Global evolutionary dynamics and resistome analysis of Clostridioides difficile ribotype 017

Abstract

Clostridioides difficile PCR ribotype (RT) 017 ranks among the most successful strains of C. difficile in the world. In the past three decades, it has caused outbreaks on four continents, more than other ‘epidemic’ strains, but our understanding of the genomic epidemiology underpinning the spread of C. difficile RT 017 is limited. Here, we performed high-resolution phylogenomic and Bayesian evolutionary analyses on an updated and more representative dataset of 282 non-clonal C. difficile RT 017 isolates collected worldwide between 1981 and 2019. These analyses place an estimated time of global dissemination between 1953 and 1983 and identified the acquisition of the ermB-positive transposon Tn6194 as a key factor behind global emergence. This coincided with the introduction of clindamycin, a key inciter of C. difficile infection, into clinical practice in the 1960s. Based on the genomic data alone, the origin of C. difficile RT 017 could not be determined; however, geographical data and records of population movement suggest that C. difficile RT 017 had been moving between Asia and Europe since the Middle Ages and was later transported to North America around 1860 (95 % confidence interval: 1622–1954). A focused epidemiological study of 45 clinical C. difficile RT 017 genomes from a cluster in a tertiary hospital in Thailand revealed that the population consisted of two groups of multidrug-resistant (MDR) C. difficile RT 017 and a group of early, non-MDR C. difficile RT 017. The significant genomic diversity within each MDR group suggests that although they were all isolated from hospitalized patients, there was probably a reservoir of C. difficile RT 017 in the community that contributed to the spread of this pathogen.

Keywords: AMR; Clostridioides difficile; evolution; outbreaks; population; ribotype 017.

Fig. 1.

Bayesian tree of 282 non-clonal C. difficile RT 017 genomes from around the world. The C. difficile RT 017 population could be divided into non-epidemic (NE; sublineages NE₁–NE₃) and epidemic (E) lineages. *The region of origin for each strain. Important genotypic AMR determinants are displayed on the right (A–E). The red star represents C. difficile M68, the reference genome in this analysis.

Fig. 2.

Comparison of motility and cell aggregation between Lineages E (pink) and NE (lilac). (a) Lineage E had a larger growth diameter in semi-solid media. (b) Lineage E displayed a lower cell aggregation as measured by the difference in OD₆₀₀ between undisturbed and disturbed broths. (c) The semisolid media for all tested strains. C. difficile IS58 (RT 033, dark grey) was used as a negative control. All error bars display 95 % confidence intervals.

Fig. 3.

Bayesian tree of 45 Thai C. difficile RT 017 strains. ‘THP’ refers to strains isolated in 2015 and ‘MAR’ to strains isolated in 2017–2018. Red boxes indicate that the patients were in the same department when the strains were isolated. Blue boxes indicate that the strains were isolated from the same patient within 2–8 weeks.