scholarly journals Automated Sampling Procedures Supported by High Persistence of Bacterial Fecal Indicators and Bacteroidetes Genetic Microbial Source Tracking Markers in Municipal Wastewater during Short-Term Storage at 5°C

2015 ◽  
Vol 81 (15) ◽  
pp. 5134-5143 ◽  
Author(s):  
R. E. Mayer ◽  
J. Vierheilig ◽  
L. Egle ◽  
G. H. Reischer ◽  
E. Saracevic ◽  
...  

ABSTRACTBecause of high diurnal water quality fluctuations in raw municipal wastewater, the use of proportional autosampling over a period of 24 h at municipal wastewater treatment plants (WWTPs) to evaluate carbon, nitrogen, and phosphorus removal has become a standard in many countries. Microbial removal or load estimation at municipal WWTPs, however, is still based on manually recovered grab samples. The goal of this study was to establish basic knowledge regarding the persistence of standard bacterial fecal indicators andBacteroidetesgenetic microbial source tracking markers in municipal wastewater in order to evaluate their suitability for automated sampling, as the potential lack of persistence is the main argument against such procedures. Raw and secondary treated wastewater of municipal origin from representative and well-characterized biological WWTPs without disinfection (organic carbon and nutrient removal) was investigated in microcosm experiments at 5 and 21°C with a total storage time of 32 h (including a 24-h autosampling component and an 8-h postsampling phase). VegetativeEscherichia coliand enterococci, as well asClostridium perfringensspores, were selected as indicators for cultivation-based standard enumeration. Molecular analysis focused on total (AllBac) and human-associated geneticBacteroidetes(BacHum-UCD, HF183 TaqMan) markers by using quantitative PCR, as well as 16S rRNA gene-based next-generation sequencing. The microbial parameters showed high persistence in both raw and treated wastewater at 5°C under the storage conditions used. Surprisingly, and in contrast to results obtained with treated wastewater, persistence of the microbial markers in raw wastewater was also high at 21°C. On the basis of our results, 24-h autosampling procedures with 5°C storage conditions can be recommended for the investigation of fecal indicators orBacteroidetesgenetic markers at municipal WWTPs. Such autosampling procedures will contribute to better understanding and monitoring of municipal WWTPs as sources of fecal pollution in water resources.

2016 ◽  
Vol 82 (5) ◽  
pp. 1625-1635 ◽  
Author(s):  
Xiang Li ◽  
Valerie J. Harwood ◽  
Bina Nayak ◽  
Jennifer L. Weidhaas

ABSTRACTPathogen identification and microbial source tracking (MST) to identify sources of fecal pollution improve evaluation of water quality. They contribute to improved assessment of human health risks and remediation of pollution sources. An MST microarray was used to simultaneously detect genes for multiple pathogens and indicators of fecal pollution in freshwater, marine water, sewage-contaminated freshwater and marine water, and treated wastewater. Dead-end ultrafiltration (DEUF) was used to concentrate organisms from water samples, yielding a recovery efficiency of >95% forEscherichia coliand human polyomavirus. Whole-genome amplification (WGA) increased gene copies from ultrafiltered samples and increased the sensitivity of the microarray. Viruses (adenovirus, bocavirus, hepatitis A virus, and human polyomaviruses) were detected in sewage-contaminated samples. Pathogens such asLegionella pneumophila,Shigella flexneri, andCampylobacter fetuswere detected along with genes conferring resistance to aminoglycosides, beta-lactams, and tetracycline. Nonmetric dimensional analysis of MST marker genes grouped sewage-spiked freshwater and marine samples with sewage and apart from other fecal sources. The sensitivity (percent true positives) of the microarray probes for gene targets anticipated in sewage was 51 to 57% and was lower than the specificity (percent true negatives; 79 to 81%). A linear relationship between gene copies determined by quantitative PCR and microarray fluorescence was found, indicating the semiquantitative nature of the MST microarray. These results indicate that ultrafiltration coupled with WGA provides sufficient nucleic acids for detection of viruses, bacteria, protozoa, and antibiotic resistance genes by the microarray in applications ranging from beach monitoring to risk assessment.


2018 ◽  
Vol 62 (5) ◽  
Author(s):  
Ryota Gomi ◽  
Tomonari Matsuda ◽  
Masaki Yamamoto ◽  
Pei-Hsin Chou ◽  
Michio Tanaka ◽  
...  

ABSTRACT Wastewater is considered a major source of antibiotic-resistant bacteria released into the environment. Here, we characterized carbapenemase-producing Enterobacteriaceae (CPE) in wastewater by whole-genome analysis. Wastewater samples ( n = 40) were collected from municipal wastewater treatment plants and hospital wastewater in Japan and Taiwan. Samples were screened for CPE using selective media, and the obtained isolates were sequenced using an Illumina MiSeq. The isolates ( n = 45) included the following microorganisms: Klebsiella quasipneumoniae ( n = 12), Escherichia coli ( n = 10), Enterobacter cloacae complex ( n = 10), Klebsiella pneumoniae ( n = 8), Klebsiella variicola ( n = 2), Raoultella ornithinolytica ( n = 1), Citrobacter freundii ( n = 1), and Citrobacter amalonaticus ( n = 1). Among the 45 isolates, 38 harbored at least one carbapenemase-encoding gene. Of these, the bla GES ( bla GES-5 , bla GES-6 , and bla GES-24 ) genes were found in 29 isolates. The genes were situated in novel class 1 integrons, but the integron structures were different between the Japanese (In1439 with bla GES-24 and In1440 with bla GES-5 ) and Taiwanese (In1441 with bla GES-5 and In1442 with bla GES-6 ) isolates. Other carbapenemase-encoding genes ( bla VIM-1 , bla NDM-5 , bla IMP-8 , bla IMP-19 , and bla KPC-2 ) were found in one to three isolates. Notably, class 1 integrons previously reported among clinical isolates obtained in the same regions as the present study, namely, In477 with bla IMP-19 and In73 with bla IMP-8 , were found among the Japanese and Taiwanese isolates, respectively. The results indicate that CPE with various carbapenemase-encoding genes in different genetic contexts were present in biologically treated wastewater, highlighting the need to monitor for antibiotic resistance in wastewater.


2013 ◽  
Vol 79 (8) ◽  
pp. 2682-2691 ◽  
Author(s):  
W. Ahmed ◽  
T. Sritharan ◽  
A. Palmer ◽  
J. P. S. Sidhu ◽  
S. Toze

ABSTRACTThis study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (BacCow-UCD and cowM3) and one viral [bovine adenovirus (B-AVs)] microbial source tracking (MST) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast Queensland, Australia. In addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal indicator bacteria (FIB),Campylobacterspp.,Escherichia coliO157, andSalmonellaspp. The overall host specificity values of the BacCow-UCD, cowM3, and B-AVs markers to differentiate between bovine and other nontarget host groups were 0.66, 0.88, and 1.00, respectively (maximum value of 1.00). The overall host sensitivity values of these markers, however, in composite bovine wastewater and individual bovine fecal DNA samples were 0.93, 0.90, and 0.60, respectively (maximum value of 1.00). Among the 36 water samples tested, 56%, 22%, and 6% samples were PCR positive for the BacCow-UCD, cowM3, and B-AVs markers, respectively. Among the 36 samples tested, 50% and 14% samples were PCR positive for theCampylobacter16S rRNA andE. coliO157rfbEgenes, respectively. Based on the results, we recommend that multiple bovine feces-associated markers be used if possible for bovine fecal pollution tracking. Nonetheless, the presence of the multiple bovine feces-associated markers along with the presence of potential zoonotic pathogens indicates bovine fecal pollution in the reservoir water samples. Further research is required to understand the decay rates of these markers in relation to FIB and zoonotic pathogens.


2013 ◽  
Vol 80 (2) ◽  
pp. 612-617 ◽  
Author(s):  
Kruti Ravaliya ◽  
Jennifer Gentry-Shields ◽  
Santos Garcia ◽  
Norma Heredia ◽  
Anna Fabiszewski de Aceituno ◽  
...  

ABSTRACTIn recent decades, fresh and minimally processed produce items have been associated with an increasing proportion of food-borne illnesses. Most pathogens associated with fresh produce are enteric (fecal) in origin, and contamination can occur anywhere along the farm-to-fork chain. Microbial source tracking (MST) is a tool developed in the environmental microbiology field to identify and quantify the dominant source(s) of fecal contamination. This study investigated the utility of an MST method based onBacteroidales16S rRNA gene sequences as a means of identifying potential fecal contamination, and its source, in the fresh produce production environment. The method was applied to rinses of fresh produce, source and irrigation waters, and harvester hand rinses collected over the course of 1 year from nine farms (growing tomatoes, jalapeño peppers, and cantaloupe) in Northern Mexico. Of 174 samples, 39% were positive for a universalBacteroidalesmarker (AllBac), including 66% of samples from cantaloupe farms (3.6 log10genome equivalence copies [GEC]/100 ml), 31% of samples from tomato farms (1.7 log10GEC/100 ml), and 18% of samples from jalapeño farms (1.5 log10GEC/100 ml). Of 68 AllBac-positive samples, 46% were positive for one of three human-specific markers, and none were positive for a bovine-specific marker. There was no statistically significant correlation betweenBacteroidalesand genericEscherichia coliacross all samples. This study provides evidence thatBacteroidalesmarkers may serve as alternative indicators for fecal contamination in fresh produce production, allowing for determination of both general contamination and that derived from the human host.


2016 ◽  
Vol 82 (18) ◽  
pp. 5505-5518 ◽  
Author(s):  
Shuai Zhi ◽  
Graham Banting ◽  
Qiaozhi Li ◽  
Thomas A. Edge ◽  
Edward Topp ◽  
...  

ABSTRACTEscherichia colihas been proposed to have two habitats—the intestines of mammals/birds and the nonhost environment. Our goal was to assess whether certain strains ofE. colihave evolved toward adaptation and survival in wastewater. Raw sewage samples from different treatment plants were subjected to chlorine stress, and ∼59% of the survivingE. colistrains were found to contain a genetic insertion element (IS30) located within theuspC-flhDCintergenic region. The positional location of the IS30element was not observed across a library of 845E. coliisolates collected from various animal hosts or within GenBank or whole-genome reference databases for human and animalE. coliisolates (n= 1,177). Phylogenetics clustered the IS30element-containing wastewaterE. coliisolates into a distinct clade, and biomarker analysis revealed that these wastewater isolates contained a single nucleotide polymorphism (SNP) biomarker pattern that was specific for wastewater. These isolates belonged to phylogroup A, possessed generalized stress response (RpoS) activity, and carried the locus of heat resistance, features likely relevant to nonhost environmental survival. Isolates were screened for 28 virulence genes but carried only thefimHmarker. Our data suggest that wastewater contains a naturalized resident population ofE. coli. We developed an endpoint PCR targeting the IS30element within theuspC-flhDCintergenic region, and all raw sewage samples (n= 21) were positive for this marker. Conversely, the prevalence of this marker inE. coli-positive surface and groundwater samples was low (≤5%). This simple PCR assay may represent a convenient microbial source-tracking tool for identification of water samples affected by municipal wastewater.IMPORTANCEThe results of this study demonstrate that some strains ofE. coliappear to have evolved to become naturalized populations in the wastewater environment and possess a number of stress-related genetic elements likely important for survival in this nonhost environment. The presence of non-host-adapted strains in wastewater challenges our understanding of usingE. colias a microbial indicator of wastewater treatment performance, suggesting that theE. colistrains present in human and animal feces may be very different from those found in treated wastewater.


2018 ◽  
Vol 84 (20) ◽  
Author(s):  
Zachery R. Staley ◽  
Rachel J. Boyd ◽  
Phoenix Shum ◽  
Thomas A. Edge

ABSTRACTAreas of concern (AOCs) around the Great Lakes are characterized by historic and ongoing problems with microbial water quality, leading to beneficial use impairments (BUIs) such as beach postings and closures. In this study, we assessed river and beach sites within the Rouge River watershed, associated stormwater outfalls, and at Rouge Beach. The concentrations ofEscherichia colias well as human- and gull-specific qPCR microbial source tracking (MST) markers were assessed at all sites. A preliminary comparison of digital PCR (dPCR) methodologies for both MST markers was conducted regarding sensitivity and specificity. Within the watershed, the outfalls were found to be a prominent source of human fecal contamination, with two outfalls particularly affected by sewage cross-connections. However, the occurrence of human fecal contamination along Rouge Beach and in the lower portions of the watershed was largely dependent on rain events. Gull fecal contamination was the predominant source of contamination at the beach, particularly during dry weather. The multiplex human/gull dPCR methodology used in this study tended to be more sensitive than the individual quantitative PCR (qPCR) assays, with only a slight decrease in specificity. Both dPCR and qPCR methodologies identified the same predominance of human and gull markers in stormwater and beach locations, respectively; however, the dPCR multiplex assay was more sensitive and capable of detecting fecal contamination that was undetected by qPCR assays. These results demonstrate the dPCR assay used in this study could be a viable tool for MST studies to increase the ability to identify low levels of fecal contamination.IMPORTANCEFecal contamination of recreational water poses a persistent and ongoing problem, particularly in areas of concern around the Great Lakes. The identification of the source(s) of fecal contamination is essential for safeguarding public health as well as guiding remediation efforts; however, fecal contamination may frequently be present at low levels and remain undetectable by certain methodologies. In this study, we utilized microbial source tracking techniques using both quantitative and digital PCR assays to identify sources of contamination. Our results indicated high levels of human fecal contamination within stormwater outfalls, while lower levels were observed throughout the watershed. Additionally, high levels of gull fecal contamination were detected at Rouge Beach, particularly during drier sampling events. Furthermore, our results indicated an increased sensitivity of the digital PCR assay to detect both human and gull contamination, suggesting it could be a viable tool for future microbial source tracking studies.


2015 ◽  
Vol 82 (4) ◽  
pp. 1316-1323 ◽  
Author(s):  
W. Ahmed ◽  
J. P. S. Sidhu ◽  
K. Smith ◽  
D. J. Beale ◽  
P. Gyawali ◽  
...  

ABSTRACTRecreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB)Escherichia coliandEnterococcusspp., HFMsBacteroidesHF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia.E. colimean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 106gene copies per ml), followed by those of HF183 (8.0 × 105gene copies per ml) andEnterococcusspp. (3.6 × 105gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated thatBacteroidesHF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters.


2012 ◽  
Vol 78 (16) ◽  
pp. 5788-5795 ◽  
Author(s):  
Marta Gómez-Doñate ◽  
Elisenda Ballesté ◽  
Maite Muniesa ◽  
Anicet R. Blanch

ABSTRACTBifidobacteriumspp. belong to the commensal intestinal microbiota of warm-blooded animals. Some strains ofBifidobacteriumshow host specificity and have thus been proposed as host-specific targets to determine the origin of fecal pollution. Most strains have been used in microbial-source-tracking (MST) studies based on culture-dependent methods. Although some of these approaches have proved very useful, the low prevalence of culturableBifidobacteriumstrains in the environment means that molecular culture-independent procedures could provide practical applications for MST. Reported here is a set of common primers and fourBifidobacteriumsp. host-associated (human, cattle, pig, and poultry) probes for quantitative-PCR (qPCR) assessment of fecal source tracking. This set was tested using 25 water samples of diverse origin: urban sewage samples, wastewater from four abattoirs (porcine, bovine, and poultry), and water from a river with a low pollution load. The selected sequences showed a high degree of host specificity. There were no cross-reactions between the qPCR assays specific for each origin and samples from different fecal origins. On the basis of the findings, it was concluded that the host-specific qPCRs are sufficiently robust to be applied in environmental MST studies.


2014 ◽  
Vol 80 (12) ◽  
pp. 3708-3720 ◽  
Author(s):  
Graham Wilkes ◽  
Julie Brassard ◽  
Thomas A. Edge ◽  
Victor Gannon ◽  
Natalie Gottschall ◽  
...  

ABSTRACTSurface waters from paired agricultural watersheds under controlled tile drainage (CTD) and uncontrolled tile drainage (UCTD) were monitored over 7 years in order to determine if there was an effect of CTD (imposed during the growing season) on occurrences and loadings of bacterial and viral pathogens, coliphages, and microbial source tracking markers. There were significantly lower occurrences of human, ruminant, and livestock (ruminant plus pig)Bacteroidalesmarkers in the CTD watershed in relation to the UCTD watershed. As for pathogens, there were significantly lower occurrences ofSalmonellaspp. andArcobacterspp. in the CTD watershed. There were no instances where there were significantly higher quantitative loadings of any microbial target in the CTD watershed, except for F-specific DNA (F-DNA) and F-RNA coliphages, perhaps as a result of fecal inputs from a hobby farm independent of the drainage practice treatments. There was lower loading of the ruminant marker in the CTD watershed in relation to the UCTD system, and results were significant at the levelP= 0.06. The odds ofSalmonellaspp. occurring increased when a ruminant marker was present relative to when the ruminant marker was absent, yet forArcobacterspp., the odds of this pathogen occurring significantly decreased when a ruminant marker was present relative to when the ruminant marker was absent (but increased when a wildlife marker was present relative to when the wildlife marker was absent). Interestingly, the odds of norovirus GII (associated with human and swine) occurring in water increased significantly when a ruminant marker was present relative to when a ruminant marker was absent. Overall, this study suggests that fecal pollution from tile-drained fields to stream could be reduced by CTD utilization.


2010 ◽  
Vol 62 (3) ◽  
pp. 719-727 ◽  
Author(s):  
T. A. Edge ◽  
S. Hill ◽  
P. Seto ◽  
J. Marsalek

Multiple microbial source tracking methods were applied to investigate spatial variation in faecal pollution sources impacting a 1.7 km freshwater beach on Lake Ontario (Canada). The highest E. coli concentrations measured in the study area were from interstitial sand pore water at Sunnyside Beach, reaching 2.6 × 106 CFU/100 ml. These E. coli concentrations exceeded those in the nearby Humber River and Black Creek, which are impacted by combined sewer overflows containing municipal wastewater and by stormwater conveying washoff from the urban area. Library-independent Bacteroidales HF183 analyses identified the more frequent occurrence of municipal wastewater contamination in the Humber River and at a Sunnyside Beach location closest to the mouth of the river. Library-dependent E. coli antibiotic resistance and rep-PCR DNA fingerprinting analyses identified the more frequent occurrence of bird faecal contamination at Sunnyside Beach locations away from the river mouth. These microbial source tracking results raise caution about managing beaches with multiple sources of contamination as a single entity without considering spatial variability in faecal pollution sources and the need for more localized beach management practices.


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