TITLE:
Metagenomic Shotgun Sequencing Provides Prevalence Data for Pathogens, and Source-Tracking Indices Useful in Public Health Risk Assessment of Environmental Waters
AUTHORS:
Brian Mercer, Karim Dawkins, Lisa Meday, Nwadiuto Esiobu
KEYWORDS:
Metagenomic Shotgun Sequencing, Water Quality, Risk Assessment, Indicator Bacteria, Environmental Microbiomes
JOURNAL NAME:
Journal of Geoscience and Environment Protection,
Vol.8 No.6,
June
30,
2020
ABSTRACT: State-approved membrane filtration (MF) techniques for water quality assessments were contrasted with metagenomic shotgun sequencing (MSS) protocols to evaluate their efficacy in providing precise health-risk indices for surface waters. Samples from a freshwater receiving pond (ABI-1002) and two upstream storm water ditches (ABI-1003) and (ABI-1004) yielded alarmingly high Fecal coliform MF densities of 220, >2000 and >2000 CFU/100ml respectively. The indicator, Enterococcus bacteria exceeded allowable limits in all but the equipment control (ABI-1001). Using MSS, the relative numerical abundance of pathogenic bacteria, virulence and antibiotic resistance genes revealed the status and potential pollution sources of each ditch. High levels of Shigella sp. (0 (ABI-1001), 4945 (ABI-1002), 55,008 (ABI-1003), and 2221 (ABI-1004) genomic reads/100ml) correlated with virulence genes and antibiotic resistance genes found in fecal samples for ABI1003 and not ABI1004. Traditional culture methods (TCM) showed possible fecal contamination in two of the four samples, and no contamination in the others. MSS clearly distinguished between fecal and environmental bacteria contamination sources, and pinpointed actual risks from pathogens. Our data underscore the potential utility of MSS in precision risk assessment for public and biodiversity health and tracking of environmental microbiomes shifts by field managers and policy makers.