Surveillance and Genomics of Toxigenic Vibrio cholerae O1 From Fish, Phytoplankton and Water in Lake Victoria, Tanzania

Abstract

The occurrence of toxigenic Vibrio cholerae O1 during a non- outbreak period in Lake Victoria was studied and genetic characteristics for environmental persistence and relatedness to pandemic strains were assessed. We analyzed 360 samples of carps, phytoplankton and water collected in 2017 during dry and rainy seasons in the Tanzanian basin of Lake Victoria. Samples were tested using PCR ( omp W and ctx A) with DNA extracted from bacterial isolates and samples enriched in alkaline peptone water. Isolates were screened with polyvalent antiserum O1 followed by antimicrobial susceptibility testing. Whole genome sequencing and bioinformatics tools were employed to investigate the genomic characteristics of the isolates. More V. cholerae positive samples were recovered by PCR when DNA was obtained from enriched samples than from isolates (69.0% vs. 21.3%, p < 0.05), irrespectively of season. We identified ten V. cholerae O1 among 22 ctx A-positive isolates. Further studies are needed to serotype the remaining ctx A-positive non-O1 strains. Sequenced strains belonged to El Tor atypical biotype of V. cholerae O1 of MLST ST69 harboring the seventh pandemic gene. Major virulence genes, ctxA, ctxB, zot, ace, tcpA, hlyA, rtxA, ompU, toxR, T6SS, alsD, makA and pathogenicity islands VPI-1, VPI-2, VSP-1, and VSP-2 were found in all strains. The strains contained Vibrio polysaccharide biosynthesis enzymes, the mshA gene and two-component response regulator proteins involved in stress response and autoinducers for quorum sensing and biofilm formation. They carried the SXT integrative conjugative element with phenotypic and genotypic resistance to aminoglycoside, sulfamethoxazole, trimethoprim, phenicol, and quinolones. Strains contained a multidrug efflux pump component and were resistant to toxic compounds with copper homeostasis and cobalt-zinc-cadmium resistance proteins. The environmental strains belonged to the third wave of the seventh pandemic and most are genetically closely related to recent outbreak strains from Tanzania, Kenya, and Uganda with as low as three SNPs difference. Some strains have persisted longer in the environment and were more related to older outbreak strains in the region. V. cholerae O1 of outbreak potential seem to persist in Lake Victoria through interactions with fish and phytoplankton supported by the optimum water parameters and intrinsic genetic features enhancing survival in the aquatic environment.

Genome-Based Analysis of Extended-Spectrum β-Lactamase-Producing Escherichia coli in the Aquatic Environment and Nile Perch (Lates niloticus) of Lake Victoria, Tanzania

“…In contrast to our study, the ESBLproducing bacteria reported in tilapia from the Mwanza region by Moremi et al (2016b) included a much more diverse population of bacterial species, a variety of ESBL genes, and no indication of a clonal relationship. The occurrence of genes encoding for resistance to metals such as copper, cobalt, zinc, cadmium, and mercury, and also genes encoding resistance to detergents is similar to previous findings in fish and aquatic environment of the Lake Victoria; the genes have been reported to play a role in environmental persistence support in bacterial survival (Moremi et al, 2016b;Hounmanou et al, 2019). Most of metal resistance genes were located on the chromosome, whereas ESBL genes were mostly located on the plasmids, except that all four ST636 isolates harbored a chromosomally located bla CTX−M−15 gene, and it is uncertain to what extent exposure to metals, for example, used as livestock feed additives and as pollutants in aquatic environments, may play a role as co-selectors of ESBL resistance.…”

Comprehensive genomic analysis of Vibrio cholerae from three outbreaks in Uganda, 2014 - 2016

“…al, 2018; also, the nding of this study in regards to most of the isolates except one belonging to the O1 serotype are consistent with other studies elsewhere, these studies attributed this to the presence of the rfbV-O1 gene in isolates classi ed as O1 (5). Unlike a similar study done in the East African region (5) in which MLST revealed that their isolates belonged to a single sequence type (ST), ST69, this study revealed that the isolates belonged to two STs namely ST69 and ST515. Strains of V. cholerae belonging to the ST515 have been reported elsewhere (9).…”

“…Despite the World Health Organization (WHO) recommendations (https://www.who.int/topics/cholera/publications/WHO_CDD_SER_91_15/en/) in regards to the management of cholera with oral rehydration salts in addition to antibiotics namely streptomycin, aminoglycosides, trimethoprim, fosfomycin, uoroquinolones, sulphonamides, chloramphenicol/ orfenicol, and tetracyclines, this study reports genotypic resistance in the isolates to the same antibiotics. Similar resistance has been reported in similar studies done in the East African region and elsewhere (5,(15)(16)(17).…”

“…The virulence genes reported in this study are similar to those reported in similar studies elsewhere (5,(10)(11)(12), these genes included among others those belonging to the Type IV secretion system, those involved in adherence, Type IV pilus genes as well as those involved in quorum sensing.…”

“…The use of these methods has been associated with several challenges (1,3). Unlike these methods, high-throughput sequencing culture-independent methods have been documented to provide an unprecedented view of pathogen biology as well as delivery of high-resolution genomic epidemiology via rapid and cheap whole-genome sequencing (4)(5)(6)(7). Despite this knowledge, sequencing remains a less desirable option for most scientists in Uganda and hence comprehensive genomic data on V. cholerae remains unavailable.…”