scholarly journals First detection of human sapoviruses in river water in South Africa

2013 ◽  
Vol 67 (12) ◽  
pp. 2776-2783 ◽  
Author(s):  
T. Y. Murray ◽  
J. Mans ◽  
M. B. Taylor
Keyword(s):  
South Africa ◽  
Water Samples ◽  
River System ◽  
Chain Reaction ◽  
Specific Primers ◽  
Potential Health ◽  
Taqman Probes ◽  
Polymerase Chain ◽  
Elution Method ◽  
Three Rivers

Over a 2-year period, from January 2009 to December 2010, water samples were collected from three rivers (Klip, Rietspruit and Suikerbosrand) in the Vaal River System, South Africa. Enteric viruses were recovered by a glass wool adsorption–elution method and concentrated using polyethylene glycol/sodium chloride precipitation. Sapoviruses (SaVs) were detected using published sapovirus (SaV)-specific primers and Taqman probes in a two-step real-time reverse transcription-polymerase chain reaction assay. Based on sequence analysis of the 5′-end of the capsid gene, SaVs were genotyped. In 2009, SaVs were detected in 39% (15/38) of samples from the Klip river, 83% (5/6) from the Rietspruit and 14% (1/7) of samples from the Suikerbosrand river. In 2010, SaVs were detected in 54% (14/26) of Klip river samples, 92% (11/12) from the Rietspruit and 20% (2/10) of samples from the Suikerbosrand river. SaV strains identified in the water samples were characterised into several GI and GII genotypes. The presence of SaVs in these rivers indicates human faecal contamination which may pose a potential health risk to persons exposed to these water sources during domestic or recreational activities.

scholarly journals Antibiotic Resistance and Sewage-Associated Marker Genes in Untreated Sewage and a River Characterized During Baseflow and Stormflow

2021 ◽  
Vol 12 ◽  
Author(s):  
Warish Ahmed ◽  
Pradip Gyawali ◽  
Kerry A. Hamilton ◽  
Sayalee Joshi ◽  
David Aster ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Antibiotic Resistance ◽  
Water Samples ◽  
Quantitative Polymerase Chain Reaction ◽  
River System ◽  
Marker Genes ◽  
Chain Reaction ◽  
E Coli ◽  
Untreated Sewage ◽  
Polymerase Chain

Since sewage is a hotspot for antibiotic resistance genes (ARGs), the identification of ARGs in environmental waters impacted by sewage, and their correlation to fecal indicators, is necessary to implement management strategies. In this study, sewage treatment plant (STP) influent samples were collected and analyzed using quantitative polymerase chain reaction (qPCR) to investigate the abundance and correlations between sewage-associated markers (i.e., Bacteroides HF183, Lachnospiraceae Lachno3, crAssphage) and ARGs indicating resistance to nine antibiotics (belonging to aminoglycosides, beta-lactams, sulfonamides, macrolides, and tetracyclines). All ARGs, except blaVIM, and sewage-associated marker genes were always detected in untreated sewage, and ermF and sul1 were detected in the greatest abundances. intl1 was also highly abundant in untreated sewage samples. Significant correlations were identified between sewage-associated marker genes, ARGs and the intl1 in untreated sewage (τ = 0.488, p = 0.0125). Of the three sewage-associated marker genes, the BIO-ENV procedure identified that HF183 alone best maximized correlations to ARGs and intl1 (τ = 0.590). Additionally, grab samples were collected from peri-urban and urban sites along the Brisbane River system during base and stormflow conditions, and analyzed for Escherichia coli, ARGs, the intl1, and sewage-associated marker genes using quantitative polymerase chain reaction (qPCR). Significant correlations were identified between E. coli, ARGs, and intl1 (τ = 0.0893, p = 0.0032), as well as with sewage-associated marker genes in water samples from the Brisbane River system (τ = 0.3229, p = 0.0001). Of the sewage-associated marker genes and E. coli, the BIO-ENV procedure identified that crAssphage alone maximized correlations with ARGs and intl1 in river samples (τ = 0.4148). Significant differences in E. coli, ARGs, intl1, and sewage-associated marker genes, and by flow condition (i.e., base vs. storm), and site types (peri-urban vs. urban) combined were identified (R = 0.3668, p = 0.0001), where percent dissimilarities between the multi-factorial groups ranged between 20.8 and 11.2%. Results from this study suggest increased levels of certain ARGs and sewage-associated marker genes in stormflow river water samples compared to base flow conditions. E. coli, HF183 and crAssphage may serve as potential indicators of sewage-derived ARGs under stormflow conditions, and this merits further investigation. Data presented in this study will be valuable to water quality managers to understand the links between sewage pollution and ARGs in urban environments.

scholarly journals Diverse norovirus genotypes identified in sewage-polluted river water in South Africa

2012 ◽  
Vol 141 (2) ◽  
pp. 303-313 ◽  
Author(s):  
J. MANS ◽  
R. NETSHIKWETA ◽  
M. MAGWALIVHA ◽  
W. B. VAN ZYL ◽  
M. B. TAYLOR
Keyword(s):  
South Africa ◽  
Polymerase Chain Reaction ◽  
Surface Water ◽  
Glass Wool ◽  
Chain Reaction ◽  
Polluted River ◽  
Potential Source ◽  
Genotype Diversity ◽  
Polymerase Chain ◽  
Three Rivers

SUMMARYThis study aimed to assess norovirus (NoV) contamination and genotype diversity in surface water in Gauteng, South Africa. Between January 2008 and December 2010, three rivers, namely Klip, Suikerbosrant, and Rietspruit were monitored for NoV genogroup (G)I and GII. Viruses were recovered using the glass wool adsorption-elution technique and detected by real-time reverse transcription–polymerase chain reaction. From 2008 to 2010, NoVs were detected in 66% (70/106) of Klip river samples. The Rietspruit and Suikerbosrant rivers were contaminated with NoV in 95% (20/21) and 21% (5/24) of samples, respectively. NoV-positive samples comprised of 33% GI, 29% GII and 38% of both GI and GII strains. Based on partial capsid gene analysis (region C), 16 NoV genotypes (6 GI, 10 GII) were identified. The major genotypes detected were GI.4, GI.5 and GII.4. These rivers could be a potential source of NoV infection for communities using the water for domestic or recreational purposes.

scholarly journals Detection of human enteric viruses in Umgeni River, Durban, South Africa

2015 ◽  
Vol 13 (4) ◽  
pp. 1098-1112 ◽  
Author(s):  
Johnson Lin ◽  
Atheesha Singh
Keyword(s):  
South Africa ◽  
Polymerase Chain Reaction ◽  
Water Samples ◽  
Nested Pcr ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Domestic Water ◽  
River Waters ◽  
Polymerase Chain ◽  
Domestic Water Supply

The prevalence of adenovirus (AdV), rotaviruses (RV) and enteroviruses (EV) in Umgeni River waters of Durban, South Africa was assessed qualitatively and quantitatively during April 2011 to January 2012 using polymerase chain reaction (PCR)/reverse transcription-polymerase chain reaction (RT-PCR), nested PCR and quantitative PCR (qPCR), as well as nested integrated cell culture PCR (nested ICC-PCR). The phylogenetic analysis of the adenovirus and enterovirus amplicons was also performed. The nested PCR results effectively detected the presence of AdV and EV in all water samples. The results of qPCR demonstrated that higher populations of EV and of AdV were widely found in the Umgeni River. Rotavirus could only be detected in the upper Umgeni River, mainly during drier seasons. Nested ICC-PCR further confirmed the presence of infectious AdV and EV particles in 100% of water samples using various cell lines. The present study identifies potential viral hazards of Umgeni River water for domestic water supply and recreational activities.

scholarly journals Occurrence of free-living amoebae (Acanthamoeba, Balamuthia, Naegleria) in water samples in Peninsular Malaysia

2018 ◽  
Vol 17 (1) ◽  
pp. 160-171 ◽  
Author(s):  
Shobana Gabriel ◽  
Naveed Ahmed Khan ◽  
Ruqaiyyah Siddiqui
Keyword(s):  
Water Samples ◽  
Tap Water ◽  
Peninsular Malaysia ◽  
Recreational Water ◽  
Chain Reaction ◽  
Specific Primers ◽  
Free Living ◽  
Polymerase Chain ◽  
Centrifugation Method ◽  
Instagene Matrix

Abstract The aim of this study was to determine the occurrence of free-living amoebae (FLA) in Peninsular Malaysia and to compare different methodologies to detect them from water samples. Water samples were collected from tap water, recreational places, water dispensers, filtered water, etc. and tested for FLA using both cultivation and polymerase chain reaction (PCR) via plating assays and centrifugation methods. Amoebae DNA was extracted using Instagene matrix and PCR was performed using genus-specific primers. Of 250 samples, 142 (56.8%) samples were positive for presence of amoebae, while 108 (43.2%) were negative. Recreational water showed higher prevalence of amoebae than tap water. PCR for the plating assays revealed the presence of Acanthamoeba in 91 (64%) samples and Naegleria in 99 (70%) of samples analysed. All samples tested were negative for B. mandrillaris. In contrast, the centrifugation method was less effective in detecting amoebae as only one sample revealed the presence of Acanthamoeba and 52 (29%) samples were positive for Naegleria. PCR assays were specific and sensitive, detecting as few as 10 cells. These findings show the vast distribution and presence of FLA in all 11 states of Peninsular Malaysia. Further studies could determine the possible presence of pathogenic species and strains of free-living amoebae in public water supplies in Malaysia.

scholarly journals Norovirus genogroups I and II in environmental water samples from Belém city, Northern Brazil

2016 ◽  
Vol 15 (1) ◽  
pp. 163-174 ◽  
Author(s):  
Dielle Monteiro Teixeira ◽  
Paula Katharine de Pontes Spada ◽  
Lena Líllian Canto de Sá Morais ◽  
Tulio Machado Fumian ◽  
Ian Carlos Gomes de Lima ◽  
...  
Keyword(s):  
Water Samples ◽  
Aquatic Ecosystems ◽  
Environmental Water ◽  
Northern Region ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Northern Brazil ◽  
Polymerase Chain ◽  
Elution Method ◽  
Different Sources

This study investigated the presence of norovirus (NoV) GI and GII in environmental samples from the northern region of Brazil. Water samples were collected monthly (November 2008/October 2010) from different sources and sewage and concentrated by the adsorption-elution method. The NoV investigation used molecular methods followed by sequencing reactions. The general positivity for NoV was 33.9% (57/168). Considering the results obtained only in the semi-nested RT-PCR (reverse transcription polymerase chain reaction) and only in the TaqMan® real-time PCR, the rates were 26.8% (45/168) and 27.4% (46/168), respectively, being for NoV GI 22.2% (10/45) and 19.6% (9/46); for GII 17.8% (8/45) and 15.2% (7/46); and for GI + GII 60% (27/45) and 65.2% (30/46), respectively. Different GI (GI.1, GI.4, GI.7 and GI.8) and GII (GII.4, GII.6, GII.9, GII.12 and GII.14) genotypes were detected. These results demonstrated the NoV was disseminated in the waters of Belém city due to a lack of sanitation that allowed the discharge of contaminated effluents into these aquatic ecosystems.

scholarly journals Detection of pork in meatballs using probe TaqMan Real-time Polymerase Chain Reaction

Food Research ◽  
2020 ◽  
Vol 4 (5) ◽  
pp. 1563-1568
Author(s):  
S. Orbayinah ◽  
A. Hermawan ◽  
Sismindari ◽  
A. Rohman
Keyword(s):  
Polymerase Chain Reaction ◽  
Wild Boar ◽  
Real Time ◽  
Chain Reaction ◽  
Specific Primers ◽  
Taqman Probes ◽  
Mitochondrial Region ◽  
D Loop ◽  
Polymerase Chain ◽  
Species Specific

This study aimed to develop a TaqMan Real-Time Polymerase Chain Reaction method, using a novel primer for detection of pork adulteration in meatballs. The study is important as it described a TaqMan method for product adulteration analysis. TaqMan is known to have a more specific result compared to SYBR green analytical method. Assay in the study combined species-specific primers and TaqMan probes to targeting 153 bp fragment of D-loop mitochondrial region of pork. A specificity test was conducted on fresh tissues of pork, beef, chicken, wild boar, dog, and mouse. Meatballs as samples were prepared from a mixture of pork-beef and wild boar-beef with concentrations as follows: 5%, 10%, 25%, 75%, 90%, and 100%. The linearity and sensitivity of the method were performed by measuring the amplification curve from the dilution series, namely 1000, 200, 100, 10, 5, 1, and 0.5 pg/μL of DNA, extracted from 100% pork meatballs. A repeatability test was conducted as many as six repetitions on 100% pork and 100% wild boar meatballs. This study showed that mitochondrial D-loop species-specific primers and TaqMan probes could identify the DNA of pork and wild boar on the fresh tissues. Additionally, it also resulted in a threshold cycle (Ct) of 17.02 and 17.95 for pork, 22.22 for wild boar, while the negative result for others. The detection limit has shown 5 pg in the meatball formulation. The Relative Standard Deviation (RSD) of repeatability was 1.936% for pork, while 2.140% for wild boar. The developed method was also applied to analyzing commercial meatballs. A TaqMan real-time PCR analytical method using specific primer targeting on 153 bp fragment of the D-loop mitochondrial region could be applied as a standard method for identifying pork and wild boar in food samples intended for halal authentication studies

scholarly journals Viruses in the environment – presence and diversity of bacteriophage and enteric virus populations in the Umhlangane River, Durban, South Africa

2017 ◽  
Vol 15 (6) ◽  
pp. 966-981 ◽  
Author(s):  
Veronna Marie ◽  
Johnson Lin
Keyword(s):  
Polymerase Chain Reaction ◽  
Enteric Viruses ◽  
River System ◽  
Enteric Virus ◽  
Water Safety ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Potential Health ◽  
Health Implications ◽  
Polymerase Chain

Abstract Due to the continued persistence of waterborne viral-associated infections, the presence of enteric viruses is a concern. Notwithstanding the health implications, viral diversity and abundance is an indicator of water quality declination in the environment. The aim of this study was to evaluate the presence of viruses (bacteriophage and enteric viruses) in a highly polluted, anthropogenic-influenced river system over a 6-month period at five sampling points. Cytopathic-based tissue culture assays revealed that the isolated viruses were infectious when tested on Hep-G2, HEK293 and Vero cells. While transmission electron microscopy (TEM) revealed that the majority of the viruses were bacteriophages, a number of presumptive enteric virus families were visualized, some of which include Picornaviridae, Adenoviridae, Polyomaviridae and Reoviridae. Finally, primer specific nested polymerase chain reaction (nested-PCR)/reverse transcription-polymerase chain reaction (RT-PCR) coupled with BLAST analysis identified human adenovirus, polyomavirus and hepatitis A and C virus genomes in river water samples. Taken together, the complexity of both bacteriophage and enteric virus populations in the river has potential health implications. Finally, a systematic integrated risk assessment and management plan to identify and minimize sources of faecal contamination is the most effective way of ensuring water safety and should be established in all future guidelines.

scholarly journals Multidrug-Resistant Listeria Species Shows Abundance in Environmental Waters of a Key District Municipality in South Africa

2021 ◽  
Vol 18 (2) ◽  
pp. 481
Author(s):  
Liyabona Mpondo ◽  
Kingsley Ehi Ebomah ◽  
Anthony Ifeanyi Okoh
Keyword(s):  
South Africa ◽  
Surface Waters ◽  
Multidrug Resistant ◽  
Eastern Cape ◽  
Environmental Waters ◽  
Potential Health ◽  
Phenotypic Resistance ◽  
Listeria Species ◽  
Polymerase Chain ◽  
Identification And Characterization

The prevalence of bacteria with multidrug-resistance (MDR) is a significant threat to public health globally. Listeria spp. are naturally ubiquitous, with L. monocytogenes particularly being ranked as important foodborne disease-causing microorganisms. This study aimed to evaluate the incidence and determine the antimicrobial resistance (AMR) profiles of multidrug-resistant Listeria spp. (MDRL) isolated from different environmental samples (river and irrigation water) in the Sarah Baartman District Municipality (SBDM), Eastern Cape Province (ECP), South Africa. Molecular identification and characterization were carried out using polymerase chain reaction (PCR) and isolates that exhibited phenotypic resistance were further screened for relevant antimicrobial-resistant genes (ARGs). Findings revealed a total of 124 presumptive Listeria isolates; 69 were molecularly confirmed Listeria species. Out of the confirmed species, 41 isolates (59%) were classified as L. monocytogenes while 9 (13%) were classified as L. welshimeri. All Listeria spp. exhibited phenotypic resistance against ampicillin, penicillin, and trimethoprim-sulphamethoxazole and further screening revealed ARGs in the following proportions: sulI (71%), blaTEM (66%), tetA (63%), and blaCIT (33%). Results confirmed the occurrence of ARGs among Listeria inhabiting surface waters of ECP. The present study indicates that the river water samples collected from SBDM are highly contaminated with MDRL, hence, constituting a potential health risk.

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