Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico

Abstract

Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica ( n =16), Chile ( n =5), Honduras ( n =3) and Mexico ( n =1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage ( n =23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8–4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA ) or antibiotic resistance (i.e. rpoB , fusA ) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n =4) than related isolates from other regions. Their unique set of ARGs includes a cfr -like gene and tetM , which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.

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

“…The molecular epidemiology of C. difficile infection (CDI) has shown that the bacterial genome and the disease have become very variable in the last decades. The incidence of CDI markedly increased worldwide at the end of the twentieth century ( Czepiel et al, 2019 ), which was associated with the rapid spread of the hypervirulent strain NAP1/B1/027/ST01 [North American Pulse field type 1/restriction endonuclease analysis type BI/ribotype 027/multilocus sequence typing (MLST)] ( Krutova et al, 2018 ; Lv et al, 2019 ; Guerrero-Araya et al, 2020 ). In addition, 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 ).…”

“…Although CDI is an important cause of hospital-acquired diarrhea and colitis in Latin America ( Muñoz et al, 2018 ; Guerrero-Araya et al, 2020 ), little is known about antibiotic resistance and molecular epidemiology of C. difficile in this region. In recent years, studies in Mexico have focused mainly on molecular typing of C. difficile strains, particularly on the identification of the hypervirulent strain RT027 using PCR ribotyping ( Camacho-Ortiz et al, 2015 ; Martínez-Meléndez et al, 2018 ).…”

Resistance of Clostridioides difficile spores (Clostridiales: Peptostreptococcaceae) to sodium dichloroisocyanurate

“…Furthermore, it is highly resistant to disinfectants due to the activity of efflux pumps and ABC transporters (Dawson et al, 2011). This genotype has circulated in Costa Rica for more than a decade (Guerrero-Araya et al, 2020). It occasionally predominates, yet it has been outnumbered by other lineages (López-Ureña et al, 2016), such as the NAP9 (MLST Clade 4) and the NAP CR1 (MLST Clade 1) strains.…”