A genomic survey of Clostridioides difficile isolates from hospitalized patients in Melbourne, Australia

Abstract

ABSTRACT 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. IMPORTANCE There has been a decrease in healthcare-associated Clostridioides difficile infection in Australia, but an increase in the genetic diversity of infecting strains, and an increase in community-associated cases. Here, we studied the genetic relatedness of C. difficile isolated from patients at a major hospital in Melbourne, Australia. Diverse ribotypes were detected, including those associated with community and environmental sources. Some types of isolates were more likely to carry antimicrobial resistance determinants, and many of these were associated with mobile genetic elements. These results correlate with those of other recent investigations, supporting the observed increase in genetic diversity and prevalence of community-associated C. difficile, and consequently the importance of sources of transmission other than symptomatic patients. Thus, they reinforce the importance of surveillance for in both hospital and community settings, including asymptomatic carriage, food, animals, and other environmental sources to identify and circumvent important sources of C. difficile transmission.

Keywords

• Clostridioides difficile
• hospital-acquired infection
• whole-genome sequencing
• genetic epidemiology