ABSTRACTVibrio 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 μm 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.SIGNIFICANCECholera 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.
Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour