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

Genomic and phenotypic studies amongClostridioides difficileisolates show a high prevalence of clade 2 and great diversity in clinical isolates from Mexican adults and children with healthcare-associated diarrhea

“…However, the epidemic keeps evolving, and new clades have emerged with a wide diversity of genotypes in different countries (Clades 1, 2, 3, 4, and 5 and one cryptic clade have been described) (23,24). Studies in large numbers of strains have shown that clade 1 is more prevalent worldwide, whereas, in Mexico, we found clade 2/ST1 strains to the more prevalent, in isolates from both adults and children (6) C. difficile isolates of the molecular type Clade2/ST1 have been associated with severe disease and in hospital outbreaks, and it has been suggested that these "hypervirulent" strains produce higher levels of TcdA and TcdB toxins besides the CDT toxin (28).In the present work, we found clade 2/ST1 as the most prevalent and extensively studied cytotoxicity, toxins profile, toxins expression, and whole-genome phylogeny.As suggested, most of these clade 2/ST1 strains presented the toxins profile tcdA+ tcdB+cdtA+ cdtB+.…”

“…Shortly after the identification of hypervirulent C. difficile strains RT 027 (B1/NAP1/ST1) in Canada, there were reports of CDI outbreaks caused by this strain in the United States and Europe and then Asia, Australia, and Latin America (3). In Mexico C. difficile RT-027 strain has been confirmed in hospitalized patients (4,5,6). The clinical outcome of C. difficile infection (CDI) ranges from mild diarrhea to lifethreatening pseudomembranous colitis, where virulence is mainly driven by the action of toxin A (TcdA) and toxin B (TcdB).…”

Genomic Characterization of Three Novel Bartonella Strains in a Rodent and Two Bat Species from Mexico

“…Each sample was used to produce a sequencing library with gDNA that was of sufficient quality (A 260/280 and A 260/230 > 1.5) with an average insert size of 350 bp according to the KAPA HyperPlus Kit protocol as described previously [ 16 , 17 , 18 , 19 ]. All samples were sequenced using HiSeq XTEN Sequencing System (Illumina, San Diego, CA, USA) [ 20 , 21 ].…”

Preventive and therapeutic effect of Lactobacillus paracasei ZFM54 on Helicobacter pylori-induced gastritis by ameliorating inflammation and restoring gastric microbiota in mice model

“…Susceptibility of H. pylori ZJC03 to amoxicillin, metronidazole, tetracycline, and clarithromycin was evaluated by the epsilometric method (E-test) ( 20 ). The E-test strip containing antibiotics was attached to the surface of the agar medium containing H. pylori (10 8 CFU/mL) and cultured in a microaerophilic tank (85 N 2 , 10 CO 2 , and 5% O 2 ) at 37°C for 48 h−72 h. The minimal inhibitory concentration (MIC) was determined by the point of the antibacterial ring and the strip.…”