Diversity of multidrug-resistant epidemic Clostridium difficile NAP1/RT027/ST01 strains in tertiary hospitals from Honduras

Hidalgo-Villeda, Fanny; Tzoc, Edgardo; Torres, Luque; Bu, Efraín; Rodríguez, César; Quesada-Gómez, Carlos

doi:10.1016/j.anaerobe.2018.06.001

Cited by 8 publications

(2 citation statements)

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“…Therefore, we anticipate that they are functional and hypothesize that they were acquired through transposition or conjugation events once the isolates entered LA. Although cfr -like genes, ermB and tetM have already been found in C. difficile from other countries [ 17, 64, 65 ] we describe here for the first time the presence of a cfr -like gene linked to ermB in a putative ICE of ca. 46 kb (Fig.…”

Section: Discussionmentioning

confidence: 63%

“…As indicated by reports from Costa Rica [ 12 ], Panama [ 13 ], Chile [ 14 ], Mexico [ 15 ], Colombia [ 16 ] and Honduras [ 17 ], the B1/NAP1/RT027/ST01 strain has been present for at least 10 years in Latin America (LA). However, since nearly all in-depth studies on the molecular epidemiology of this epidemic strain have been conducted in Europe and the USA, the origin, date of introduction, diversity and microevolution of the B1/NAP1/RT027/ST01 strain in LA remains obscure.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2020

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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.

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Section: Discussionmentioning

confidence: 63%