Molecular Epidemiology and Antimicrobial Resistance of Clostridioides difficile in Hospitalized Patients From Mexico

Emmanuel Aguilar-Zamora; Bart C Weimer; Roberto C Torres; Alejandro Gómez-Delgado; Nayeli Ortiz-Olvera; Gerardo Aparicio-Ozores; Varenka J Barbero-Becerra; Javier Torres; Margarita Camorlinga-Ponce

doi:10.3389/fmicb.2021.787451

Molecular Epidemiology and Antimicrobial Resistance of Clostridioides difficile in Hospitalized Patients From Mexico

Front Microbiol. 2022 Mar 10:12:787451. doi: 10.3389/fmicb.2021.787451. eCollection 2021.

Authors

Emmanuel Aguilar-Zamora^{1

2}, Bart C Weimer³, Roberto C Torres¹, Alejandro Gómez-Delgado¹, Nayeli Ortiz-Olvera⁴, Gerardo Aparicio-Ozores⁵, Varenka J Barbero-Becerra⁶, Javier Torres¹, Margarita Camorlinga-Ponce¹

Affiliations

¹ Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico.
² Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico.
³ Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States.
⁴ Departamento de Gastroenterología, UMAE Hospital de Especialidades, Instituto Mexicano del Seguro Social, México City, Mexico.
⁵ Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico.
⁶ Translational Research Unit, Medica Sur Clinic and Foundation, México City, Mexico.

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.

Keywords: Clostridioides difficile; adults and children; antibiotic resistance; multilocus sequence typing; mutation; whole-genome sequencing.