Abstract
Clostridioides difficile is a global public health problem, which is a primary cause of antibiotic-associated diarrhea in humans. The emergence of hypervirulent and antibiotic-resistant strains is associated with the increased incidence and severity of the disease. There are limited studies on genomic characterization of C. difficile in Latin America. We aimed to learn about the molecular epidemiology and antimicrobial resistance in C. difficile strains from adults and children in hospitals of México. We studied 94 C. difficile isolates from seven hospitals in Mexico City from 2014 to 2018. Whole-genome sequencing (WGS) was used to determine the genotype and examine the toxigenic profiles. Susceptibility to antibiotics was determined by E-test. Multilocus sequence typing (MLST) was used to determine allelic profiles. Results identified 20 different sequence types (ST) in the 94 isolates, mostly clade 2 and clade 1. ST1 was predominant in isolates from adult and children. Toxigenic strains comprised 87.2% of the isolates that were combinations of tcdAB and cdtAB (tcdA+/tcdB+/cdtA+/cdtB+, followed by tcdA+/tcdB+/cdtA−/cdtB−, tcdA−/tcdB+/cdtA−/ cdtB−, and tcdA−/tcdB−/cdtA+/cdtB+). Toxin profiles were more diverse in isolates from children. All 94 isolates were susceptible to metronidazole and vancomycin, whereas a considerable number of isolates were resistant to clindamycin, fluroquinolones, rifampicin, meropenem, and linezolid. Multidrug-resistant isolates (≥3 antibiotics) comprised 65% of the isolates. The correlation between resistant genotypes and phenotypes was evaluated by the kappa test. Mutations in rpoB and rpoC showed moderate concordance with resistance to rifampicin and mutations in fusA substantial concordance with fusidic acid resistance. cfrE, a gene recently described in one Mexican isolate, was present in 65% of strains linezolid resistant, all ST1 organisms. WGS is a powerful tool to genotype and characterize virulence and antibiotic susceptibility patterns.
Highlights
Clostridioides (Clostridium) difficile is a spore-forming, grampositive, and anaerobic bacillus found in the environment and in the intestinal tract of animals and humans
The toxin profile tcdA+/tcdB+/cdtB−/cdtB− was more frequent in children (25.8%) than adults (12%) (p = 0.067)
The tcdA−/tcdB+/cdtA−/cdtB− was present in five C. difficile isolates
Summary
Clostridioides (Clostridium) difficile is a spore-forming, grampositive, and anaerobic bacillus found in the environment and in the intestinal tract of animals and humans. CDI cases attributed to other ribotypes such as RT078, RT001, RT018, and RT126 are emerging in Europe (Couturier et al, 2018), and, currently, CDI is the most frequently identified health care– associated infection in the United States (Guh and Kutty, 2018). A number of major factors contribute to the virulence of C. difficile including the production of toxin A (TcdA) and toxin B (TcdB), which are monoglycosyltransferases that disrupt the gut epithelium (Monot et al, 2015), as well as other factors that participate in colonization like adhesins, pili, and flagella (Janoir, 2016). The toxins are encoded by tcdA and tcdB genes that are situated in the pathogenicity locus (PaLoc) and are implicated in progression and severity of CDI (Monot et al, 2015). Some C. difficile strains express an ADP-ribosylating toxin named C. difficile transferase (CDT) that modifies actin and is encoded by the genes cdtA and cdtB located in the CdTLoc locus (Gerding et al, 2014)
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