A Metagenomic Approach to Evaluating Surface Water Quality in Haiti

Abstract

The cholera epidemic that occurred in Haiti post-earthquake in 2010 has resulted in over 9000 deaths during the past eight years. Currently, morbidity and mortality rates for cholera have declined, but cholera cases still occur on a daily basis. One continuing issue is an inability to accurately predict and identify when cholera outbreaks might occur. To explore this surveillance gap, a metagenomic approach employing environmental samples was taken. In this study, surface water samples were collected at two time points from several sites near the original epicenter of the cholera outbreak in the Central Plateau of Haiti. These samples underwent whole genome sequencing and subsequent metagenomic analysis to characterize the microbial community of bacteria, fungi, protists, and viruses, and to identify antibiotic resistance and virulence associated genes. Replicates from sites were analyzed by principle components analysis, and distinct genomic profiles were obtained for each site. Cholera toxin converting phage was detected at one site, and Shiga toxin converting phages at several sites. Members of the Acinetobacter family were frequently detected in samples, including members implicated in waterborne diseases. These results indicate a metagenomic approach to evaluating water samples can be useful for source tracking and the surveillance of pathogens such as Vibrio cholerae over time, as well as for monitoring virulence factors such as cholera toxin.

A comparative analysis of drinking water employing metagenomics

“…Metagenomic samples were sequenced with an average of 1.5 x 10 7 (min = 4.8 x 10 6 ; max = 3.0 x 10 7 ) sequence read depth across samples ( Table 2). The low DNA input observed in BW samples B and C resulted in a slightly lower number of reads, 4.8 x 10 6 and 5.6 x 10 6 , respectively, compared to the number of reads observed in samples A, D, E, and F and that employed in similar metagenomic investigations employing Ion Torrent chemistry [26].…”

“…Base-calling error probabilities (P) were evaluated using Phred Quality Score (Q), defined by: Q = −10log 10 (P). Residual primer and adapter content were trimmed using the Joint Genome Institute Bestus Bioinformatics Decontamination Using Kmers (BBDuk) tool (v.38.07) [36] with a previously defined read quality trimming threshold [26]. Reads were trimmed from both ends until the mean quality value across each base position in the reads for all sample read libraries were above a Phred Quality Score of 17 for at least 80% of the read lengths, i.e., probability of correct base call was at least 98%.…”

“…Unassembled metagenomic sequencing reads, with P. pnomenusa sequences removed, were analyzed as previously described [26,[40][41][42] using the CosmosID Metagenomics Cloud Application [43] to achieve microbial identification to species, subspecies, and/or strain level and quantification of microorganism relative abundance. Analogously, antibiotic and virulenceassociated genes present in each sample were identified by querying unassembled sequence reads against GenBook1, a proprietary series of extensive databases curated by CosmosID Inc. (CosmosID Inc., Rockville, MD, USA).…”

“…Thus, bacteria, viruses, fungi, and protists now can be detected, identified to sub-species level, and characterized. A significant benefit is detection of microorganisms in water that were previously missed or not identified by culture-dependent methods [22,26,27]. Metagenomic surveys carried out by other investigators have provided evidence that ingested dietborne components can have short-and long-term effects on the human microbiota [28][29][30][31].…”

New strategies for the enumeration of enteric pathogens in water

“…Nevertheless, Roy et al . () showed that shotgun metagenomics (sequencing all of the DNA in a sample) could be used to monitor surface waters for Vibrio cholerae ; however, this was done in a region with a recent cholera epidemic, and the target might be assumed to be present at a high concentration. In contrast use of this method for surveillance of enteric pathogens, which might be present in very small number, is problematic.…”