Comparison of the efficacy of an existing versus a locally developed metabolic fingerprint database to identify non-point sources of faecal contamination in a coastal lake

Enterococci populations of a metropolitan river after an extreme flood event: prevalence, persistence and virulence determinants

We investigated the prevalence, persistence and virulence determinants of enterococci populations in water samples collected over three rounds following an extreme flood event in a metropolitan river. Enterococci (n = 482) were typed using the high resolution biochemical fingerprinting method (PhP typing) and grouped into common (C) or single (S) biochemical phenotypes (BPTs). In all, 23 C-BPTs (72.6% of isolates) were found across the sites. A representative isolate of each C-BPT was identified to the species level and tested for the presence of seven virulence genes (VGs), biofilm formation and resistance to 14 antibiotics. The enterococci concentrations in samples collected during the first two rounds were above national recreational water guidelines. By round three, enterococci concentrations decreased significantly (P < 0.05). However, 11 C-BPTs (55.5% of isolates) persisted across all sampling rounds. E. casseliflavus and E. mundtii were the most common enterococci populations comprising of >57% of all isolates. Ten of the 11 most dominant C-BPTs were resistant to multiple antibiotics and harboured one or more VGs. The high prevalence of antibiotic resistance and VGs among enterococci isolates in this catchment not only provides them with niche advantages but also poses a risk to public health.

Assessing the population dynamics of Escherichia coli in a metropolitan river after an extreme flood event

We investigated Escherichia coli populations in a metropolitan river after an extreme flood event. Between nine and 15 of the 23 selected sites along the river were sampled fortnightly over three rounds. In all, 307 E. coli were typed using the PhP typing method and were grouped into common (C) or single (S) biochemical phenotypes (BPTs). A representative from each of the 31 identified C-BPTs was tested for 58 virulence genes (VGs) associated with intestinal and extra-intestinal E. coli, resistance to 22 antibiotics, production of biofilm and cytotoxicity to Vero cells. The number of E. coli in the first sampling round was significantly (P < 0.01) higher than subsequent rounds, whereas the number of VGs was significantly (P < 0.05) higher in isolates from the last sampling round when compared to previous rounds. Comparison of the C-BPTs with an existing database from wastewater treatment plants (WWTPs) in the same catchment showed that 40.6% of the river isolates were identical to the WWTP isolates. The relatively high number of VGs and antibiotic resistance among the C-BPTs suggests possessing and retaining these genes may provide niche advantages for those naturalised and/or persistent E. coli populations which may pose a health risk to the community.

In vitro Effectiveness of Commercial Bacteriophage Cocktails on Diverse Extended-Spectrum Beta-Lactamase Producing Escherichia coli Strains

The objective of this study is to determine the in vitro susceptibility of Georgian bacteriophage cocktails on multidrug resistant (MDR) extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC) isolated from patients’ blood and urine cultures. A total of 615 E. coli isolates were included in this study. Phene Plate (PhP)-typing and phylogenetic grouping were used for the typing. Antimicrobial resistance profiles and ESBL production of all isolates were confirmed according to Clinical and Laboratory Standards Institute (CLSI) criteria. The activities of four bacteriophage cocktails (Enko-phage, SES-bacteriophage, Pyo-bacteriophage, and Intesti-bacteriophage) were determined against 142 ESBL-EC using in vitro spot tests. According to this, Enko-phage were active against 87.3% of the tested strains while that ratio was 81.7% for Intesti-bacteriophage, 81.7% for Pyo-bacteriophage, and 59.2% for SES-bacteriophage cocktails. Based on the contingency tests, the phage cocktails were observed to be statistically significantly (p < 0.001) more effective on ESBL-EC strains belonging to phylogenetic groups D and B2. The employed phage cocktails were found to be affective against all tested resistant types. These results are promising especially for the infections that are caused by MDR pathogens that are difficult to treat. As this is a preliminary step to the potential clinical trials to be designed for the country, in vitro confirmation of their success on a MDR ESBL-EC collection should be accepted as an initial action, which is encouraging to consider clinical trials of phage therapy especially in countries which are not introduce phage therapy.

A combination of PhP typing and β-d-glucuronidase gene sequence variation analysis for differentiation of Escherichia coli from humans and animals

We investigated the usefulness of the β-d-glucuronidase gene variance in Escherichia coli as a microbial source tracking tool using a novel algorithm for comparison of sequences from a prescreened set of host-specific isolates using a high-resolution PhP typing method. A total of 65 common biochemical phenotypes belonging to 318 E. coli strains isolated from humans and domestic and wild animals were analysed for nucleotide variations at 10 loci along a 518 bp fragment of the 1812 bp β-d-glucuronidase gene. Neighbour-joining analysis of loci variations revealed 86 (76.8%) human isolates and 91.2% of animal isolates were correctly identified. Pairwise hierarchical clustering improved assignment; where 92 (82.1%) human and 204 (99%) animal strains were assigned to their respective cluster. Our data show that initial typing of isolates and selection of common types from different hosts prior to analysis of the β-d-glucuronidase gene sequence improves source identification. We also concluded that numerical profiling of the nucleotide variations can be used as a valuable approach to differentiate human from animal E. coli. This study signifies the usefulness of the β-d-glucuronidase gene as a marker for differentiating human faecal pollution from animal sources.

Evaluating sewage-associated JCV and BKV polyomaviruses for sourcing human fecal pollution in a coastal river in Southeast Queensland, Australia

In this study, the host-sensitivity and host-specificity of JC virus (JCV) and BK virus (BKV) polyomaviruses were evaluated by testing wastewater and fecal samples from nine host groups in Southeast Queensland, Australia. The JCV and BKV polyomaviruses were detected in 63 human wastewater samples collected from primary and secondary effluent, suggesting high sensitivity of these viruses in human wastewater. In the 81 animal wastewater and fecal samples tested, 80 were polymerase chain reaction (PCR) negative for the JCV and BKV markers. Only one sample (out of 81 animal wastewater and fecal samples) from pig wastewater was positive. Nonetheless, the overall host-specificity of these viruses to differentiate between human and animal wastewater and fecal samples was 0.99. To our knowledge, this is the first study in Australia that reports on the high specificity of JCV and BKV polyomaviruses. To evaluate the field application of these viral markers for detecting human fecal pollution, 20 environmental samples were collected from a coastal river. In the 20 samples tested, 15% (3/20) and 70% (14/20) samples exceeded the regulatory guidelines for Escherichia coli and enterococci levels for marine waters. In all, five (25%) samples were PCR positive for JCV and BKV, indicating the presence of human fecal pollution in the coastal river investigated. The results suggest that JCV and BKV detection using PCR could be a useful tool for identifying human-sourced fecal pollution in coastal waters.

Comparison of molecular markers to detect fresh sewage in environmental waters

Human-specific Bacteroides HF183 (HS-HF183), human-specific Enterococci faecium esp (HS-esp), human-specific adenoviruses (HS-AVs) and human-specific polyomaviruses (HS-PVs) assays were evaluated in freshwater, seawater and distilled water to detect fresh sewage. The sewage spiked water samples were also tested for the concentrations of traditional fecal indicators (i.e., Escherichia coli, enterococci and Clostridium perfringens) and enteric viruses such as enteroviruses (EVs), sapoviruses (SVs), and torquetenoviruses (TVs). The overall host-specificity of the HS-HF183 marker to differentiate between humans and other animals was 98%. However, the HS-esp, HS-AVs and HS-PVs showed 100% host-specificity. All the human-specific markers showed >97% sensitivity to detect human fecal pollution. E. coli, enterococci and, C. perfringens were detected up to dilutions of sewage 10(-5), 10(-4) and 10(-3) respectively. HS-esp, HS-AVs, HS-PVs, SVs and TVs were detected up to dilution of sewage 10(-4) whilst EVs were detected up to dilution 10(-5). The ability of the HS-HF183 marker to detect fresh sewage was 3-4 orders of magnitude higher than that of the HS-esp and viral markers. The ability to detect fresh sewage in freshwater, seawater and distilled water matrices was similar for human-specific bacterial and viral marker. Based on our data, it appears that human-specific molecular markers are sensitive measures of fresh sewage pollution, and the HS-HF183 marker appears to be the most sensitive among these markers in terms of detecting fresh sewage. However, the presence of the HS-HF183 marker in environmental waters may not necessarily indicate the presence of enteric viruses due to their high abundance in sewage compared to enteric viruses. More research is required on the persistency of these markers in environmental water samples in relation to traditional fecal indicators and enteric pathogens.

Phenotypic variations of enterococci in surface waters: analysis of biochemical fingerprinting data from multi-catchments

AIMS

The aim of this study was to identify the prevalence of environmentally adapted enterococci strains by analysing biochemical fingerprinting (BF) data of 3952 enterococci isolates collected over 5 years from the six catchments in Southeast Queensland, Australia.

METHODS AND RESULTS

A BF method was used to type 3952 enterococci isolates from six catchments. The environmental isolates were compared with a large existing BF library comprised of 5803 enterococci isolates from 10 host groups. Environmental isolates belonged to 801 biochemical phenotypes (BPTs), of which, an average of 29.2% was specific to each catchment. When compared with the BF library, an average of 79.5% BPTs from each catchment was identical to those in the library (i.e. host-origin BPTs). The remaining 20.5% was regarded as non-host origin BPTs, as they were not in the library and constituted only 5.3% of the total isolates tested for each catchment.

CONCLUSIONS

Our data suggest that less than 5% of studied environmental strains was not identical to those in the library and seemed to be of environmental origin. From a microbial source tracking context, such low level of environmentally adapted strains can have a minimal impact on the performance of the library-based methods if a large number of isolates were tested from both the host groups and environmental waters.

SIGNIFICANCE AND IMPACT OF THE STUDY

These data shed light on the importance of the size and representativeness of library-based source-tracking methods and their implications for the identification of faecal pollution in environmental waters.

Genotype diversity of Escherichia coli isolates in natural waters determined by PFGE and ERIC-PCR

Most library-dependent bacterial source tracking studies using Escherichia coli (E. coli) have focused on strain diversity of isolates obtained from known human and animal faecal sources for library development. In contrast, this study evaluated the genotype variation of E. coli isolated from natural surface water using pulsed field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus sequence polymerase chain reaction (ERIC-PCR) to better understand these naturally occurring populations. A total of 650 water samples were collected over a nine month period from eleven sampling stations from Lake Waco and Belton Lake in Central Texas. Of the 650 water samples collected, 412 were positive for E. coli, yielding a total of 631 E. coli isolates (1-12 isolates collected per sample). PFGE and ERIC-PCR patterns were successfully generated for 555 isolates and were compared using the curve-based Pearson's product-moment correlation coefficient. The 555 E. coli isolates represented 461 PFGE genotypes, with 84% (386/461) of the genotypes being represented by individual isolates. The remaining 75 genotypes were represented by 2-5 isolates each. Using ERIC-PCR, the 555 E. coli isolates represented 175 genotypes, with 63% (109/175) of the genotypes being represented by individual isolates. In contrast to the PFGE results, two ERIC-PCR genotypes represented 37% of the E. coli isolates, (83 and 124 isolates, respectively), and were found throughout the watersheds both spatially and temporally. Based on the PFGE genotype diversity of water isolates, there is little evidence that a small number of environmentally-adapted E. coli represent dominant populations in the studied waterbodies. However, with the lower discriminatory power technique ERIC-PCR, an opposing conclusion might have been drawn. These results emphasize the importance of considering the resolving power of the source tracking technique being used when assessing strain diversity and geographical stability.

Sourcing faecal pollution: a combination of library-dependent and library-independent methods to identify human faecal pollution in non-sewered catchments

Library-dependent (LD) (biochemical fingerprinting of Escherichia coli and enterococci) and library-independent (LI) (PCR detection of human-specific biomarkers) methods were used to detect human faecal pollution in three non-sewered catchments. In all, 550 E. coli isolates and 700 enterococci isolates were biochemically fingerprinted from 18 water samples and compared with metabolic fingerprint libraries of 4508 E. coli and 4833 enterococci isolates. E. coli fingerprints identified human unique biochemical phenotypes (BPTs) in nine out of 18 water samples; similarly, enterococci fingerprints identified human faecal pollution in 10 water samples. Seven samples were tested by PCR for the detection of biomarkers. Human-specific HF134 Bacteroides and enterococci surface protein (esp) biomarkers were detected in five samples. Four samples were also positive for HF183 Bacteroides biomarker. The combination of biomarkers detected human faecal pollution in six out of seven water samples. Of the seven samples analysed for both the indicators/markers, at least one indicator/marker was detected in every sample. Four of the seven PCR-positive samples were also positive for one of the human-specific E. coli or enterococci BPTs. The results indicated human faecal pollution in the studied sub-catchments after storm events. LD and LI methods used in this study complimented each other and provided additional information regarding the polluting sources when one method failed to detect human faecal pollution. Therefore, it is recommended that a combination of methods should be used to identify the source(s) of faecal pollution where possible.

Monitoring source water for microbial contamination: evaluation of water quality measures

Watershed management programs often rely on monitoring for a large number of water quality parameters to define contaminant issues. While coliforms have traditionally been used to identify microbial contamination, these indicators cannot discriminate among potential contaminant sources. Microbial source tracking (MST) can provide the missing link that implicates the sources of contamination. The objective of this study was to use a weight-of-evidence approach (land use analysis using GIS, sanitary surveys, traditional water quality monitoring, and MST targets) to identify sources of pollution within a watershed that contains a raw drinking water source. For the study watersheds, statistical analyses demonstrated that one measure each of particulate matter (turbidity, particle counts), organic matter (total organic carbon, dissolved organic carbon, UV(254) absorbance), and indicator organisms (fecal coliforms, enterococci) were adequate for characterizing water quality. While these traditional parameters were useful for assessing overall water quality, they were not intended to differentiate between microbial sources at different locations. In contrast, the MST targets utilized (Rhodococcus coprophilus, sorbitol-fermenting Bifidobacteria, and male-specific coliphages) pinpointed specific sources of microbial pollution. However, these targets could not be used for routine monitoring due to a high percentage of non-detects.