Publications by authors named "Jatinder Sidhu"

20 Publications

  • Page 1 of 1

Assessment of competence in local anaesthetic thoracoscopy: development and validity investigation of a new assessment tool.

J Thorac Dis 2021 Jul;13(7):3998-4007

Copenhagen Academy for Medical Education and Simulation, Centre for HR and Education, The Capital Region of Denmark, Copenhagen, Denmark.

Background: The aims of the study were to develop an assessment tool in local anaesthetic thoracoscopy (LAT), investigate validity evidence, and establish a pass/fail standard.

Methods: Validity evidence for the assessment tool was gathered using the unified Messick framework. The tool was developed by five experts in respiratory medicine and medical education. Doctors with varying experience performed two consecutive procedures in a standardized, simulation-based setting using a newly developed thorax/lung silicone model. Performances were video-recorded and assessed by four expert raters using the new tool. Contrasting groups' method was used to set a pass/fail standard.

Results: Nine novices and 8 experienced participants were included, generating 34 recorded performances and 136 expert assessments. The tool had a high internal consistency (Cronbach's alpha =0.94) and high inter-rater reliability (Cronbach's alpha =0.91). The total item score significantly correlated with the global score (r=0.86, P<0.001). Participants' first performance correlated to second performance (test-retest reliability) with a Pearson's r of 0.93, P<0.001. Generalisability (G) study showed a G-coefficient of 0.92 and decision (D) study estimated that one performance assessed by two raters or four performances assessed by one rater are needed to reach an acceptable reliability, i.e., G-coefficient >0.80. The tool was able to discriminate between the two groups in both performances: experienced mean score =30.8±4.2; novice mean score =15.8±2.3, P<0.001. Pass/fail standard was set at 22 points.

Conclusions: The newly developed assessment tool showed solid evidence of validity and can be used to ensure competence in LAT.
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http://dx.doi.org/10.21037/jtd-20-3560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8339737PMC
July 2021

Virological Characterization of Roof-Harvested Rainwater of Densely Urbanized Low-Income Region.

Food Environ Virol 2021 Sep 29;13(3):412-420. Epub 2021 Jun 29.

Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.

Roof-harvested rainwater (RHRW) is considered relatively clean water, even though the possible presence of pathogens in the water may pose human health risks. In this study, we investigated the occurrence of enteric viruses in the first flush (10 mm) of RHRW from a densely populated and low-income urbanized region of Rio de Janeiro. One hundred samples (5 L) were collected from 10 rainfall events between April 2015 and March 2017. RNA and DNA viruses were concentrated using the skimmed milk flocculation method and analyzed using the TaqMan® quantitative RT-qPCR and qPCR. Human adenoviruses, noroviruses, rotaviruses A, and avian parvoviruses were detected in 54%, 31%, 12%, and 12% of the positive samples. JC polyomavirus, also targeted, was not detected. Virus concentrations ranged from 1.09 × 10 to 2.58 × 10 genome copies/Liter (GC/L). Partial nucleotide sequence confirmed the presence of HAdV type 41, norovirus genotype GII.4, and avian parvovirus 1. The results suggest that the first flush diversion devices may not adequately remove enteric virus from the rainwater. Additional treatment of RHRW is required to mitigate potential health risks from potable use of captured water.
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http://dx.doi.org/10.1007/s12560-021-09484-yDOI Listing
September 2021

Characterization of Lung Tumors that the Pulmonologist can Biopsy from the Esophagus with Endosonography (EUS-B-FNA).

Respiration 2021;100(2):135-144. Epub 2021 Jan 21.

Department of Internal Medicine, Zealand University Hospital, Roskilde, Denmark.

Background: According to guidelines, it is possible to biopsy lung tumors "immediately adjacent to the esophagus" with EUS-B-FNA. However, it is unknown what "immediately adjacent" exactly means.

Objective: to investigate the possibility of achieving EUS-B-FNA biopsies from a lung tumor depending on the distance from the esophagus and to establish the maximal allowable distance between the tumor and the esophagus.

Methods: In a prospective observational study, we included patients with a lung tumor located maximum 6 cm from the esophagus and indication of EUS-B-FNA from the tumor. The tumors were of different sizes. In a plot presenting the tumor size-distance relationship in cases with (biopsy) versus without (non-biopsy) successful EUS-B-FNA, a separation line representing the threshold between the groups were identified and a biopsy-index equation established. The maximal tumor-size corrected distance (TSCD) was calculated using the residuals to the separation line.

Results: In total, 70 patients were included. EUS-B-FNA from the lung tumor was possible in 46 patients. All tumors with a distance from the esophagus below 19 mm could be biopsied. The maximal allowable esophagus-tumor distance depended on tumor size. From the separation line, a biopsy-index equation was established with the sensitivity of 93.5%, a specificity of 100%, and total accuracy of 95.7%. The TSCD was 31 mm (sensitivity: 95.7%, specificity 75.0%, and accuracy: 88.6%).

Conclusion: We established a biopsy-index equation to predict the achievability of a lung tumor using EUS-B-FNA depending on distance to esophagus and tumor size. A general maximal TSCD was 31 mm.
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http://dx.doi.org/10.1159/000512074DOI Listing
January 2021

EUS-B for suspected left adrenal metastasis in lung cancer.

J Thorac Dis 2020 Mar;12(3):258-263

Department of Internal Medicine, Unit of Respiratory Medicine, Zealand University Hospital, Roskilde, Denmark.

Background: Several studies have reported the efficacy of esophageal ultrasound-guided fine needle aspiration (EUS-FNA) for the detection of metastases in the left adrenal gland (LAG) in patients with lung cancer. Currently we have only limited evidence based on small studies on the usefulness of EUS-B [endobronchial ultrasound (EBUS) scope into the esophagus] to provide tissue proof of suspected LAG metastases. The objectives of this study are to investigate feasibility, safety and diagnostic yield of EUS-B-FNA in LAG analysis in patients with proven or suspected lung cancer.

Methods: In two Danish hospitals, a systematic search in the electronic database for patients who underwent EUS-B-FNA of the LAG for suspected or proven lung cancer was performed retrospectively between January 1st, 2015 and December 31st, 2017. Computed tomography (CT), positron emission tomography-CT, endoscopy, pathology and follow-up data were acquired.

Results: One hundred and thirty-five patients were included; the prevalence of biopsy proven LAG malignancy was 30% (40/135). A total of 87% (117/135) of EUS-B-FNA samples were adequate (i.e., containing adrenal or malignant cells). No complications were observed.

Conclusions: We present the largest cohort of patients ever reported showing that EUS-B-FNA of the LAG is a safe and feasible procedure and should therefore be used for staging purposes in patients with lung cancer and a suspicious LAG.
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http://dx.doi.org/10.21037/jtd.2020.01.43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7139040PMC
March 2020

Fluoroscopy guided percutaneous biopsy in combination with bronchoscopy and endobronchial ultrasound in the diagnosis of suspicious lung lesions - the triple approach.

Eur Clin Respir J 2020 7;7(1):1723303. Epub 2020 Feb 7.

Department of Respiratory Medicine, Naestved Hospital, Naestved, Denmark.

Flexible bronchoscopy and endobronchial ultrasound guided transbronchial needle aspiration (EBUS-TBNA) are the pulmonologists´ basic procedures for the biopsy of suspicious lung lesions. If inconclusive, other guiding-modalities for tissue sampling are needed, computed tomography performed by a radiologist, or - if available - radial EBUS or electromagnetic navigation biopsy. We wanted to investigate if same-day X-ray fluoroscopy-guided transthoracic fine-needle aspiration biopsy (F-TTNAB) performed by the pulmonologist immediately after bronchoscopy and EBUS is a feasible alternative. We retrospectively identified consecutive patients in whom F-TTNAB followed a bronchoscopy and EBUS in the same séance. Patients in whom the suspicion of malignancy was invalidated after complete work up were followed for six months to identify false-negative cases. In total 125 patients underwent triple approach (bronchoscopy, EBUS and F-TTNAB) during the same séance. Malignancy was diagnosed in 86 (69%), and 77 of these (90%) were primary lung cancers. The diagnostic yield of F-TTNAB for malignancy was 77%, and sensitivity was 90%. Pneumothorax occurred in 35 (28%) patients, and was administered with pleural drainage in 22 (18% of all patients). No cases of prolonged haemoptysis were observed. The risk of pneumothorax differed insignificantly with lesion size ≤2.0 cm (27%) >2.0 cm (29%). We conclude that it is feasible for pulmonologist to perform F-TTNAB immediately after endoscopy as a combined triple approach in a fast-track workup of suspected lung cancer.
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http://dx.doi.org/10.1080/20018525.2020.1723303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7034437PMC
February 2020

Optimization of sampling strategy to determine pathogen removal efficacy of activated sludge treatment plant.

Environ Sci Pollut Res Int 2017 Aug 28;24(23):19001-19010. Epub 2017 Jun 28.

CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, 4102, Australia.

Large-scale wastewater schemes rely on multi-barrier approach for the production of safe and sustainable recycled water. In multi-barrier wastewater reclamation systems, conventional activated sludge process (ASP) often constitutes a major initial treatment step. The main aim of this research was to determine most appropriate sampling approach to establish pathogen removal efficacy of ASP. The results suggest that ASP is capable of reducing human adenovirus (HAdV) and polyomavirus (HPyV) by up to 3 log. The virus removal data suggests that HAdV removal is comparable to somatic bacteriophage belonging to Microviridae family. Due to the high removal of Escherichia coli (>3 log) and very poor correlation with the enteric virus, it is not recommended that E. coli be used as a surrogate for enteric virus removal. The results also demonstrated no statistically significant differences (t test, P > 0.05) in calculated log removal values (LRVs) for HAdV, HPyV, and Microviridae from samples collected on hydraulic retention time (HRT) or simultaneous paired samples collected for influent and effluent. This indicates that a more practical approach of simultaneous sampling for influent and effluent could be used to determine pathogen removal efficiency of ASP. The results also suggest that a minimum of 10, preferably 20 samples, are required to fully capture variability in the removal of virus. In order to cover for the potential seasonal prevalence of viruses such as norovirus and rotavirus, sampling should be spread across all seasons.
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http://dx.doi.org/10.1007/s11356-017-9557-5DOI Listing
August 2017

Quantification of hookworm ova from wastewater matrices using quantitative PCR.

J Environ Sci (China) 2017 Jul 24;57:231-237. Epub 2017 Feb 24.

CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld 4102, Australia; School of Public Health, The University of Queensland, Herston Road, Qld 4006, Australia.

A quantitative PCR (qPCR) assay was used to quantify Ancylostoma caninum ova in wastewater and sludge samples. We estimated the average gene copy numbers for a single ovum using a mixed population of ova. The average gene copy numbers derived from the mixed population were used to estimate numbers of hookworm ova in A. caninum seeded and unseeded wastewater and sludge samples. The newly developed qPCR assay estimated an average of 3.7×10 gene copies per ovum, which was then validated by seeding known numbers of hookworm ova into treated wastewater. The qPCR estimated an average of (1.1±0.1), (8.6±2.9) and (67.3±10.4) ova for treated wastewater that was seeded with (1±0), (10±2) and (100±21) ova, respectively. The further application of the qPCR assay for the quantification of A. caninum ova was determined by seeding a known numbers of ova into the wastewater matrices. The qPCR results indicated that 50%, 90% and 67% of treated wastewater (1L), raw wastewater (1L) and sludge (~4g) samples had variable numbers of A. caninum gene copies. After conversion of the qPCR estimated gene copy numbers to ova for treated wastewater, raw wastewater, and sludge samples, had an average of 0.02, 1.24 and 67 ova, respectively. The result of this study indicated that qPCR can be used for the quantification of hookworm ova from wastewater and sludge samples; however, caution is advised in interpreting qPCR generated data for health risk assessment.
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http://dx.doi.org/10.1016/j.jes.2016.10.019DOI Listing
July 2017

Comparative prevalence of Escherichia coli carrying virulence genes and class 1 and 2 integrons in sub-tropical and cool temperate freshwater.

Environ Sci Pollut Res Int 2017 Aug 21;24(22):18263-18272. Epub 2017 Jun 21.

CSIRO Land and Water Flagship, Ecosciences Precinct, 41 Boggo Road, Dutton Park, Brisbane, QLD, 4102, Australia.

Aquatic environments are now recognized secondary habitat of potentially pathogenic Escherichia coli. In this study, PCR-based analyses were used to determine the phylogenetic composition and frequency of occurrence of eight clinically significant virulence genes (VGs) in E. coli isolates from sub-tropical Brisbane and cool temperate Tasmania freshwater in Australia. In Brisbane, non-commensal E. coli isolates belonging to the B2 and D phylogenetic group were dominant (72%). A significantly higher number (P < 0.05) of E. coli carrying VGs were detected in the sub-tropical freshwaters compared to the cool temperate water. Furthermore, diarrheagenic pathotype (EHEC) was also observed in the sub-tropical freshwater. The genes east1 and eaeA were significantly more common (P < 0.00001) than other VGs. The eaeA gene which codes for intimin protein along with toxin genes east1, stx , stx , and LT1 were mostly detected in phylogenetic groups B2 and D. The ANOVA results also suggested a statistically significant difference (P < 0.016) between the VGs carried by phylogenetic groups B2 and D. Class 1 integrase (intl1) and class 2 integrase (intl2) genes were detected in 38 (24.83%) and 23 (15.03%) of E. coli isolates, respectively. The Gretna site (Tasmania) with known fecal input from bovine and ovine sources had the highest number of E. coli carrying intl1 (29%) and intl2 (13%) genes. In addition, class 2 integron was more commonly detected in the phylogenetic group B2. The results of this study highlight the need to better understand sources and reasons for the high prevalence of E. coli carrying clinically significant VGs in a sub-tropical environment and its public health implications.
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http://dx.doi.org/10.1007/s11356-017-9497-0DOI Listing
August 2017

Pesticide occurrence and spatio-temporal variability in urban run-off across Australia.

Water Res 2017 05 6;115:245-255. Epub 2017 Mar 6.

Cooperative Research Centre for Water Sensitive Cities, Clayton, VIC, 3800, Australia; The University of Queensland, Advanced Water Management Centre, St. Lucia, QLD, 4072, Australia; Catalan Institute for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain; Catalan Institute for Water Research (ICRA), 17003, Girona, Spain. Electronic address:

Stormwater is a major driving factor of aquatic ecosystem degradation as well as one of the largest untapped urban freshwater resources. We present results from a long-term, multi-catchment study of urban stormwater pesticides across Australia that addresses this dichotomous identity (threat and resource), as well as dominant spatial and temporal patterns in stormwater pesticide composition. Of the 27 pesticides monitored, only 19 were detected in Australian stormwater, five of which (diuron, MCPA, 2,4-D, simazine, and triclopyr) were found in >50% of samples. Overall, stormwater pesticide concentrations were lower than reported in other countries (including the United States, Canada and Europe), and exceedances of public health and aquatic ecosystem standards were rare (<10% of samples). Spatio-temporal patterns were investigated with principal component analysis. Although stormwater pesticide composition was relatively stable across seasons and years, it varied significantly by catchment. Common pesticide associations appear to reflect 1) user application of common registered formulations containing characteristic suites of active ingredients, and 2) pesticide fate properties (e.g., environmental mobility and persistence). Importantly, catchment-specific occurrence patterns provide opportunities for focusing treatment approaches or stormwater harvesting strategies.
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http://dx.doi.org/10.1016/j.watres.2017.03.010DOI Listing
May 2017

Amplicon-based profiling of bacteria in raw and secondary treated wastewater from treatment plants across Australia.

Appl Microbiol Biotechnol 2017 Feb 12;101(3):1253-1266. Epub 2016 Nov 12.

CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Brisbane, QLD, 4102, Australia.

In this study, we investigated the use of Illumina high-throughput sequencing of 16S ribosomal RNA (rRNA) amplicons to explore microbial diversity and community structure in raw and secondary treated wastewater (WW) samples from four municipal wastewater treatment plants (WWTPs A-D) across Australia. Sequence reads were analyzed to determine the abundance and diversity of bacterial communities in raw and secondary treated WW samples across the four WWTPs. In addition, sequence reads were also characterized to phenotypic features and to estimate the abundance of potential pathogenic bacterial genera and antibiotic-resistant genes in total bacterial communities. The mean coverage, Shannon diversity index, observed richness (S ), and abundance-based coverage estimate (ACE) of richness for raw and secondary treated WW samples did not differ significantly (P > 0.05) among the four WWTPs examined. Generally, raw and secondary treated WW samples were dominated by members of the genera Pseudomonas, Arcobacter, and Bacteroides. Evaluation of source contributions to secondary treated WW, done using SourceTracker, revealed that 8.80-61.4% of the bacterial communities in secondary treated WW samples were attributed to raw WW. Twenty-five bacterial genera were classified as containing potential bacterial pathogens. The abundance of potentially pathogenic genera in raw WW samples was higher than that found in secondary treated WW samples. Among the pathogenic genera identified, Pseudomonas and Arcobacter had the greatest percentage of the sequence reads. The abundances of antibiotic resistance genes were generally low (<0.5%), except for genes encoding ABC transporters, which accounted for approximately 3% of inferred genes. These findings provided a comprehensive profile of bacterial communities, including potential bacterial pathogens and antibiotic-resistant genes, in raw and secondary treated WW samples from four WWTPs across Australia and demonstrated that Illumina high-throughput sequencing can be an alternative approach for monitoring WW quality in order to protect environmental and human health.
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http://dx.doi.org/10.1007/s00253-016-7959-9DOI Listing
February 2017

Biofouling potential and material reactivity in a simulated water distribution network supplied with stormwater recycled via managed aquifer recharge.

Water Res 2016 Nov 31;105:110-118. Epub 2016 Aug 31.

CSIRO Land and Water, CSIRO, Private Bag 10, Clayton South, Vic, 3169, Australia.

The injection of stormwater into aquifers for storage and recovery during high water demand periods is a promising technology for augmenting conventional water reserves. Limited information exists regarding the potential impact of aquifer treated stormwater in distribution system infrastructure. This study describes a one year pilot distribution pipe network trial to determine the biofouling potential for cement, copper and polyvinyl chloride pipe materials exposed to stormwater stored in a limestone aquifer compared to an identical drinking water rig. Median alkalinity (123 mg/L) and colour (12 HU) in stormwater was significantly higher than in drinking water (82 mg/L and 1 HU) and pipe discolouration was more evident for stormwater samples. X-ray Diffraction and Fluorescence analyses confirmed this was driven by the presence of iron rich amorphous compounds in more thickly deposited sediments also consistent with significantly higher median levels of iron (∼0.56 mg/L) in stormwater compared to drinking water (∼0.17 mg/L). Water type did not influence biofilm development as determined by microbial density but faecal indicators were significantly higher for polyvinyl chloride and cement exposed to stormwater. Treatment to remove iron through aeration and filtration would reduce the potential for sediment accumulation. Operational and verification monitoring parameters to manage scaling, corrosion, colour, turbidity and microbial growth in recycled stormwater distribution networks are discussed.
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http://dx.doi.org/10.1016/j.watres.2016.08.066DOI Listing
November 2016

Attachment and Detachment Behavior of Human Adenovirus and Surrogates in Fine Granular Limestone Aquifer Material.

J Environ Qual 2015 Sep;44(5):1392-401

The transport of human adenovirus, nanoparticles, and PRD1 and MS2 bacteriophages was tested in fine granular limestone aquifer material taken from a borehole at a managed aquifer recharge site in Adelaide, South Australia. Comparison of transport and removal of virus surrogates with the pathogenic virus is necessary to understand the differences between the virus and surrogate. Because experiments using pathogenic viruses cannot be done in the field, laboratory tests using flow-through soil columns were used. Results show that PRD1 is the most appropriate surrogate for adenovirus in an aquifer dominated by calcite material but not under high ionic strength or high pH conditions. It was also found that straining due to size and the charge of the colloid were not dominant removal mechanisms in this system. Implications of this study indicate that a certain surrogate may not represent a specific pathogen solely based on similar size, morphology, and/or surface charge. Moreover, if a particular surrogate is representative of a pathogen in one aquifer system, it may not be the most appropriate surrogate in another porous media system. This was apparent in the inferior performance of MS2 as a surrogate, which is commonly used in virus transport studies.
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http://dx.doi.org/10.2134/jeq2015.01.0052DOI Listing
September 2015

Urban stormwater harvesting and reuse: a probe into the chemical, toxicology and microbiological contaminants in water quality.

Environ Monit Assess 2013 Aug 21;185(8):6645-52. Epub 2012 Dec 21.

CSIRO Land and Water, Ecosciences Precinct, Boggo Rd, Dutton Park, Queensland, 4102, Australia.

Stormwater is one of the last major untapped urban water resources that can be exploited as an alternative water source in Australia. The information in the current Australian Guidelines for Water Recycling relating to stormwater harvesting and reuse only emphasises on a limited number of stormwater quality parameters. In order to supply stormwater as a source for higher value end-uses, a more comprehensive assessment on the potential public health risks has to be undertaken. Owing to the stochastic variations in rainfall, catchment hydrology and also the types of non-point pollution sources that can provide contaminants relating to different anthropogenic activities and catchment land uses, the characterisation of public health risks in stormwater is complex, tedious and not always possible through the conventional detection and analytical methods. In this study, a holistic approach was undertaken to assess the potential public health risks in urban stormwater samples from a medium-density residential catchment. A combined chemical-toxicological assessment was used to characterise the potential health risks arising from chemical contaminants, while a combination of standard culture methods and quantitative polymerase chain reaction (qPCR) methods was used for detection and quantification of faecal indicator bacteria (FIB) and pathogens in urban stormwater. Results showed that the concentration of chemical contaminants and associated toxicity were relatively low when benchmarked against other alternative water sources such as recycled wastewater. However, the concentrations of heavy metals particularly cadmium and lead have exceeded the Australian guideline values, indicating potential public health risks. Also, high numbers of FIB were detected in urban stormwater samples obtained from wet weather events. In addition, qPCR detection of human-related pathogens suggested there are frequent sewage ingressions into the urban stormwater runoff during wet weather events. Further water quality monitoring study will be conducted at different contrasting urban catchments in order to undertake a more comprehensive public health risk assessment for urban stormwater.
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http://dx.doi.org/10.1007/s10661-012-3053-7DOI Listing
August 2013

Sensitive detection of human adenovirus from small volume of primary wastewater samples by quantitative PCR.

J Virol Methods 2013 Feb 23;187(2):395-400. Epub 2012 Nov 23.

CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld 4102, Australia.

An accurate quantitative detection of enteric viruses from the primary wastewater requires, sample concentration followed by extraction of nucleic acid with high purity. A highly efficient and sensitive method was developed for the concentration and quantitative detection of human adenovirus (HAdv) from wastewater samples. The two-step method which combines concentration of virus from 10 mL sample with centrifugal filters followed by extraction and purification of DNA with commercially available nucleic acid extraction kit resulted in high purity DNA for downstream quantitative PCR (qPCR). The results obtained on analytical sensitivities of five commercial nucleic acid extraction kits show that they differ in their ability for DNA yield and purity. Nevertheless, despite variable analytical sensitivities extracted nucleic acid was found to be relatively PCR inhibition free. The genomic copy numbers of HAdv detected from the same concentrated wastewater sample were significantly higher (P<0.01) when Qiagen Blood and Tissue kit (1.54×10(6) L(-1)) was used as compared to Mo-Bio PowerSoil kit (5.30×10(5) L(-1)) which suggests that the nucleic acid extraction kit can influence the sensitivity of qPCR assays. The method developed in this study is simple, rapid, sensitive, and can be applicable for the qPCR detection of adenovirus and other DNA virus in wastewater.
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http://dx.doi.org/10.1016/j.jviromet.2012.11.002DOI Listing
February 2013

Occurrence of virulence genes associated with Diarrheagenic pathotypes in Escherichia coli isolates from surface water.

Appl Environ Microbiol 2013 Jan 2;79(1):328-35. Epub 2012 Nov 2.

CSIRO Land and Water, Ecosciences Precinct, Queensland, Australia.

Escherichia coli isolates (n = 300) collected from six sites in subtropical Brisbane, Australia, prior to and after storm events were tested for the presence of 11 virulence genes (VGs) specific to diarrheagenic pathotypes. The presence of eaeA, stx(1), stx(2), and ehxA genes specific for the enterohemorrhagic E. coli (EHEC) pathotype was detected in 56%, 6%, 10%, and 13% of isolates, respectively. The VGs astA (69%) and aggR (29%), carried by enteroaggregative (EAEC) pathotypes, were frequently detected in E. coli isolates. The enteropathogenic E. coli (EPEC) gene bfp was detected in 24% of isolates. In addition, enteroinvasive E. coli (EIEC) VG ipaH was also detected in 14% of isolates. During dry periods, isolates belonging to the EAEC pathotype were most commonly detected (23%), followed by EHEC (11%) and EPEC (11%). Conversely, a more uniform prevalence of pathotypes, EPEC (14%), EAEC (12%), EIEC (10%), EHEC (7%), and ETEC (7%), was observed after the storm events. The results of this study highlight the widespread occurrence of potentially diarrheagenic pathotypes in the urban aquatic ecosystems. While the presence of VGs in E. coli isolates alone is insufficient to determine pathogenicity, the presence of diarrheagenic E. coli pathotypes in high frequency after the storm events could lead to increased health risks if untreated storm water were to be used for nonpotable purposes and recreational activities.
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http://dx.doi.org/10.1128/AEM.02888-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536071PMC
January 2013

Incorporating parameter uncertainty into Quantitative Microbial Risk Assessment (QMRA).

J Water Health 2011 Mar;9(1):10-26

Queensland University of Technology, George Street, Brisbane, QLD 4000, Australia.

Modern statistical models and computational methods can now incorporate uncertainty of the parameters used in Quantitative Microbial Risk Assessments (QMRA). Many QMRAs use Monte Carlo methods, but work from fixed estimates for means, variances and other parameters. We illustrate the ease of estimating all parameters contemporaneously with the risk assessment, incorporating all the parameter uncertainty arising from the experiments from which these parameters are estimated. A Bayesian approach is adopted, using Markov Chain Monte Carlo Gibbs sampling (MCMC) via the freely available software, WinBUGS. The method and its ease of implementation are illustrated by a case study that involves incorporating three disparate datasets into an MCMC framework. The probabilities of infection when the uncertainty associated with parameter estimation is incorporated into a QMRA are shown to be considerably more variable over various dose ranges than the analogous probabilities obtained when constants from the literature are simply 'plugged' in as is done in most QMRAs. Neglecting these sources of uncertainty may lead to erroneous decisions for public health and risk management.
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http://dx.doi.org/10.2166/wh.2010.073DOI Listing
March 2011

Risk assessment of aquifer storage transfer and recovery with urban stormwater for producing water of a potable quality.

J Environ Qual 2010 Nov-Dec;39(6):2029-39

CSIRO Land and Water, Private Bag No 2, Glen Osmond, SA 5064, Australia.

The objective of the Parafield Aquifer Storage Transfer and Recovery research project in South Australia is to determine whether stormwater from an urban catchment that is treated in a constructed wetland and stored in an initially brackish aquifer before recovery can meet potable water standards. The water produced by the stormwater harvesting system, which included a constructed wetland, was found to be near potable quality. Parameters exceeding the drinking water guidelines before recharge included small numbers of fecal indicator bacteria and elevated iron concentrations and associated color. This is the first reported study of a managed aquifer recharge (MAR) scheme to be assessed following the Australian guidelines for MAR. A comprehensive staged approach to assess the risks to human health and the environment of this project has been undertaken, with 12 hazards being assessed. A quantitative microbial risk assessment undertaken on the water recovered from the aquifer indicated that the residual risks posed by the pathogenic hazards were acceptable if further supplementary treatment was included. Residual risks from organic chemicals were also assessed to be low based on an intensive monitoring program. Elevated iron concentrations in the recovered water exceeded the potable water guidelines. Iron concentrations increased after underground storage but would be acceptable after postrecovery aeration treatment. Arsenic concentrations in the recovered water continuously met the guideline concentrations acceptable for potable water supplies. However, the elevated concentration of arsenic in native groundwater and its presence in aquifer minerals suggest that the continuing acceptable residual risk from arsenic requires further evaluation.
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http://dx.doi.org/10.2134/jeq2010.0078DOI Listing
February 2011

Detection of antibiotic resistance and tetracycline resistance genes in Enterobacteriaceae isolated from the Pearl rivers in South China.

Environ Pollut 2010 Jun 30;158(6):2101-9. Epub 2010 Mar 30.

State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 511 Kehua Street, Tianhe District, Guangzhou 510640, China.

This study investigated antibiotic resistance profiles and tetracycline resistance genes in Enterobacteriaceae family isolates from the Pearl rivers. The Enterobacteriaceae isolates were tested for susceptibility to seven antibiotics ampicillin, chloramphenicol, ciprofloxacin, levofloxacin, sulphamethoxazole/trimethoprim, tetracycline and trimethoprim. In Liuxi reservoir, with an exception to ampicillin resistant strains (11%) no other antibiotic resistance bacterial strains were detected. However, multiple drug resistance in bacterial isolates from the other sites of Pearl rivers was observed which is possibly due to sewage discharge and input from other anthropogenic sources along the rivers. Four tetracycline resistance genes tet A, tet B, tet C and tet D were detected in the isolates from the rivers. The genes tet A and tet B were widely detected with the detection frequencies of 43% and 40% respectively. Ciprofloxacin and levofloxacin resistant enteric bacteria were also isolated from the pig and duck manures which suggest a wider distribution of human specific drugs in the environment. This investigation provided a baseline data on antibiotic resistance profiles and tetracycline resistance genes in the Pearl rivers delta.
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http://dx.doi.org/10.1016/j.envpol.2010.03.004DOI Listing
June 2010

Use of static Quantitative Microbial Risk Assessment to determine pathogen risks in an unconfined carbonate aquifer used for Managed Aquifer Recharge.

Water Res 2010 Feb 27;44(4):1038-49. Epub 2009 Aug 27.

CSIRO Water for a Healthy Country, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Brisbane, QLD 4067, Australia.

Managed Aquifer Recharge (MAR) is becoming a mechanism used for recycling treated wastewater and captured urban stormwater and is being used as a treatment barrier to remove contaminants such as pathogens from the recharged water. There is still a need, however, to demonstrate the effectiveness of MAR to reduce any residual risk of pathogens in the recovered water. A MAR research site recharging secondary treated wastewater in an unconfined carbonate aquifer was used in conjunction with a static Quantitative Microbial Risk Assessment (QMRA) to assess the microbial pathogen risk in the recovered water following infiltration and aquifer passage. The research involved undertaking a detailed hydrogeological assessment of the aquifer at the MAR site and determining the decay rates of reference pathogens from an in-situ decay study. These variables along with literature data were then used in the static QMRA which demonstrated that the recovered water at this site did not meet the Australian Guidelines for recycled water when used for differing private green space irrigation scenarios. The results also confirmed the importance of obtaining local hydrogeological data as local heterogeneity can influence of residence time in the aquifer which, in turn, influences the outcomes. The research demonstrated that a static QMRA can be used to determine the residual risk from pathogens in recovered water and showed that it can be a valuable tool in the preliminary design and operation of MAR systems and the incorporation of complementary engineered treatment processes to ensure that there is acceptable health risk from the recovered water.
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http://dx.doi.org/10.1016/j.watres.2009.08.028DOI Listing
February 2010

Human pathogens and their indicators in biosolids: a literature review.

Environ Int 2009 Jan 13;35(1):187-201. Epub 2008 Sep 13.

CSIRO Land and Water, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia.

A growing beneficial reuse of biosolids in agriculture has led to concerns about potential contamination of water resources and the food chain. In order to comprehend the potential risks of transmission of diseases to the human population, an advanced quantitative risk assessment is essential. This requires good quantitative data which is currently limited due to the methodological limitations. Consequently, further development and standardization of methodologies for the detection, enumeration and viability assessment of pathogens in biosolids is required. There is a paucity of information on the numbers and survival of enteric virus and protozoan pathogens of concern in biosolids. There is a growing urgency for the identification of more reliable alternative indicators, both index and model microorganisms, which could be used for potential public health risk assessment. In this review, we have summarized reported literature on the numbers and fate of enteric pathogens and indicators in biosolids. The advantages and limitations of the use of conventional and alternative index and model microorganisms for the prediction of pathogen presence in biosolids are also discussed.
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http://dx.doi.org/10.1016/j.envint.2008.07.006DOI Listing
January 2009
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