scholarly journals Distribution and Differential Survival of Traditional and Alternative Indicators of Fecal Pollution at Freshwater Beaches

2016 ◽  
Vol 83 (4) ◽  
Author(s):  
Danielle D. Cloutier ◽  
Sandra L. McLellan
Keyword(s):  
Water Samples ◽  
Environmental Samples ◽  
High Sensitivity ◽  
Fecal Pollution ◽  
Source Material ◽  
Beach Sand ◽  
Differential Survival ◽  
Content Type ◽  
Volume Comparison ◽  
E Coli

ABSTRACT Alternative indicators have been developed that can be used to identify host sources of fecal pollution, yet little is known about how their distribution and fate compare to traditional indicators. Escherichia coli and enterococci were widely distributed at the six beaches studied and were detected in almost 95% of water samples (n = 422) and 100% of sand samples (n = 400). Berm sand contained the largest amount of E. coli (P < 0.01), whereas levels of enterococci were highest in the backshore (P < 0.01). E. coli and enterococci were the lowest in water, using a weight-to-volume comparison. The gull-associated Catellicoccus marimammalium (Gull2) marker was found in over 80% of water samples, regardless of E. coli levels, and in 25% of sand samples. Human-associated Bacteroides (HB) and Lachnospiraceae (Lachno2) were detected in only 2.4% of water samples collected under baseflow and post-rain conditions but produced a robust signal after a combined sewage overflow, despite low E. coli concentrations. Burdens of E. coli and enterococci in water and sand were disproportionately high in relation to alternative indicators when comparing environmental samples to source material. In microcosm studies, Gull2, HB, and Lachno2 quantitative PCR (qPCR) signals were reduced twice as quickly as those from E. coli and enterococci and approximately 20% faster than signals from culturable E. coli. High concentrations of alternative indicators in source material illustrated their high sensitivity for the identification of fecal sources; however, differential survival and the potential for long-term persistence of traditional fecal indicators complicate the use of alternative indicator data to account for the levels of E. coli and enterococci in environmental samples. IMPORTANCE E. coli and enterococci are general indicators of fecal pollution and may persist in beach sand, making their use problematic for many applications. This study demonstrates that gull fecal pollution is widespread at Great Lakes beaches, whereas human and ruminant contamination is evident only after major rain events. An exploration of sand as a reservoir for indicators found that E. coli was ubiquitous, while gull host markers were detected in only 25% of samples. In situ sand beach microcosms provided decay rate constants for E. coli and enterococci relative to alternative indicators, which establish comparative benchmarks that would be helpful to distinguish recent from past pollution. Overall, alternative indicators are useful for identifying sources and assessing potentially high health risk contamination events; however, beach managers should be cautious in attempting to directly link their detection to the levels of E. coli or enterococci.

scholarly journals Characterization of Extended-Spectrum β-Lactamase Genes Found among Escherichia coli Isolates from Duck and Environmental Samples Obtained on a Duck Farm

2012 ◽  
Vol 78 (10) ◽  
pp. 3668-3673 ◽  
Author(s):  
Junying Ma ◽  
Jian-Hua Liu ◽  
Luchao Lv ◽  
Zhiyong Zong ◽  
Yan Sun ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Water Samples ◽  
Environmental Samples ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Hypothetical Protein ◽  
M Gene ◽  
Content Type ◽  
E Coli ◽  
Extended Spectrum

ABSTRACTIn this study, we focused on evaluating the occurrence of extended-spectrum β-lactamase (ESBL)-producingEscherichia coliin fecal samples of healthy ducks and environmental samples from a duck farm in South China. Duck cloacal swabs and pond water samples were cultivated on MacConkey agar plates supplemented with ceftiofur. Individual colonies were examined for ESBL production. Bacteria identified asE. coliwere screened for the presence of ESBL and plasmid-borne AmpC genes. The genetic relatedness, plasmid replicon type, and genetic background were determined. Of 245 samples analyzed, 123 hadE. coliisolates with ceftiofur MICs higher than 8 μg/ml (116 [50.4%] from 230 duck samples and 7 [46.7%] from 15 water samples).blaCTX-M,blaSHV-12,blaCMY-2, andblaDHA-1were identified in 108, 5, 9, and 1 isolates, respectively. The most commonblaCTX-Mgenes wereblaCTX-M-27(n= 34),blaCTX-M-55(n= 27),blaCTX-M-24e(n= 22), andblaCTX-M-105(n= 20), followed byblaCTX-M-14a,blaCTX-M-14b,blaCTX-M-24a, andblaCTX-M-24b. Although most of the CTX-M producers had distinct pulsotypes, clonal transmission between duck and water isolates was observed.blaCTX-Mgenes were carried by transferable IncN, IncF, and untypeable plasmids. The novel CTX-M geneblaCTX-M-105was flanked by two hypothetical protein sequences, partial ISEcp1upstream and truncated IS903D,iroN,orf1, and a Tn1721-like element downstream. It is suggested that the horizontal transfer ofblaCTX-Mgenes mediated by mobile elements and the clonal spread of CTX-M-producingE. coliisolates contributed to the dissemination ofblaCTX-Min the duck farm. Our findings highlight the importance of ducks for the dissemination of transferable antibiotic resistance genes into the environment.

Modern nanobiotechnologies for efficient detection and remediation of mercury

Sensor Review ◽  
2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Mulayam Singh Gaur ◽  
Rajni Yadav ◽  
Mamta Kushwah ◽  
Anna Nikolaevna Berlina
Keyword(s):  
Heavy Metals ◽  
Water Samples ◽  
Low Cost ◽  
High Sensitivity ◽  
Environmental Water ◽  
Mercury Ions ◽  
Content Type ◽  
Efficient Detection ◽  
Sensitivity And Selectivity ◽  
Selection Of

Purpose This information will be useful in the selection of materials and technology for the detection and removal of mercury ions at a low cost and with high sensitivity and selectivity. The purpose of this study is to provide the useful information for selection of materials and technology to detect and remove the mercury ions from water with high sensitivity and selectivity. The purpose of this study is to provide the useful information for selection of materials and technology to detect and remove the mercury ions from water with high sensitivity and selectivity. Design/methodology/approach Different nano- and bio-materials allowed for the development of a variety of biosensors – colorimetric, chemiluminescent, electrochemical, whole-cell and aptasensors – are described. The materials used for their development also make it possible to use them in removing heavy metals, which are toxic contaminants, from environmental water samples. Findings This review focuses on different technologies, tools and materials for mercury (heavy metals) detection and remediation to environmental samples. Originality/value This review gives up-to-date and systemic information on modern nanotechnology methods for heavy metal detection. Different recognition molecules and nanomaterials have been discussed for remediation to water samples. The present review may provide valuable information to researchers regarding novel mercury ions detection sensors and encourage them for further research/development.

scholarly journals Ecological and Technical Mechanisms for Cross-Reaction of Human Fecal Indicators with Animal Hosts

2019 ◽  
Vol 86 (5) ◽  
Author(s):  
Shuchen Feng ◽  
Warish Ahmed ◽  
Sandra L. McLellan
Keyword(s):  
False Positive ◽  
Marker Gene ◽  
Fecal Pollution ◽  
Marker Genes ◽  
Indicator Organisms ◽  
Sequencing Data ◽  
Content Type ◽  
E Coli ◽  
Cross Reactions ◽  
Nonspecific Amplification

ABSTRACT Quantitative PCR (qPCR) assays for human/sewage marker genes have demonstrated sporadic positive results in animal feces despite their high specificities to sewage and human feces. It is unclear whether these positive reactions are caused by true occurrences of microorganisms containing the marker gene (i.e., indicator organisms) or nonspecific amplification (false positive). The distribution patterns of human/sewage indicator organisms in animals have not been explored in depth, which is crucial for evaluating a marker gene’s true- or false-positive reactions. Here, we analyzed V6 region 16S rRNA gene sequences from 257 animal fecal samples and tested a subset of 184 using qPCR for human/sewage marker genes. Overall, specificities of human/sewage marker genes within sequencing data were 99.6% (BacV6-21), 96.9% (Lachno3), and 96.1% (HF183, indexed by its inferred V6 sequence). Occurrence of some true cross-reactions was associated with atypical compositions of organisms within the genera Blautia or Bacteroides. For human/sewage marker qPCR assays, specificities were 96.7% (HF183/Bac287R), 96.2% (BacV6-21), 95.6% (human Bacteroides [HB]), and 94.0% (Lachno3). Select assays duplexed with either Escherichia coli or Enterococcus spp. were also validated. Most of the positive qPCR results in animals were low level and, on average, 2 orders of magnitude lower than the copy numbers of E. coli and Enterococcus spp. The lower specificity in qPCR assays compared to sequencing data was mainly caused by amplification of sequences highly similar to the marker gene and not the occurrence of the exact marker sequence in animal fecal samples. IMPORTANCE Identifying human sources of fecal pollution is critical to remediate sanitation concerns. Large financial investments are required to address these concerns; therefore, a high level of confidence in testing results is needed. Human fecal marker genes validated in this study showed high specificity in both sequencing data and qPCR results. Human marker sequences were rarely found in individual animals, and in most cases, the animals had atypical microbial communities. Sequencing also revealed the presence of closely related organisms that could account for nonspecific amplification in certain assays. Both the true cross-reactions and the nonspecific amplification had low signals well below E. coli or Enterococcus levels and likely would not impact the assay’s ability to reliably detect human fecal pollution. No animal source had multiple human/sewage marker genes present; therefore, using a combination of marker genes would increase the confidence of human fecal pollution detection.

Salmonella Contamination during Production of Cantaloupe: A Binational Study

2004 ◽  
Vol 67 (4) ◽  
pp. 713-720 ◽  
Author(s):  
A. CASTILLO ◽  
I. MERCADO ◽  
L. M. LUCIA ◽  
Y. MARTÍNEZ-RUIZ ◽  
J. PONCE de LEÓN ◽  
...  
Keyword(s):  
United States ◽  
Water Samples ◽  
Environmental Samples ◽  
Rio Grande Valley ◽  
The United States ◽  
South Texas ◽  
Pcr Analysis ◽  
E Coli ◽  
Binational Study ◽  
Valley Area

Six cantaloupe farms and packing plants in South Texas (950 cantaloupe, 140 water, and 45 environmental samples), including the Rio Grande Valley area, and three farms in Colima State, Mexico (300 cantaloupe, 45 water, and 15 environmental samples), were sampled to evaluate cantaloupe contamination with Salmonella and Escherichia coli during production and processing. Samples collected from external surfaces of cantaloupes, water, and the environments of packing sheds on cantaloupe farms were examined for the presence of Salmonella and E. coli. Of a total of 1,735 samples collected, 31 (1.8%) tested positive for Salmonella. Fifteen Salmonella serotypes were isolated from samples collected in Texas, and nine from samples collected in Colima. Two serotypes (Poona and Oranienburg) that have been associated with three large Salmonella outbreaks in the United States and Canada linked to the consumption of contaminated cantaloupe were found in water samples collected at four farms (three from the United States). Susceptibility of Salmonella isolates to 10 antimicrobials was evaluated by disk diffusion. Eighty-eight percent of the isolates from the United States and Mexico were pansusceptible to the antimicrobials tested; eight isolates from the United States demonstrated an intermediate susceptibility to streptomycin and only two isolates were resistant to the same antimicrobial. From Mexico, four isolates showed an intermediate susceptibility to streptomycin and one isolate was resistant to nalidixic acid and streptomycin. Repetitive sequence-based PCR analysis of Salmonella isolates helped to trace potential sources of Salmonella contamination in source water and in subsequent water samples obtained after the filtration systems of U.S. and Mexican cantaloupe farms. No differences could be seen between the levels of Salmonella contamination in melons from both countries.

scholarly journals Evaluation of Bovine Feces-Associated Microbial Source Tracking Markers and Their Correlations with Fecal Indicators and Zoonotic Pathogens in a Brisbane, Australia, Reservoir

2013 ◽  
Vol 79 (8) ◽  
pp. 2682-2691 ◽  
Author(s):  
W. Ahmed ◽  
T. Sritharan ◽  
A. Palmer ◽  
J. P. S. Sidhu ◽  
S. Toze
Keyword(s):  
Host Specificity ◽  
Water Samples ◽  
Microbial Source Tracking ◽  
Fecal Pollution ◽  
Decay Rates ◽  
Source Tracking ◽  
Content Type ◽  
Zoonotic Pathogens ◽  
Maximum Value ◽  
Bovine Feces

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.

scholarly journals Methanobrevibacter ruminantium as an Indicator of Domesticated-Ruminant Fecal Pollution in Surface Waters

2007 ◽  
Vol 73 (21) ◽  
pp. 7118-7121 ◽  
Author(s):  
Jennifer A. Ufnar ◽  
Shiao Y. Wang ◽  
David F. Ufnar ◽  
R. D. Ellender
Keyword(s):  
Surface Waters ◽  
Water Samples ◽  
Environmental Samples ◽  
Environmental Water ◽  
Fecal Pollution ◽  
Environmental Water Samples ◽  
Amplification Product ◽  
Methanobrevibacter Ruminantium

ABSTRACT A PCR-based assay (Mrnif) targeting the nifH gene of Methanobrevibacter ruminantium was developed to detect fecal pollution from domesticated ruminants in environmental water samples. The assay produced the expected amplification product only when the reaction mixture contained DNA extracted from M. ruminantium culture, bovine (80%), sheep (100%), and goat (75%) feces, and water samples from a bovine waste lagoon (100%) and a creek contaminated with bovine lagoon waste (100%). The assay appears to be specific and sensitive and can distinguish between domesticated- and nondomesticated-ruminant fecal pollution in environmental samples.

scholarly journals FORENSIC: an Online Platform for Fecal Source Identification

mSystems ◽  
2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Adélaïde Roguet ◽  
Özcan C. Esen ◽  
A. Murat Eren ◽  
Ryan J. Newton ◽  
Sandra L. McLellan
Keyword(s):  
Water Quality ◽  
Random Forest ◽  
Source Identification ◽  
Environmental Samples ◽  
Fecal Pollution ◽  
Rrna Gene ◽  
Content Type ◽  
Random Forest Classification ◽  
Forest Classification ◽  
Reference Signature

ABSTRACT Sewage overflows, agricultural runoff, and stormwater discharges introduce fecal pollution into surface waters. Distinguishing these sources is critical for evaluating water quality and formulating remediation strategies. With the falling costs of sequencing, microbial community-based water quality assessment tools are under development. However, their application is limited by the need to build reference libraries, which requires extensive sampling of sources and bioinformatic expertise. Here, we introduce FORest Enteric Source IdentifiCation (FORENSIC; https://forensic.sfs.uwm.edu/), an online, library-independent source tracking platform based on random forest classification and 16S rRNA gene amplicon sequences to identify in environmental samples common fecal contamination sources, including humans, domestic pets, and agricultural animals. FORENSIC relies on a broad reference signature database of Bacteroidales and Clostridiales, two predominant bacterial groups that have coevolved with their hosts. As a result, these groups demonstrate cohesive and reliable assemblage patterns within mammalian species or among species sharing the same diet/physiology. We created a scalable and extensible platform that we tested for global applicability using samples collected in distant geographic locations. This Web application offers a fast and intuitive approach for fecal source identification, particularly in sewage-contaminated waters. IMPORTANCE FORENSIC is an online platform to identify sources of fecal pollution without the need to create reference libraries. FORENSIC is based on the ability of random forest classification to extract cohesive source microbial signatures to create classifiers despite individual variability and to detect the signatures in environmental samples. We primarily focused on defining sewage signals, which are associated with a high human health risk in polluted waters. To test for fecal contamination sources, the platform only requires paired-end reads targeting the V4 or V6 regions of the 16S rRNA gene. We demonstrated that we could use V4V5 reads trimmed to the V4 positions to generate the reference signature. The systematic workflow we describe to create and validate the signatures could be applied to many disciplines. With the increasing gap between advancing technology and practical applications, this platform makes sequence-based water quality assessments accessible to the public health and water resource communities.

scholarly journals Evaluation of the Biotoxis qPCR Detection Kit for Francisella tularensis Detection in Clinical and Environmental Samples

2020 ◽  
Vol 59 (1) ◽  
pp. e01434-20
Author(s):  
Aurélie Hennebique ◽  
Fabienne Gas ◽  
Hélène Batina ◽  
Cécilia De Araujo ◽  
Karine Bizet ◽  
...  
Keyword(s):  
Francisella Tularensis ◽  
Water Samples ◽  
Environmental Samples ◽  
Limit Of Detection ◽  
Bacterial Species ◽  
Environmental Water ◽  
Type B ◽  
Content Type ◽  
Clinical Specimens ◽  
Real Time Quantitative Pcr

ABSTRACTRapid and reliable detection and identification of Francisella tularensis (a tier 1 select agent) are of primary interest for both medical and biological threat surveillance purposes. The Biotoxis qPCR detection kit is a real-time quantitative PCR (qPCR) assay designed for the detection of Bacillus anthracis, Yersinia pestis, and F. tularensis in environmental or biological samples. Here, we evaluated its performance for detecting F. tularensis in comparison to previously validated qPCR assays. The Biotoxis qPCR was positive for 87/87 F. tularensis subsp. holarctica (type B) strains but also for F. tularensis subsp. novicida. It was negative for Francisella philomiragia and 24/24 strains belonging to other bacterial species. For 31 tularemia clinical specimens, the Biotoxis qPCR displayed a sensitivity between 90.32% and 96.55%, compared to qPCR tests targeting ISFtu2 or a type B-specific DNA sequence, respectively. All 30 nontularemia clinical specimens were Biotoxis qPCR negative. For water samples, the Biotoxis qPCR limit of detection was 1,000 CFU/liter of F. tularensis. For 57 environmental water samples collected in France, the Biotoxis qPCR was positive for 6/15 samples positive for ISFtu2 qPCR and 4/4 positive for type B qPCR. In conclusion, the Biotoxis qPCR detection kit demonstrated good performances for F. tularensis detection in various biological and environmental samples, although cross-amplification of F. tularensis subsp. novicida must be considered. This plate format assay could be useful to test a large number of clinical or environmental specimens, especially in the context of natural or intentional tularemia outbreaks.

scholarly journals Selective survival of Escherichia coli phylotypes in freshwater beach sand

2020 ◽  
Author(s):  
Natalie A. Rumball ◽  
HannahRose C. Mayer ◽  
Sandra L. McLellan
Keyword(s):  
Escherichia Coli ◽  
Lake Michigan ◽  
Fecal Pollution ◽  
Pollution Monitoring ◽  
Beach Sand ◽  
Environmental Drivers ◽  
Nutrient Inputs ◽  
Term Survival ◽  
E Coli

Escherichia coli is used as an indicator of fecal pollution at beaches despite evidence of long-term survival in sand. This work investigated the basis for survival of E. coli through field microcosm experiments and phylotypic characterization of more than >1400 E. coli isolated from sand, sewage, and gulls, enabling identification of long-surviving populations and environmental drivers of their persistence. Microcosms containing populations of E. coli from each source (n=176) were buried in the backshore of Lake Michigan for 45 & 96 days under several different nutrient treatments, including unaltered native sand, sterile autoclaved sand and baked nutrient depleted sand. Availability of carbon and nitrogen and competition with the indigenous community were major factors that influenced E. coli survival. E. coli Clermont phylotypes B1 and A were the most dominant phylotypes surviving seasonally (>6 weeks), regardless of source and nutrient treatment, whereas cryptic clade and D/E phylotypes survived over winter (>300 days). Autoclaved sand, presumably supplying nutrients through increased availability, promoted growth and the presence of the indigenous microbial community reduced this effect. Screening of 849 sand E. coli from four freshwater beaches demonstrated that B1, but also D/E, were the most common phylotypes recovered. Analysis by qPCR for the Gull2, Lachno3 and HB human markers demonstrated only 25% of the samples had evidence of gull waste and none of the samples had evidence of human waste. These findings suggest prevalence of E. coli in the sand could be attributed more to long term surviving populations than to new fecal pollution. IMPORTANCE Fecal pollution monitoring still relies upon the enumeration of E. coli, despite the fact that this organism can survive for prolonged periods and has been shown to be easily transported from sand into surrounding waters through waves and runoff, thus no longer represents recent fecal pollution events. Here, we experimentally demonstrate that regardless of host source, certain genetically distinct subgroups, or phylotypes, survive longer than others under conditions typical of Great Lakes beach sites. We found nutrients were a major driver of survival and could actually promote growth, and the presence of native microorganisms modulated these effects. These insights into the dynamics and drivers of survival will improve the interpretation of E. coli measurements at beaches and inform strategies that could focus on reducing nutrient inputs to beaches or maintaining a robust natural microbiome in beach sand.

scholarly journals Quantification of Human and Animal Viruses to Differentiate the Origin of the Fecal Contamination Present in Environmental Samples

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Sílvia Bofill-Mas ◽  
Marta Rusiñol ◽  
Xavier Fernandez-Cassi ◽  
Anna Carratalà ◽  
Ayalkibet Hundesa ◽  
...  
Keyword(s):  
Environmental Samples ◽  
Fecal Contamination ◽  
Fecal Pollution ◽  
Human Polyomavirus ◽  
Source Tracking ◽  
E Coli ◽  
Bacterial Indicator ◽  
Low Concentrations ◽  
Polyomavirus Jc ◽  
Viral Indicators

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 asE. coliand 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.

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