Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018

Abstract

43Vibrio cholerae is a human pathogen which is transmitted by the consumption of contaminated 44 food or water. V. cholera strains belonging to the serogroups O1 and O139 can cause cholera 45 outbreaks and epidemics, a severe life-threatening diarrheal disease. In contrast, serogroups 46 other than O1 and O139, denominated as non-O1/non-O139, have been mainly associated with 47 sporadic cases of moderate or mild diarrhea, bacteremia and wound infections. Here we 48 investigated the virulence determinants and phylogenetic origin of a non-O1/non-O139 Vibrio 49 cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018. We found that this 50 outbreak strain lacks the classical virulence genes harbored by O1 and O139 strains, including 51 the cholera toxin (CT) and the toxin-coregulated pilus (TCP). However, this strain carries genomic 52 islands (GIs) encoding Type III and Type VI secretion systems (T3SS/T6SS) and antibiotic 53 resistance genes. Moreover, we found these GIs are wide distributed among several lineages of 54 non-O1/non-O139 strains. Our results suggest that the acquisition of these GIs may enhance the 55 virulence of non-O1/non-O139 strains that lack the CT and TCP-encoding genes. Our results 56 highlight the pathogenic potential of these V. cholerae strains.

Analysis of the antimicrobial resistance gene frequency in whole-genome sequenced Vibrio from Latin American countries

“…Despite the limited number of studies that have analysed the antimicrobial resistance of Vibrio strains in Latin America [18][19][20][21][22][23][24][25][26] and the fact that the present study did not comprehended phenotypic resistance results, our findings agree with previous reports on both genotypic and phenotypic data from these countries. Our data also reinforce the accuracy of WGS and its capacity to predict phenotypic antimicrobial resistance profiles.…”

“…The present study also demonstrated that 99.8 % of the strains harboured at least one resistance gene and 52.4 % of the strains harboured three or more resistance genes for different antimicrobial classes (Table 2). The last information suggested that the isolates may also display a possible phenotypic MDR profile, as previously reported for Vibrio strains of different species [18][19][20][21][22][23][24][25][26]. Our findings are worrisome because these drug-resistant Vibrio strains may have been causing infections with particular resistance to drugs indicated for human therapy, which in turn may also increase the risk of treatment failure and death of infected individuals.…”

“…The isolates from human, environmental, animal and food sources included in this study also harboured genes that confer resistance to antimicrobials usually not recommended for human therapy, such as amphenicols, streptogramin, rifamycin, fosfomycin and antibiotic peptides (Table 2). Previous studies have reported similar resistance profiles using phenotypic and genotypic methods [18][19][20][21][22][23][24][25][26]. The most plausible explanation is that these genes, and even the ones that confer resistant to antimicrobials used in human therapy, may have been acquired by horizontal *The percentages of the frequency of resistance genes and sequence types were calculated according to the number of strains present for each country, source and period of isolation.…”

Antibiotic Resistance in Vibrio cholerae: Mechanistic Insights from IncC Plasmid-Mediated Dissemination of a Novel Family of Genomic Islands Inserted at trmE

“…Given the presence of MGI Vch Hai6-like elements integrated at different chromosomal sites and across a wide range of Vibrionaceae and other species of Gammaproteobacteria , IncC plasmids and their subordinate GIs can be concluded to comprise a potent driving force in the gene flow circulating in many bacterial pathogens. In fact, this is superbly exemplified by the recently reported presence of an MGI Vch Hai6-like GI in V. cholerae Santiago-089, a non-O1/non-O139 clinical isolate harboring many virulence genes scattered throughout chromosome 1 ( 52 ). Not only is the GI itself poised to be mobilized by an incoming IncC plasmid—along with the GI-borne antibiotic and mercury resistance genes—but it is also plausible that it may, in fact, usher transfer of downstream elements GI Vch -T3SS and VPI-2, thus simultaneously contributing to dissemination of virulence determinants.…”

“…The geographical range of V. cholerae is expected to expand dramatically as climate change renders the marine environment increasingly hospitable to this pathogen ( 54 , 55 ). While the ability to promote epidemic outbreaks was traditionally regarded as an appanage of O1 and O139 strains ( 56 ), it is becoming increasingly clear that the actual picture is far more nuanced ( 52 , 57 – 60 ). In various species, cumulative acquisition of antibiotic resistance and/or virulence determinants through exchange of genomic islands has time and again allowed emergence of virulent strains, some of which lack canonical virulence hallmarks ( 61 – 63 ).…”