Clostridioides difficile in Honduras: a genomic and phenotypic characterization of the persistent RT027 and emergent RT002 genotypes.

Abstract

Background: Clostridioides (C.) difficile is an anaerobic enteropathogen of clinical relevance in hospital and community settings. Its ubiquitous presence in pets, livestock, food, and the environment, together with its ability to form spores, facilitates its survival and spread. Hypervirulent and multidrug-resistant genotypes have been previously reported from Central America.

Aim: To characterize thirty-one isolates from patients of two major hospitals in Honduras.

Methods: second- and third-generation whole genome sequencing (WGS) and phenotypic antimicrobial susceptibility testing (AST).

Findings: Two toxigenic PCR-ribotypes RT027 (ST1) and RT002 (ST8) were detected. All RT027/ST1 isolates (n=29) were resistant to moxifloxacin, tetracycline and linezolid, whereas RT002/ST8 isolates (n=2) were susceptible. In addition, a number of mobile genetic elements (MGE) associated with antimicrobial resistance were found in all RT027 isolates. Notably, core genome multilocus sequence typing and core genome single nucleotide polymorphism analysis demonstrated the close genetic relationship among RT027/ST1 isolates, their persistence since 2016, and an interhospital transfer event with unknown sanitary and economic consequences. In addition, RT002, a genotype with known implications for community-acquired C. difficile infection (CA-CDI) and possible zoonotic implications, is a remarkable finding in the national epidemiologic context.

Conclusions: Taken together, our findings highlight the presence of persistent and community-relevant C. difficile strains and the consequent need to adopt and develop interventions to control and prevent CDI in the Honduran national health system within a One Health research approach.