In:
Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 29 ( 2012-07-17)
Abstract:
The present study speaks to the critical need for an up-to-date, properly curated, and publicly available reference genomic database (including geographically diverse and circulating strains from regions where cholera is endemic) reflecting quality coverage of global phylogenetic diversity as well as diversity within this heterogeneous clade and its phylogenetic near-neighbors. The need for such a qualified database is critically important if investigations of future V. cholerae epidemics are to be effective and timely for public health applications. Moreover, it may also be necessary to generate the database during an epidemic, as the apposite comparator if SNP data are to be used to assign attribution in outbreak investigations. Results of comprehensive genomic analysis showed that V. cholerae O1 populations were clonal, resembling epidemic isolates from South Asia and Africa, whereas V. cholerae non-O1/O139 populations were not clonal and harbor a genomic backbone similar to that of toxigenic V. cholerae O1 circulating in the western hemisphere ( Fig. P1 ). Of interest, V. cholerae O1 strains from Zimbabwe, Zambia, Mexico, Thailand, Bangladesh, and Haiti contained a distinct genotype (8.3.6.n.n) not observed previously. Environmental V. cholerae non-O1/O139 isolates exhibited diverse VNTR genotypes with variability at all five loci. However, the clinical V. cholerae non-O1/O139 isolates possessed an identical VNTR genotype, akin to, but distinct from, the clinical V. cholerae O1 isolates. We observed a single amino acid residue deletion in the rst B gene of the Haitian V. cholerae O1 strains. This deletion, a unique feature for a classical biotype of V. cholerae , was not detected in any of the Altered El Tor, Hybrid, or El Tor variants of V. cholerae , except V. cholerae CP1048 (Bangladesh, 2010) and CP1032 (Mexico, 1991), INDRE 91/1 (Mexico, 1991), and RC27 (Indonesia, 1991), proving that this deletion is not singularly a characteristic of western hemisphere isolates. Moreover, PCR amplification and sequence analysis of rst B gene identified two unique polymorphisms. Whole-genome mapping of the selected isolates also demonstrated polymorphisms within the Haitian outbreak strains and between Haitian and the other reference strains. Genome similarity clustering of both chromosomes reinforced the conclusion that the Haitian outbreak isolates did not differ substantially from isolates from Zimbabwe (CP1038) and Bangladesh (CP1048). The core genome phylogeny ( Fig. P1 ) of the Haitian V. cholerae isolates demonstrates that the majority of V. cholerae non-O1/O139 strains cluster with toxigenic V. cholerae O1 strains (e.g., Amazonia and TM11079-80) ( 2 , 4 ) implicated in sporadic cases and epidemics originating in the western hemisphere (Brazil, 1991 and 1980), indicating potential indigenous origin of these strains. The Haitian V. cholerae O1 strains, on the contrary, tightly clustered together, along with the clinical isolates from Zimbabwe (CP1038) and Bangladesh (CP1048 and CP1050). This observation agrees with a recent report of shared ancestry of Haiti, India, and Cameroon isolates. Phylogenetic analysis also reveals that within the short span of 3 wk, early in the cholera epidemic, substantial genomic diversity accumulated in the circulating population ( Fig. P1 ). In the present study, we report the analysis of clinical samples from 81 patients showing symptoms of cholera with varying severity from 18 towns across eight Arrondissements of Haiti, spanning 3 wk in November 2010, very early in the outbreak. Bacteriological analysis identified V. cholerae O1 and V. cholerae non-O1/O139 as pathogen in 48% and 21% of the samples, respectively. V. cholerae O1 and non-O1/O139 were cocultured from 7% of the O1 positive samples. We sequenced whole genomes of 47 V. cholerae O1 and 29 V. cholerae non-O1/O139 isolates from patients and the environment in Haiti as well as eight reference strains of V. cholerae O1 isolated in concurrent epidemics outside Haiti. Our analysis of these Haitian isolates, along with 27 V. cholerae genomes ( 2 , 3 ) available in public databases, demonstrates the utility of combining multiple approaches [multilocus variable-number tandem repeat (VNTR) analysis, SNP, mobile genetic elements, core genome phylogeny, and whole-genome mapping, formerly known as optical mapping] in defining genetic diversity for a given population. The results revealed that two distinct Vibrio populations, V. cholerae O1 and V. cholerae non-O1/O139, contributed to the cholera epidemic in Haiti. Because non-O1/O139 V. cholerae was the sole pathogen isolated from 21% of the clinical specimens, its role in this epidemic, either alone or in concert with V. cholerae O1, cannot be dismissed. Cholera is a disease endemic in many developing countries, and its causative agent, Vibrio cholerae , is indigenous to estuaries and river systems worldwide ( 1 ). The devastating 2010 cholera epidemic in Haiti generated worldwide attention. Assignation of potential source was explored in several published works, but a definitive assignment was not established. In this study, genomes of V. cholerae isolates from Haitian patients with cholera were examined to explore diversity within this species. V. cholerae O1 and non-O1/O139 were isolated repeatedly from patients in early weeks of the outbreak, underscoring the difficulty in verifying the ultimate source and origin of outbreak strain(s). Our analysis indicates the importance of maintaining up-to-date public databases of pathogen genome sequences to combat and even prevent future outbreaks of cholera.
Type of Medium:
Online Resource
ISSN:
0027-8424
,
1091-6490
DOI:
10.1073/pnas.1207359109
Language:
English
Publisher:
Proceedings of the National Academy of Sciences
Publication Date:
2012
detail.hit.zdb_id:
209104-5
detail.hit.zdb_id:
1461794-8
SSG:
11
SSG:
12
