Genomic and Evolutionary Insights into Australian Toxigenic Vibrio cholerae O1 Strains

Abstract

Australia has its own indigenous V. cholerae strains, both toxigenic and nontoxigenic, that are associated with disease. Exotic strains are also detected in Australian patients returning from overseas travel.

Clinical and Environmental Vibrio cholerae Non-O1, Non-O139 Strains from Australia Have Similar Virulence and Antimicrobial Resistance Gene Profiles

“…In a similar way, genotype 2 ctxB -containing CTX prophage was previously reported in outbreak-related V. cholerae O1 El Tor strains from Australia ( 34 ) and is also observed in clinical NOVC strains in this study. Notably, three of the toxigenic NOVC clinical and environmental strains, M12590, M138351, and 243712, had single or double copies of the genotype 2-containing CTX phage region as shown in Table 2 .…”

“…This study has extensively investigated the genotypic features of clinical and environmental NOVC strains from Australia as having similar virulence potential. Interestingly, in this study we confirmed the presence of ctxB genotype 2, CTX phage region, among environmental NOVC strains from Australia similar to toxigenic Queensland outbreak-related O1 El Tor V. cholerae clinical and environmental strains from our previous study ( 34 ). Thus, based on our characterization of these strains QLD waterways harbor genetically diverse V. cholerae strains, which may be due to the mechanism of horizontal gene transfer and the bipartite architecture of V. cholerae ’s genome.…”

“…Among the 87 V. cholerae clinical and environmental strains used in this study ( Fig. 1 ; see also Data Set S1 in the supplemental material), serotype O1 strains ( n = 5), NOVC strains (clinical = 39, environmental = 15) from Australia, and international travel-associated NOVC strains ( n = 2) (61 in total) were sequenced, characterized, and compared to seven previously sequenced strains representing a different disease cluster ( 34 ), reference (N16961) O1 strains, and 18 additional publicly available Australian and international NOVC strains. As shown in the maximum likelihood phylogenetic tree ( Fig.…”

“…De novo assemblies were generated with the SPAdes assembler v3.12.0 ( 58 ), the quality of the assemblies was analyzed using QUAST 4.6.3, and annotation was performed by using Prokka. The quality of assemblies was determined based on the number of contigs with a length of ≥500 bp being less than 500 and the total length of the assembled contigs being similar (within 30%) to the expected genome median from the NCBI genome ( 34 ).…”

“…All the V. cholerae strains selected for this study were previously identified and characterized using a combination of biochemical, serological, and molecular methods. Furthermore, in this study, whole-genome sequences of all the strains were characterized by using the CholeraFinder ( https://cge.food.dtu.dk/services/CholeraeFinder/ ) database as described in our previous study ( 34 ) (online tool CholeraFinder v1.0). This tool uses BLAST as a search engine and was used to determine the presence of the species-specific gene ( ompW ), serogroup-specific genes ( rfbV -O1, wbfZ -O139), biotype-specific genes ( ctxB , rstR , tcpA ), seventh-pandemic-specific gene ( VC2346 ), several virulence genes ( ctxA , ctxB , zot , ace , tcpA , hlyA , stn , chxA , rtxA , ompU , toxR , mshA , makA , als , TTSS, T6SS), and pathogenic islands (VPI-1, VPI-2, VSP-I, VSP-II) with a threshold equal to 95% identity and 60% coverage as previously described ( 40 ).…”