Recent mixing of Vibrio parahaemolyticus populations

Abstract

20Background Humans have profoundly affected the ocean environment but little is known 21 about anthropogenic effects on the distribution of microbes. Vibrio parahaemolyticus is found 22 in warm coastal waters and causes gastroenteritis in humans and economically significant 23 disease in shrimps. 24Results Based on data from 1,103 genomes, we show that V. parahaemolyticus is divided 25 into four diverse populations, VppUS1, VppUS2, VppX and VppAsia. The first two are 26 largely restricted to the US and Northern Europe, while the others are found worldwide, with 27 VppAsia making up the great majority of isolates in the seas around Asia. Patterns of 28 diversity within and between the populations are consistent with them having arisen by 29 progressive divergence via genetic drift during geographical isolation. However, we find that 30 there is substantial overlap in their current distribution. These observations can be reconciled 31 without requiring genetic barriers to exchange between populations if dispersal between 32 oceans has increased dramatically in the recent past. We found that VppAsia isolates from the 33 US have an average of 1.01% more shared ancestry with VppUS1 and VppUS2 isolates than 34 VppAsia isolates from Asia itself. Based on time calibrated trees of divergence within 35 epidemic lineages, we estimate that recombination affects about 0.017% of the genome per 36year, implying that the genetic mixture has taken place within the last few decades. 37Conclusions These results suggest that human activity, such as shipping and aquatic products 38 trade, are responsible for the change of distribution pattern of this marine species. 39 40 Keywords 41 Vibrio parahaemolyticus, population structure, biogeography, anthropogenic change, ocean 42 dispersal 43 44 3 45 Background 46 Hospitable environments for particular marine microbes can be separated by large distances 47 but whether dispersal barriers substantially influence their distribution and evolution is 48 unknown. There are many studies of distribution of marine microbes e.g. [1-4], but these 49 typically survey patterns of macro-scale diversity. Differences in species level or genus level 50 composition between locations are as likely to reflect environmental heterogeneity as 51 dispersal, making the patterns difficult to interpret. Recent spread of microbes between 52 continents has been documented for lineages that cause pathogenic infection of humans, 53 including notorious clonal groups within Vibrio parahaemolyticus and Vibrio cholerae [5-8]. 54 However, these lineages are unusual in using humans as vectors, which might facilitate long-55 range dispersal as in the case of the Haitian cholera outbreak [9]. We currently have little 56 information on rates of spread of the great majority of environmental organisms that do not 57 colonize large-animal hosts. 58 59 V. parahaemolyticus prefers warm coastal waters and causes gastroenteritis in humans [10, 60 11]. Disease outbreaks became common from 1990s and became global, due to spread of 61 pa...

The landscape of coadaptation in Vibrio parahaemolyticus

“…For each interaction group, we investigated how genetic variation was structured within the V. parahaemolyticus population using a larger “non-redundant” set of 469 strains, which includes isolates from all four of the populations identified in (8), but excludes closely related isolates, differing at less than 2,000 SNPs. We performed hierarchical clustering of the strains based on the interaction group variants (Figure 3, 4, 5, S2).…”

“…Totally 1,103 global V. parahaemolyticus genomes were used in this work (Table S1), which also were analyzed in our other studies (8, 10). To reduce clonal signals, we firstly made a “non-redundant” dataset of 469 strains, in which no sequence differed by less than 2,000 SNPs in the core genome.…”

“…It is capable of replicating in less than 10 minutes in appropriate conditions (6), while the doubling time in the wild of the related bacteria Vibrio cholerae has been estimated as slightly over an hour (7). Approximately 0.017% of the genome recombines each year (8), implying that there are approximately 50 million generations on average between recombination events at a given genetic locus. As a result, mutations that are beneficial only on specific backgrounds have a chance to rise to high frequency on those backgrounds even if they are harmful on others.…”

Separating Functions of the Phage-Encoded Quorum-Sensing-Activated Antirepressor Qtip

“…As phage VP882 has the capacity to activate lysis in response to host DPO production, we wondered whether mutations in the phage-encoded QS pathway similarly arise. As one example, we identified a curious 8.5 kb contig (GenBank: NNHH01000051.1) in a recent dataset from mixed V. parahaemolyticus populations (Yang et al, 2019) (Figure S6B). The contig spans the region where vqmAPhage and qtip are located in phage VP882, between two conserved genes, repA and telN (Silpe and Bassler, 2019a).…”

Managing the risk of Vibrio parahaemolyticus infections associated with oyster consumption: A review

“…A study by Rehnstam‐Holm, Atnur, and Godhe (2014) also reported that the occurrence of V. parahaemolyticus in offshore areas of the southwest coast of India in the Arabian Sea was positively correlated with the abundance of copepods. Evidence suggests that zooplankton and copepods facilitate the oceanic dispersal of V. parahaemolyticus populations (Martinez‐Urtaza et al., 2012; Rehnstam‐Holm et al., 2014), which facilitates the spread of V. parahaemolyticus infections (Raszl, Froelich, Vieira, Blackwood, & Noble, 2016; Yang et al., 2019). A study by Martinez‐Urtaza et al.…”