to be predominant (64/71), with most strains (63/71) encoding both toxins A and B (A+B+). Despite these similarities, only two isolates were genetically related (≤2 SNPs) and a diverse range of ribotypes was detected, with those predominating including ribotypes commonly found in community-associated cases. Five non-toxigenic (A−B−CDT−) clade 1 strains were identified, all in asymptomatic patients. Three clade 4 (A−B+CDT−) and four clade 5 (A+B+CDT+) strains were detected also, with these strains more likely to carry antimicrobial resistance determinants, many of which were associated with mobile genetic elements. Overall, within a single hospital, C. difficile-associated disease was caused by a diverse range of strains, including many strain types associated with community and environmental sources. While strains carried asymptomatically were more likely to be non-toxigenic, toxigenic strains were isolated also from asymptomatic patients, which together suggest the presence of diverse sources of transmission, potentially including asymptomatic patients.
AB - There has been a decrease in healthcare-associated Clostridioides difficile infection (CDI) in Australia, coupled with an increase in the genetic diversity of strains isolated in these settings, and an increase in community-associated cases. To explore this changing epidemiology, we studied the genetic relatedness of C. difficile isolated from patients at a major hospital in Melbourne, Australia. Whole-genome sequencing of C. difficile isolates from symptomatic (n = 61) and asymptomatic (n = 10) hospital patients was performed. Genomic comparisons were made using single-nucleotide polymorphism (SNP) analysis, ribotyping, and toxin, resistome, and mobilome profiling. C. difficle clade 1 strains were found to be predominant (64/71), with most strains (63/71) encoding both toxins A and B (A+B+). Despite these similarities, only two isolates were genetically related (≤2 SNPs) and a diverse range of ribotypes was detected, with those predominating including ribotypes commonly found in community-associated cases. Five non-toxigenic (A−B−CDT−) clade 1 strains were identified, all in asymptomatic patients. Three clade 4 (A−B+CDT−) and four clade 5 (A+B+CDT+) strains were detected also, with these strains more likely to carry antimicrobial resistance determinants, many of which were associated with mobile genetic elements. Overall, within a single hospital, C. difficile-associated disease was caused by a diverse range of strains, including many strain types associated with community and environmental sources. While strains carried asymptomatically were more likely to be non-toxigenic, toxigenic strains were isolated also from asymptomatic patients, which together suggest the presence of diverse sources of transmission, potentially including asymptomatic patients.
KW - Clostridioides difficile
KW - genetic epidemiology
KW - hospital-acquired infection
KW - whole-genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85180011675&partnerID=8YFLogxK
U2 - 10.1128/spectrum.01352-23
DO - 10.1128/spectrum.01352-23
M3 - Article
C2 - 37815385
AN - SCOPUS:85180011675
SN - 2165-0497
VL - 11
JO - Microbiology Spectrum
JF - Microbiology Spectrum
IS - 6
M1 - e0135223
ER -