Relationship of human-associated microbial source tracking markers with Enterococci in Gulf of Mexico waters

Spatiotemporal assessment of pathogenic Leptospira in subtropical coastal watersheds

The World Health Organization classifies leptospirosis as a significant public health concern, predominantly affecting impoverished and unsanitary regions. By using the Pensacola Bay System as a case study, this study examines the underappreciated susceptibility of developed subtropical coastal ecosystems such as the Pensacola Bay System to neglected zoonotic pathogens such as Leptospira. We analyzed 132 water samples collected over 12 months from 44 distinct locations with high levels of Escherichia coli (>410 most probable number/100 mL). Fecal indicator bacteria (FIB) concentrations were assessed using IDEXX Colilert-18 and Enterolert-18, and an analysis of water physiochemical characteristics and rainfall intensity was conducted. The LipL32 gene was used as a quantitative polymerase chain reaction (qPCR) indicator to identify the distribution of Leptospira interrogans. The results revealed 12 instances of the presence of L. interrogans at sites with high FIB over various land cover and aquatic ecosystem types. Independent of specific rainfall events, a seasonal relationship between precipitation and elevated rates of fecal bacteria and leptospirosis was found. These findings highlight qPCR's utility in identifying pathogens in aquatic environments and the widespread conditions where it can be found in natural and developed areas.

Occurrence of a human-associated microbial source tracking marker and its relationship with faecal indicator bacteria in an urban estuary

One of the main impacts of urban sprawl in rapidly growing countries has been contamination of coastal environments by waterborne pathogens, posing a critical risk to ecosystem and human health. Microbial source tracking (MST) has been a robust tool to identify the origin of these pathogens globally. This study compared the occurrence of a human-associated Bacteroides marker (BT-α) with faecal indicator bacteria (FIB) in an urban estuary (Golden Horn, Istanbul, Turkey). Faecal coliform (culture method), enterococci (both culture and qPCR method) concentrations and physicochemical variables were compared with the BT-α concentrations in monthly collected samples for a year (n = 108). Enterococci concentrations detected by culture and qPCR were positively correlated (r = 0·86, P < 0·01) suggesting that qPCR can be an alternative method for monitoring. BT-α marker was positive for 30% of the samples and positively correlated with enterococci (r = 0·61 and r = 0·64 for culture and qPCR methods respectively, P < 0·01). Rainfall had a moderate positive correlation with all faecal/MST indicators suggesting combined sewer overflows also severely impacted estuarine water quality. The high FIB and BT-α concentrations at upper estuary suggested that faecal pollution mainly originated from the peri-urban settlements around two creeks entering the estuary.

Natural attenuation of indicator bacteria in coastal streams and estuarine environments

One of the most significant causes of poor water quality is the presence of pathogens. To reduce the cost of human exposure to microbial contamination, monitoring of Fecal Indicator Bacteria (FIB), as a surrogate for the presence of pathogens in natural waters, has become the norm. A total maximum daily load (TMDL) framework is used to establish limits for microbial concentrations in impaired waterbodies. In order to meet microbial loads determined by the TMDLs, reductions in microbial sources varying from 50% to almost complete elimination are required. Such targets are fairly difficult, if not impossible, to achieve. A natural attenuation (NA) framework is proposed that takes into account the connectivity between freshwater streams and their receiving coastal estuaries. The framework accounts for destructive and non-destructive mechanisms and defines three regimes: NA 1 - reaction-dilution mixing at the freshwater-tidal interface, NA 2 - advection-reactions within the tidally influenced coastal stream, and NA 3 - dilution-discharge at the interface with the estuary. The framework was illustrated using the Houston Metropolitan area freshwater streams, their discharge into the Houston Ship Channel (HSC) and into Galveston Bay. FIB concentrations in Galveston Bay were much lower when compared to FIB concentrations in Houston streams. Lower enterococci concentrations in tributary tidal waters were found compared to their counterparts in fresh waters (NA1 regime). Additionally, 70% reduction in FIB loads within the HSC was demonstrated as well as a decreasing trend in enterococci geometric means, from upstream to downstream, on the order of 0.092 day^-1 (NA2 regime). Lower enterococci concentrations in Galveston Bay at the confluence with the HSC were also demonstrated (NA3 regime). Statistical testing showed that dilution, tide-associated processes, and salinity are the most important NA mechanisms and indicated the significant effect of ambient temperature and rainfall patterns on FIB concentrations and the NA mechanisms.

Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters

Stormwater contamination can threaten the health of aquatic ecosystems and human exposed to runoff via nutrient and pathogen influxes. In this study, the concentrations of 11 bacterial pathogens and 47 antibiotic resistance genes (ARGs) were determined by using high-throughput microfluidic qPCR (MFQPCR) in several storm drain outfalls (SDOs) during dry and wet weather in Tampa Bay, Florida, USA. Data generated in this study were also compared with the levels of fecal indicator bacteria (FIB) and sewage-associated molecular markers (i.e., Bacteroides HF183 and crAssphage markers) in same SDOs collected in a recent study (Ahmed et al., 2018). Concentration of FIB, sewage-associated markers, bacterial pathogens and many ARGs in water samples were relatively high and SDOs may be potentially hotspots for microbial contamination in Tampa Bay. Mean concentrations of culturable E. coli and Enterococcus spp. were tenfold higher in wet compared to dry weather. The majority of microbiological contaminants followed this trend. E. coli eaeA, encoding the virulence factor intimin, was correlated with levels of 20 ARGs, and was more frequently detected in wet weather than dry weather samples. The bla_KPC gene associated with carbapenem resistant Enterobacteriaceae and the beta-lactam resistant gene (bla_NPS) were only detected in wet weather samples. Frequency of integron genes Intl2 and Intl3 detection increased by 42% in wet weather samples. Culturable E. coli and Enterococcus spp. significantly correlated with 19 of 47 (40%) ARG tested. Sewage-associated markers crAssphage and HF183 significantly correlated (p < 0.05) with the following ARGs: intl1, sul1, tet(M), ampC, mexB, and tet(W). The presence of sewage-associated marker genes along with ARGs associated with sewage suggested that aging sewage infrastructure contributed to contaminant loading in the Bay. Further research should focus on collecting spatial and temporal data on the microbiological contaminants especially viruses in SDOs.

Toward Forensic Uses of Microbial Source Tracking

The science of microbial source tracking has allowed researchers and watershed managers to go beyond general indicators of fecal pollution in water such as coliforms and enterococci, and to move toward an understanding of specific contributors to water quality issues. The premise of microbial source tracking is that characteristics of microorganisms that are strongly associated with particular host species can be used to trace fecal pollution to particular animal species (including humans) or groups, e.g., ruminants or birds. Microbial source tracking methods are practiced largely in the realm of research, and none are approved for regulatory uses on a federal level. Their application in the conventional sense of forensics, i.e., to investigate a crime, has been limited, but as some of these methods become standardized and recognized in a regulatory context, they will doubtless play a larger role in applications such as total maximum daily load assessment, investigations of sewage spills, and contamination from agricultural practices.

Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces

The aim of this study was to judge the legal duty of pollution liabilities by assessing a duck faeces-specific marker, which can exclude distractions of residual bacteria from earlier contamination accidents. With the gene sequencing technology and bioinformatics method, we completed the comparative analysis of Faecalibacterium sequences, which were associated with ducks and other animal species, and found the sequences unique to duck faeces. Polymerase chain reaction (PCR) and agarose gel electrophoresis techniques were used to verify the reliability of both human and duck faeces-specific primers. The duck faeces-specific primers generated an amplicon of 141 bp from 43.3 % of duck faecal samples, 0 % of control samples and 100 % of sewage wastewater samples that contained duck faeces. We present here the initial evidence of Faecalibacterium-based applicability as human faeces-specificity in China. Meanwhile, this study represents the initial report of a Faecalibacterium marker for duck faeces and suggests an independent or supplementary environmental biotechnology of microbial source tracking (MST).

Human health risk implications of multiple sources of faecal indicator bacteria in a recreational waterbody

We simulate the influence of multiple sources of enterococci (ENT) as faecal indicator bacteria (FIB) in recreational water bodies on potential human health risk by considering waters impacted by human and animal sources, human and non-pathogenic sources, and animal and non-pathogenic sources. We illustrate that risks vary with the proportion of culturable ENT in water bodies derived from these sources and estimate corresponding ENT densities that yield the same level of health protection that the recreational water quality criteria in the United States seeks (benchmark risk). The benchmark risk is based on epidemiological studies conducted in water bodies predominantly impacted by human faecal sources. The key result is that the risks from mixed sources are driven predominantly by the proportion of the contamination source with the greatest ability to cause human infection (potency), not necessarily the greatest source(s) of FIB. Predicted risks from exposures to mixtures comprised of approximately 30% ENT from human sources were up to 50% lower than the risks expected from purely human sources when contamination is recent and ENT levels are at the current water quality criteria levels (35 CFU 100 mL(-1)). For human/non-pathogenic, human/gull, human/pig, and human/chicken faecal mixtures with relatively low human contribution, the predicted culturable enterococci densities that correspond to the benchmark risk are substantially greater than the current water quality criteria values. These findings are important because they highlight the potential applicability of site specific water quality criteria for waters that are predominantly un-impacted by human sources.

Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the upper Mississippi river

The sanitary quality of recreational waters that may be impacted by sewage is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); these organisms are found in the gastrointestinal tracts of humans and many other animals, and hence their presence provides no information about the pollution source. Microbial source tracking (MST) methods can discriminate between different pollution sources, providing critical information to water quality managers, but relatively little is known about factors influencing the decay of FIB and MST genetic markers following release into aquatic environments. An in situ mesocosm was deployed at a temperate recreational beach in the Mississippi River to evaluate the effects of ambient sunlight and biotic interactions (predation, competition, and viral lysis) on the decay of culture-based FIB, as well as molecularly based FIB (Entero1a and GenBac3) and human-associated MST genetic markers (HF183 and HumM2) measured by quantitative real-time PCR (qPCR). In general, culturable FIB decayed the fastest, while molecularly based FIB and human-associated genetic markers decayed more slowly. There was a strong correlation between the decay of molecularly based FIB and that of human-associated genetic markers (r(2), 0.96 to 0.98; P < 0.0001) but not between culturable FIB and any qPCR measurement. Overall, exposure to ambient sunlight may be an important factor in the early-stage decay dynamics but generally was not after continued exposure (i.e., after 120 h), when biotic interactions tended to be the only/major influential determinant of persistence.

A proposal for source tracking of fecal pollution in recreational waters by pulsed-field gel electrophoresis

This study aimed to identify specific river sources of fecal contamination by applying pulsed-field gel electrophoresis (PFGE) to environmental water samples from a recreational beach in Japan. The genotypes of all Enterococcus faecium and Enterococcus faecalis strains used as indicators of fecal pollution on the recreational beach and rivers were analyzed by PFGE, and the PFGE profiles of the strains were classified at a 0.9 similarity level using dendrogram analysis. PFGE types of E. faecium isolated from Sakai River or urban drainage were classified in the same cluster. Therefore, the probable sources of fecal pollution on the recreational beach were Sakai River and urban drainage. The approaches for microbial source tracking employed in this study used PFGE with Enterococcus species as an indicator can be a potential tool to specify the source(s) of fecal pollution and contribute to improved public health in coastal environments.

Microbial water quality in freshwater lakes with different land use

AIMS

The relationship between land use (undeveloped, cattle grazing, urban), faecal indicator bacteria (FIB) levels and microbial source tracking (MST) marker detection was investigated in lakes created following phosphate mining.

METHODS AND RESULTS

Faecal coliforms and enterococci were cultured, and MST markers were detected by PCR [Methanobrevibacter smithii, human polyomaviruses (HPyVs), ruminant, human (HF183) and general Bacteroidales]. FIB levels varied significantly by sampling date and were correlated with antecedent rainfall. FIB levels varied with land use category only in the case of faecal coliform levels in sediments of urban lakes, which were significantly greater than those in undeveloped or cattle-impacted lakes. Ruminant Bacteroidales were detected consistently in cattle-impacted lakes (57%) and rarely in other lakes. HPyVs was the only human source marker detected.

CONCLUSIONS

Rainfall was more strongly associated with FIB levels than land use category. The detection frequency of only the ruminant MST marker was associated with land use.

SIGNIFICANCE AND IMPACT OF STUDY

Microbial source tracking (MST) can fine-tune the assessment of human health risk from recreational use of inland waters, particularly when similar FIB levels but different surrounding land use and probable impacts exist.

Quantification of human and animal viruses to differentiate the origin of the fecal contamination present in environmental samples

Many different viruses are excreted by humans and animals and are frequently detected in fecal contaminated waters causing public health concerns. Classical bacterial indicator such as E. coli and enterococci could fail to predict the risk for waterborne pathogens such as viruses. Moreover, the presence and levels of bacterial indicators do not always correlate with the presence and concentration of viruses, especially when these indicators are present in low concentrations. Our research group has proposed new viral indicators and methodologies for determining the presence of fecal pollution in environmental samples as well as for tracing the origin of this fecal contamination (microbial source tracking). In this paper, we examine to what extent have these indicators been applied by the scientific community. Recently, quantitative assays for quantification of poultry and ovine viruses have also been described. Overall, quantification by qPCR of human adenoviruses and human polyomavirus JC, porcine adenoviruses, bovine polyomaviruses, chicken/turkey parvoviruses, and ovine polyomaviruses is suggested as a toolbox for the identification of human, porcine, bovine, poultry, and ovine fecal pollution in environmental samples.