Biology subjects

Boucher, Y. F.

Publications and source records attributed to Boucher, Y. F..

6 recordsLinked to original sources

bioRxiv2026

Culture-enriched metagenomics enables genome-resolved detection of low abundance ESKAPE and Vibrio pathogens in coastal habitats

Coastal marine environments are increasingly recognised as reservoirs of antimicrobial-resistant (AMR) pathogens. However, it remains challenging to recover high-quality genomes of clinically relevant bacteria present at low abundance from complex natural systems. Here, we applied culture-enriched metagenomics to systematically track the diversity and dynamics of major AMR pathogens within the coastal marine system of St. Johns Island, Singapore, as a model ecosystem for pathogen surveillance. Selective media-based enrichment recovered 773 metagenome-assembled genomes (MAGs) from 92 multi-matrix environmental samples, which includes coastal water, sediment, and seaweed, capturing diverse AMR ESKAPE and Vibrio species. Distinct bacterial signatures and dispersal patterns were observed in each niche, for example, microbes that signal human impact was detected at the beach, while fish-associated pathogens were present at the aquaculture facility outlet. Notably, the high-quality MAGs enabled subspecies-level identification and supported the AMR gene detection across six distinct coastal habitats. Detailed differences in the recovery of specific pathogens across enrichment media were also identified, demonstrating the methods efficacy in finding media suitable for surveillance of specific organisms, such as deciding between liquid or solid formulations. MAGs recovered from culture-enriched metagenomics were highly similar to genomes obtained from pure isolates, as demonstrated for Klebsiella pneumoniae. The preserved culture-enriched stocks were capable of recovering organisms of interest when individual isolates were required for further study. Overall, our findings highlight the utility of culture-enriched metagenomics as a cost-effective, sensitive approach to uncovering the genomic landscape of pathogens with environmental reservoirs, with implications for AMR surveillance and ecological risk assessment.

microbiology↗

bioRxiv2026

Lessons from the equator: a window on the future of vibriosis in a warming Earth

Vibrios are important aquatic human pathogens, causing gastroenteritis, wound infections, and cholera. Vibriosis (non-cholera infection) has been increasing in temperate climates due to correlation between Vibrio abundance and water temperature. However, how warming oceans differentially influence various Vibrio species, and whether incidence is higher in tropical regions, remains understudied. We assembled the first comprehensive dataset of culture-confirmed vibriosis cases outside a temperate climate from equatorial Singapore. Comparison to cases from the detailed United States (US) CDC COVIS system revealed that vibriosis incidence is over two times higher in Singapore than the United States. Causative species also differ markedly, with Vibrio fluvialis and non-toxigenic Vibrio cholerae dominating in Singapore (>40%) but are much less prominent in the United States (<15%). Singapore cases have remained stable in the last decade, while US incidence is rising rapidly, especially for V. fluvialis and V. cholerae (13% and 17% per year). Differences in causative species in Singapore and the United States suggest ecological factors may shape infection dynamics, with some species benefitting more from warming oceans, raising their equatorial prominence. Incidence is stable in Singapore, likely due to slower warming of waters near the equator. In contrast, vibriosis in the United States will likely continue to increase steadily, with changing species composition, likely becoming tropicalized.

microbiology↗

bioRxiv2022

Vibrio tarriae sp. nov., a novel member of the Cholerae clade isolated from across the United States

A number of bacteria with close resemblance to Vibrio cholerae has been isolated over the years by the Centers for Disease Control and Prevention (CDC), which could not be assigned a proper taxonomic designation based on preliminary identification methods. Nine such isolates have been found to share 16S rRNA gene identity exceeding 99% with V. cholerae, yet DNA-DNA hybridization (60.4-62.1%) and average nucleotide identity values (94.4-95.1%) were below the species cut-off, indicating a potentially novel species. Phylogenetic analysis of core genomes places this group of isolates in a monophyletic clade, within the "Cholerae clade," but distinct from any other species. Extensive phenotypic characterization reveals unique biochemical properties that distinguish this novel species from V. cholerae. Comparative genomic analysis reveals a unique set of siderophore genes, suggesting that iron acquisition strategies could be vital for the divergence of the novel species from a common ancestor with V. cholerae. Based on genetic, phylogenetic, and phenotypic differences observed, we propose these isolates represent a novel species of the genus Vibrio, for which the name Vibrio tarriae sp. nov. is proposed. Strain 2521-89 (= DSM 112461 = CCUG 75318), isolated from lake water, is the type strain. Author NotesThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain 2521-89 is MW773202.1. The genome sequences (genome assemblies) of strains 2521-89, 2523-88, 2015V-1076, 2016V-1018, 2016V-1062, 2017V-1038, 2017V-1070 and 2017V-1124 are deposited under the accession number NZ_CP022353.1, QKKG01000001.1, QKKH00000000.1, QKKI00000000.1, QKKJ00000000.1, QKKK00000000.1, QKKM00000000.1, and QKKN00000000.1, respectively. All the whole genome sequences are deposited under bioproject ID: PRJNA391152.

microbiology↗

bioRxiv2021

Population analysis of Vibrio cholerae in aquatic reservoirs reveals a novel sister species (Vibrio paracholerae sp. nov.) with a history of association with human infections

Most efforts to understand the biology of Vibrio cholerae have focused on a single group, the pandemic-generating lineage harbouring the strains responsible for all known cholera pandemics. Consequently, little is known about the diversity of this species in its native aquatic environment. To understand the differences in the V. cholerae populations inhabiting in regions with varying history of cholera cases and how that might influence the abundance of pandemic strains, a comparative analysis of population composition was performed. Little overlap was found in lineage compositions between those in Dhaka (cholera endemic) located in the Ganges delta, and of Falmouth (no known history of cholera), a small coastal town on the US East Coast. The most striking difference was the presence of a group of related lineages at high abundance in Dhaka which was completely absent from Falmouth. Phylogenomic analysis revealed that these lineages form a cluster at the base of the phylogeny of V. cholerae species, sufficiently differentiated genetically and phenotypically to form a novel species. Strains from this species have been anecdotally isolated from around the world and were isolated as early as 1916 from a British soldier in Egypt suffering from choleraic diarrhoea. In 1935 Gardner and Venkatraman unofficially referred to a member of this group as Vibrio paracholerae. In recognition of this earlier designation, we propose the name Vibrio paracholerae, sp. nov. for this bacterium. Genomic analysis suggests a link with human populations for this novel species and substantial interaction with its better-known sister species. ImportanceCholera continues to remain a major public health threat around the globe. Understanding the ecology, evolution and environmental adaptation of the causative agent Vibrio cholerae and tracking the emergence of novel lineages with pathogenic potential are essential to combat the problem. In this study, we investigated the population dynamics of Vibrio cholerae in an inland locality which is known as endemic for cholera and compared with that of a cholera free coastal location. We found the consistent presence of the pandemic generating V. cholerae in cholera-endemic Dhaka and an exclusive presence of a lineage phylogenetically distinct from other V. cholerae. Our study suggests that this lineage represents a novel species having pathogenic potential and a human link to its environmental abundance. The possible association with human population, co-existence and interaction with toxigenic V. cholerae in the natural environment make this potential human pathogen an important subject for future studies.

microbiology↗

bioRxiv2020

A Vibrio Cholerae Core Genome Multilocus Sequence Typing Scheme to Facilitate the Epidemiological Study of Cholera

Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive dataset of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates which could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/). IMPORTANCEToxigenic Vibrio cholerae of the O1 and O139 serogroups are the causative agent of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing (cgMLST) scheme for V. cholerae. Using cgMLST, we established an outbreak threshold that can efficiently identify outbreak related strains and potential sources of introduction. We also defined a sublineage threshold that is similar to traditional MLST sequence type which will provide context to this new typing method by relating it to previous MLST results. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use, making this scheme the most suitable method for V. cholerae typing and surveillance worldwide.

microbiology↗

bioRxiv2019

Simultaneous quantification of Vibrio metoecus and Vibrio cholerae with its O1 serogroup and toxigenic subpopulations in environmental reservoirs

Vibrio metoecus is a recently described and little studied causative agent of opportunistic infections in humans, often coexisting with V. cholerae in aquatic environments. However, the relative abundance of V. metoecus with V. cholerae and their population dynamics in aquatic reservoirs is still unknown. We developed a multiplex qPCR assay with a limit of detection of three copies per reaction to simultaneously quantify total V. metoecus and V. cholerae abundance, as well as the toxigenic and O1 serogroup subpopulations of V. cholerae from environmental samples. Four different genes were targeted as specific markers for individual Vibrio species or subpopulations; viuB, a gene encoding a vibriobactin utilization protein, was used to quantify the total V. cholerae population. The cholera toxin gene ctxA provided an estimation of toxigenic V. cholerae abundance, while the rfbO1 gene specifically detected and quantified V. cholerae belonging to the O1 serogroup, which includes almost all lineages of the species responsible for the majority of past and ongoing cholera pandemics. To measure V. metoecus abundance, the gene mcp, encoding methyl accepting chemotaxis protein, was used. Marker specificity was confirmed by testing several isolates of V. cholerae and V. metoecus alongside negative controls of isolates within and outside of the Vibrio genus. Analysis of environmental water samples collected from four different geographic locations including cholera-endemic (Dhaka, Kuakata and Mathbaria in Bangladesh) and non-endemic (Oyster Pond in Falmouth, Massachusetts, USA) regions showed that V. metoecus was only present in the USA site, recurring seasonally. Within the coastal USA site, the non-toxigenic O1 serogroup represented up to [~]18% of the total V. cholerae population. V. cholerae toxigenic O1 serogroup was absent or present in low abundance in coastal Bangladesh (Kuakata and Mathbaria) but constituted a relatively high proportion of the total V. cholerae population sustained throughout the year in inland Bangladesh (Dhaka). A preference for host/particle attachment was observed, as the majority of cells from both Vibrio species (>90%) were identified in the largest water size fraction sampled, composed of particles or organisms >63 m and their attached bacteria. This is the first study to apply a culture-independent method to quantify V. cholerae or V. metoecus directly in environmental reservoirs of areas endemic and non-endemic for cholera on significant temporal and spatial scales.\n\nSIGNIFICANCECholera is a life-threatening disease that requires immediate intervention; it is of prime importance to have fast, accurate and sensitive means to detect V. cholerae. Consistent environmental monitoring of the abundance of V. cholerae along with its toxigenic and O1 serogroup subpopulations could facilitate the determination of the actual distribution of this organism in aquatic reservoirs and thus help to predict an outbreak before it strikes. The lack of substantial temporal and spatial environmental sampling, along with specific quantitative measures, has made this goal elusive so far. The same is true for V. metoecus, a close relative of V. cholerae which has been associated with several clinical infections and could likely pose an emerging threat, readily exchanging genetic material with its more famous relative.

microbiology↗