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

Abstract

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

Keywords: gastroenteritis outbreak; multidrug resistance genomic island; non-O1/non-O139Vibrio cholerae; type III secretion system (T3SS); type VI secretion system (T6SS).

Fig. 1.

Phylogenetic relationship between 70 V . cholerae strains. (a) Maximum likelihood phylogenetic tree (midpoint rooted) based on whole-genome SNPs (146 534 SNPs within 2 483 145 positions, which were found in all analysed genomes). The genome of the V. cholerae str. N16961 was used as the reference. Bayesian analysis of population structure grouped the strains into five sequence clusters (SC; SC1 to SC5), which were further divided into 12 lineages. The epidemiological data of each strain is shown, including country and year of isolation. MLST sequence types (STs) are shown. (b) Heat map showing the presence, absence and variation of major virulence-associated genes distributed among the strains. Presence and variation (nucleotide identity levels, ranging from 80 to 100 %) for each gene are indicated by colour intensity (red to yellow), as shown in the legend. The analysis was performed using blastn. Absence was defined as an identity and/or gene coverage of less than 80 and 60 %, respectively and is indicated in grey.

Fig. 2.

Comparison of the genomes of the V. cholerae str. Santiago-089 and 48 representative V. cholerae strains. The genomes are compared against the reference genome of V. cholerae str. N16961. The outermost ring (blue) shows the genome of V. cholerae str. Santiago-089. All other genomes are shown in red rings. blastn comparisons between reference genome and query genomes are shown as % identity according to the legend at the right. White regions indicate absence of genes or identity levels below 85 %. The location of the major genomic islands is indicated as black bars. VSP, Vibrio seventh pandemic island; VPI, Vibrio pathogenicity island; CTX/TLC, cholera toxin/toxin-linked cryptic. The figure was prepared using brig [23].

Fig. 3.

Comparison of the genetic structures of genomic islands carried by the V. cholerae str. Santiago-089. Predicted genes and the direction of transcription are represented as block arrows. Genes are colour-coded according to gene function, as indicated in the legends at the bottom. The names of some genes are indicated. Conserved regions are shaded in grey and the intensity of the colour indicates nucleotide identity levels, as indicated in the legends at the right. Contig boundaries are shown as red lines. (a) Genomic islands encoding a T3SS. GenBank accessions: GIVch-T3SS_AM-19226 (AATY02000004 and AATY02000003), GIVch-T3SS_10432-62 (CP010812), GIVch-T3SS_Santiago-089 (SRLP00000000). (b) Genomic islands encoding CRISPR-Cas and T6SS genes. GenBank accessions: GIVch-T6SS_HC-36A1 (AXDR01000008.1), GIVch-T6SS_Santiago-089 (SRLP00000000), GIVchS12 (KU722393). ORFs of the GIVch-T6SS_Santiago-089 are listed in Table S3. (c) Multidrug resistance (MDR) islands. The GIVch-MDR_Santiago-089 (GenBank accession: SRLP00000000) harbours the sul1 and dfrA15 genes, which confer resistance to sulfonamide and trimethoprim, respectively. ORFs of the GIVch-MDR_Santiago-089 are listed in Table S4. GIVchHai6 (GenBank accession: AXDR01000001).