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.
Highlights
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
For over 50 years, microbiological risk assessment of environmental samples has been based on monitoring the prevalence of indicator organisms that are generally not harmful, but indicate the possible presence of pathogenic bacteria, viruses and protozoans (EPA 822-R-10-005, 2010)
The lowest run dilution for these samples was 10 ml, making the highest possible detection limit to be 2000 Colony Forming Units (CFU)/100ml. As such all results that are at 2000 CFU/100ml are presumed to be greater than 2000 CFU/100ml, because the plates were too numerous to count. Results reported for these culturing techniques are based on the most accurate number calculated from the volume of sample filtered
Summary
For over 50 years, microbiological risk assessment of environmental samples has been based on monitoring the prevalence of indicator organisms that are generally not harmful, but indicate the possible presence of pathogenic bacteria, viruses and protozoans (EPA 822-R-10-005, 2010). The US Environmental Protection Agency (EPA) manual for monitoring (EPA 5.11 Fecal Bacteria, 2012; EPA-820-R-14-010, 2014; EPA-820-R-14-011, 2014) justified the indicator system because “it is difficult, time-consuming, and expensive to test directly for the presence of a large variety of pathogens; water is usually tested for coliforms and fecal Streptococci instead” In some instances, these relatively inexpensive culture techniques provide data considered sufficient to accurately assess (at least in part) the public health risk of water samples. To address the many challenges that remain unsolved, emerging technologies such as the metagenomic shotgun sequencing, which can detect virulence genes and all microbial life forms—viruses, bacteria, fungi and protozoans in a single assay are being developed These permit a direct rather than an indirect assessment of public health risks. Cabral et al (2018) employed sequencing technologies to successfully characterize microbial communities in water ways while other recent studies (Mohiuddin et al, 2017; Roy et al, 2018; Cocolin et al, 2018; Li et al, 2018) have demonstrated the utility of genera-
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