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Warish Ahmed, PhD

Warish Ahmed, PhD
Research Scientist
CSIRO Land and Water
Water for a Healthy Country Flagship
Queensland Biosciences Precinct
306 Carmody Rd. St. Lucia Qld 4067
E. mail:shuhat@yahoo.com
Warish.Ahmed@csiro.au
Ph: (+ 617) 3214 2238
Fax: (+617) 3214 2308


Warish.Ahmed@csiro.au
Research interests:

[1] Microbial Source Tracking
[2] Quantitative Microbial Risk Assessment (QMRA)
[3] Direct Monitoring of Pathogens in Environmental Waters
[4] Microbiological Quality of Roof-Harvested Rainwater and stormwater
[5] Detection and Quantification of Enteric Viruses in Food and Environmental Waters Using Molecular Based Methods

Journal articles

2014
2013
2012
2011
2010
D SULLIVAN, P BROOKS, N TINDALE, S CHAPMAN, W AHMED (2010)  Faecal Sterols Analysis for the Identification of Human Faecal Pollution in a Non-Sewered Catchment   Water Science and Technology 61: 1355-1361 (ISI Impact Factor 1.122)  
Abstract: In this study, faecal sterols were used to identify human faecal pollution in a non-sewered catchment in Southeast Queensland, Australia. In all, 36 water samples were collected from six sites on six occasions and the concentration of sterols were determined using gas chromatography and mass spectrometry. The stanols concentration in water samples generally increased with increased catchment runoff. After moderate rainfall, high coprostanols levels found in water samples indicated human faecal pollution via defective septic systems. In contrast, it appears that during dry weather human faecal pollution is not occurring in the study catchment. Sterol profiles also pointed to a cattle farm polluting during modest catchment runoff. The method used in this study was able to identify the sources of faecal pollution to the catchment due to rainfall.
Notes:
2009
2008
W AHMED, J STEWART, D POWELL, T GARDNER (2008)  Evaluation of Bacteroides Markers for the Detection of Human Faecal Pollution   Letters in Applied Microbiology 46: 237-242 (ISI Impact Factor 1.622)  
Abstract: AIMS: This paper reports on the results of a study aimed at evaluating the specificity and sensitivity of human-specific HF183 and HF134 Bacteroides markers in various host groups and their utility to detect human faecal pollution in storm water samples collected from nonsewered catchments in Southeast Queensland, Australia. METHODS AND RESULTS: The specificity and sensitivity of the HF183 and HF134 Bacteroides markers was evaluated by testing 207 faecal samples from 13 host groups, including 52 samples from human sources (via sewage and septic tanks). Polymerase chain reaction analysis of these samples revealed the presence/absence of HF183 and HF134 across these host groups, demonstrating their suitability for distinguishing between human and animal faecal pollution. The HF183 marker was found to be more reliable than that of HF134, which was also found in dogs. CONCLUSIONS: Based on our data, it appears that the HF183 marker is specific to sewage and is a reliable marker for detecting human faecal pollution, while the use of HF134 marker alone may not be sufficient enough to provide the evidence of human faecal pollution. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study in Australia that rigorously evaluated the specificity and sensitivity of Bacteroides markers. Based on our findings, we suggest that the HF183 marker could reliably be used to detect the sources of human faecal pollution in Southeast Queensland region.
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W AHMED, J STEWART, D POWELL, T GARDNER (2008)  Evaluation of the Host-specificity and Prevalence of Enterococci Surface Protein (esp) Marker in Sewage and its Application for Sourcing Human Fecal Pollution   Journal of Environmental Quality 37: 1583-1588 (ISI Impact Factor 2.324)  
Abstract: The suitability of the enterococci surface protein (esp) marker to detect human fecal pollution was evaluated by testing 197 fecal samples from 13 host groups in Southeast Queensland, Australia. Overall, this marker was detected in 90.5% of sewage and septic system samples and could not be detected in any fecal samples from 12 animal host groups. The sensitivity of the esp primer to detect the human-specific esp marker in sewage and septic samples was 100% and 67%, respectively. The overall specificity of this marker to distinguish between human and animal faecal pollution was 100%. Its prevalence in sewage was also determined by testing samples from the raw sewage, secondary effluent, and treated effluent of a sewage treatment plant (STP) over five consecutive days. Of the 15 samples tested, 12 (80%) were found to be positive for this marker. In contrast, it was not found in three samples from the treated effluent and these samples did not contain any culturable enterococci. The PCR limit of detection of this marker in freshwater samples was up to dilution 1 X 10-4 and the number of culturable enterococci at this dilution was 4.8 X 101 ± 7.0 X 100 colony forming unit (CFU). The utility of this marker was evaluated by testing water samples from three non-sewered catchments in Pine Rivers in Southeast Queensland. Of the thirteen samples tested, eight were positive for this marker with the number of enterococci ranging between 1.8 X 103 to 8.5 X 103 CFU per 100 mL of water. Based on the results, it can be concluded that the esp marker appears to be sewage specific and could be used as a reliable marker to detect human fecal pollution in surface waters in Southeast Queensland, Australia.
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W AHMED, M KATOULI (2008)  Phenotypic Variations of Enterococci in Surface Waters: Analysis of Biochemical Fingerprinting Data from Multi-Catchments   Journal of Applied Microbiology 105: 452-458 (ISI Impact Factor 2.337)  
Abstract: We analysed biochemical fingerprinting data, collected over five years from the six catchments to identify the prevalence of environmentally adopted enterococci strains and their impacts on the performance of an existing metabolic fingerprinting library comprised of 5,803 isolates from 10 host groups. Comparison of enterococci isolates from the six catchments (i.e. 3952 isolates) showed that they belonged to 801 biochemical phenotypes (BPTs) and 29.2% of these BPTs were specific to each catchment. When compared with the existing library, on average 79.5% BPTs from each catchment were found to be host-origin. The remaining 20.5% were regarded as non-host origin BPTs and constituted only 5.3% (ranging between 2.4% to 7.3% in different catchments) of the total isolates tested for each catchment. To identify the occurrence and prevalence of these non-host origin-BPTs, they were compared with each other. On average, 18% (ranging between 14.4% and 23%) of these were unique BPTs and constituted only 3.7% (ranging between 2.3% to 5%) of the total isolates tested for each catchment. The remaining non-host origin BPTs were shared between two or more catchments and constituted 1.6% of the total isolates tested. These data suggests that environmentally adopted strains of enterococci constitute a small portion of enterococci isolates in each watershed and could have a minimal impact on the validity of the results obtained by library-based methods if the numbers of isolates tested from both the host groups and the environment are high. We also conclude that our existing metabolic fingerprinting library can be used to trace the sources of faecal pollution beyond local catchments with minimal impact from catchments specific BPTs of enterococci.
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J HARPER, W AHMED, A NELLER, N TINDALE, R NELLER, I KURTBOKE (2008)  The Efficacy of Vermicomposting on the Population Structure of Enterococci in Domestic Biosolids in a Residential Resort Community   The Journal of Environmental Health Australia 8: 11-21  
Abstract: The effects that vermiculture (VC) treatment had on population and community structure of enterococci in domestic biosolids in a residential resort in southeast Queensland were investigated by enumerating and typing enterococci with a biochemical fingerprinting method. Vermiculture beds with a substrate consisting of non-amended biosolids from an activated sludge sewage treatment plant were established. Various treatments (earthworms added and earthworms excluded) beds were sampled on 3 occasions. Enterococci numbers were significantly lower in the earthworm treatments than those without. Of the 300 isolates biochemically fingerprinted, 106 different biochemical phenotypes (BPTs) were identified. The overall mean diversity of enterococci in all beds was high (0.87 ± 0.13; maximum is 1), indicating a diverse enterococci population. The overall mean population similarity (Sp) value amongst beds was quite low (0.16 ± 0.10) also indicating a diverse population. Antibiotic resistance patterns (ARPs) of the 106 BPTs revealed that 83.6% were resistant to rifampicin, 59.6% were resistant to erythromycin, 21.9% were resistant to tetracycline, 7.7% were resistant to ampicillin and 2.9% were resistant to gentamicin and vancomycin. The results indicate that the current VC methods used in the residential resort to create worm castings for potting mixture may not satisfactorily pasteurize the biosolids and significant number of pathogenic microorganisms could be present. There remains a potential health risk to workers and guests and routine monitoring of pathogens is recommended for improved management of stockpiled biosolids.
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W AHMED, M HARGREAVES, A GOONETILLEKE, M KATOULI (2008)  Population Similarity Analysis of Indicator Bacteria for Source Prediction of Fecal Pollution in a Coastal Lake   Marine Pollution Bulletin 56: 1469-1475 (ISI Impact Factor 2.503)  
Abstract: Biochemical fingerprinting (BF) databases comprising of 524 enterococci and 571 Escherichia coli isolates and an antibiotic resistance analysis (ARA) database comprising of 380 E. coli isolates from four suspected sources (i.e. dogs, chickens, waterfowls and a sewage treatment plant [STP]) were developed to predict the sources of faecal pollution in a recreational coastal lake. Twenty water samples representing four sampling episodes were collected from five sites in the lake and the enterococci and E. coli populations from each site were compared with those of the databases. The degree of similarity between bacterial populations was measured as population similarity (Sp) coefficient. Using the BF-databases, bacterial populations of waterfowl showed the highest similarity (mean Sp coefficient ± SD; 0.46 ± 0.09 for enterococci, and 0.32 ± 0.03 for E. coli) with the water samples followed by STP (0.31 ± 0.06 for enterococci and 0.27 ± 0.09 for E. coli). Higher population similarities were found between samples from STP and water samples especially at sites T2 and T3 which were located near the sewerage pipes collecting wastewater from the study area. When using the ARA database, the highest similarity was found between E. coli populations of STP and water samples at sites T2 and T4. When datasets from two databases (i.e. BF and ARA) were combined together, E. coli populations from STP (0.14 ± 0.09) and waterfowl (0.09 ± 0.02) showed higher similarities with water samples. Both faecal indicators as well as methods predicted human faecal pollution possibly through leakage from submerged sewerage pipes. The results indicated that the Sp-analysis of faecal indicator bacterial populations from suspected sources and water samples can be used as simple tool to predict the source(s) of faecal pollution in surface waters.
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W AHMED, J STEWART, T GARDNER, D POWELL (2008)  A Real-time Polymerase Chain Reaction Assay for Quantitative Detection of the Human-specific Enterococci Surface Protein Marker in Sewage and Environmental Waters   Environmental Microbiology 10: 3255-3264 (ISI Impact Factor 5.843)  
Abstract: A real-time PCR assay using SYBR Green I dye was developed to quantify the E. faecium esp marker in sewage (n=16) and environmental waters (n=16). The concentration of culturable enterococci in raw sewage samples ranged between 1.3 X 105 and 5.6 X 105 cfu/100 ml. The real-time PCR detected 9.8 X 103 to 3.8 X 104 gene copies of the esp marker /100 ml of sewage. However, the concentration of culturable enterococci and the esp marker in secondary effluent was two orders of magnitude lower than raw sewage. Surface water samples were collected from a non-sewered catchment after storm events and the real-time PCR was applied to quantify the esp marker. Of the 16 samples tested 6 (38%) were PCR positive and the concentration of the esp marker ranged between 1.1 X 102 and 5.3 X 102 gene copies/100 ml of water samples. The newly developed real-time PCR method was successfully used to quantify the esp marker in samples collected from sewage and environmental waters. The presence of the esp marker in water samples immediate after storm events not only indicated human faecal pollution but also provided evidence of the degree of human faecal pollution. To our knowledge, this is the first study that reports the use of a real-time PCR assay to quantify the esp marker in sewage and surface waters. Such study would provide valuable information for managers for the improved management of water quality.
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W AHMED, D POWELL, A GOONETILLEKE, T GARDNER (2008)  Detection and Source Identification of Fecal Pollution in Non-sewered Catchment by Means of Host-Specific Molecular Markers   Water Science and Technology 58: 579-586 (ISI Impact Factor 1.122)  
Abstract: Multiple host-specific molecular markers were used to detect the sources of faecal pollution in a mixed land use non-sewered catchment in Southeast Queensland, Australia. These markers included human-specific Bacteroides (HF183 and HF134), cattle-specific Bacteroides (CF128), dog-specific Bacteroides (BacCan) and human-specific enterococci surface protein (esp) markers. The sensitivity and specificity of these markers were determined by testing 197 faecal samples from 13 host groups. The overall sensitivity and specificity of these markers was high (sensitivity ≥ 85% and specificity ≥ 93%) indicating their suitability for detecting the sources of faecal pollution. Of the 16 samples collected from the study area, 14 (87%) were positive for at least one of the molecular marker tested. Amongst all the markers, cattle-specific CF128 was more prevalent than others, followed by human-specific HF183 which was consistently detected in samples collected from sites within close proximity to urban development. Significant correlations were found between E. coli and enterococci concentrations with the positive/negative results of human-specific Bacteroides HF183 (p < 0.001, p < 0.0001) and HF134 (p < 0.001, p < 0.004) markers. No correlations were found between faecal indicators (E. coli or enterococci) with the CF128 or BacCan markers. A significant correlation was also found between enterococci concentrations and the presence/absence of the esp marker (p < 0.02). Based on the results, it appears that the host-specific markers are a sensitive measure of sources of faecal pollution in surface waters in Southeast Queensland, Australia
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2007
W AHMED (2007)  Limitations of Library-dependent Microbial Source Tracking Methods   AWA Water 34: 96-101  
Abstract: Over the past 15 years, microbial source tracking (MST) methods have emerged as a management tool for water quality authorities to identify the sources of faecal contamination in receiving waters. The majority of the MST methods require the development of a library of target strains or faecal indicator bacteria from suspected sources by using various genotypic or phenotypic methods. Phenotypic or genotypic patterns of target strains are then compared to the library to identify their likely sources. None of these library-dependent methods are regarded as a 'gold standard'. Significant limitations include the size and representativeness of the developed library, temporal and geographical stability of target strains, host specificity of target strains, relative persistence of target strains in receiving waters and differences in statistical methods used. This paper reviews the various assumptions and limitation of library dependent methods currently used for source tracking.
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W AHMED, J TUCKER, K BETTELHEIM, R NELLER, M KATOULI (2007)  Detection of Virulence Genes in Escherichia coli of an Existing Metabolic Fingerprint Database to Predict the Sources of pathogenic E. coli in Surface Waters   Water Research 41: 3785-3791 (ISI Impact Factor 4.865)  
Abstract: A collection of 366 Escherichia coli strains from 10 host groups and surface waters were tested for the presence of 15 virulence genes associated with strains causing intestinal and extra-intestinal infections. The virulence genes included eaeA, VT1, 2 and 2e, LT1, ST1 and 2, Einv gene, EAgg gene, CNF1 and 2, papC, O111 and O157 side chain LPS. Of the 262 strains obtained from nine different hosts, 39 (15%) carried one or more of these virulence genes. These included six strains from humans, two from horses, eight from dogs, two from ducks, five from cattle, seven from chickens, four from pigs, two from sheep and three from deer. Of the remaining 104 strains obtained from water samples, 10 (10%) also carried one or more of the tested virulence genes. Of these, six had identical biochemical phenotypes (BPTs) to strains isolated from humans (two strains), dogs (two strains), chickens (one strain) and sheep (one strain) with 4 BPTs also carrying same virulence genes. Our results indicate that the sources of clinically important E. coli strains found in surface waters due to faecal contamination can be predicted by using a combination of biochemical fingerprinting method and the detection of virulence genes. From the public health point of view this information will be of great importance for evaluating the risk associated with public use of the catchment.
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W AHMED, J STEWART, T GARDNER, D POWELL, P BROOKS, D SULLIVAN, N TINDALE (2007)  Sourcing Faecal Pollution: A Combination of Library-dependent and Library-independent Methods to Identify Human Faecal Pollution in Non-sewered Catchments   Water Research 41: 3771-3779 (ISI Impact Factor 4.865)  
Abstract: Library-dependent (LD) (biochemical fingerprinting of Escherichia coli and enterococci) and library-independent (LI) (PCR detection of human-specific biomarkers) methods were used to detect human faecal pollution in three non-sewered catchments. In all, 550 E. coli isolates and 700 enterococci isolates were biochemically fingerprinted from 18 water samples and compared with metabolic fingerprint libraries of 4508 E. coli and 4833 enterococci isolates. E. coli fingerprints identified human unique biochemical phenotypes (BPTs) in nine out of 18 water samples; similarly, enterococci fingerprints identified human faecal pollution in 10 water samples. Seven samples were tested by PCR for the detection of biomarkers. Human-specific HF134 Bacteroides and enterococci surface protein (esp) biomarkers were detected in five samples. Four samples were also positive for HF183 Bacteroides biomarker. The combination of biomarkers detected human faecal pollution in six out of seven water samples. Of the seven samples analysed for both the indicators/markers, at least one indicator/marker was detected in every sample. Four of the seven PCR-positive samples were also positive for one of the human-specific E. coli or enterococci BPTs. The results indicated human faecal pollution in the studied sub-catchments after storm events. LD and LI methods used in this study complimented each other and provided additional information regarding the polluting sources when one method failed to detect human faecal pollution. Therefore, it is recommended that a combination of methods should be used to identify the source(s) of faecal pollution where possible.
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2006
W AHMED, R NELLER, M KATOULI (2006)  Population Similarity of Enterococci and Escherichia coli in Surface Waters: A Predictive Tool to Trace the Sources of Fecal Contamination   Journal of Water and Health 4: 347-356 (ISI Impact Factor 1.367)  
Abstract: A biochemical fingerprinting method (the PhPlate system) was used to compare similarities between Escherichia coli and enterococci populations from surface water samples with those found in different animal species during the wet and the dry seasons in order to predict the dominant source(s) of fecal contamination in a local creek. A significant increase in the number and diversity of enterococci was observed in the creek during the wet season. Enterococci population from water samples also showed a higher population similarity with animal species than did E. coli. A higher population similarity was found between both indicator bacteria and animal species during the wet season with highest population similarities found in dogs, horses, cows and kangaroos. In contrast, a low population similarity was found for both fecal indicator bacteria from humans with water samples during the wet and the dry seasons, indicating that humans are not a major source of contamination in the studied creek. The results also indicate that the population similarity analysis of enterococci population has an advantage over E. coli in tracing the possible source(s) of contamination in the studied creek and that population similarity analysis as used in this study can be used to predict the source(s) of fecal contamination in surface waters.
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W AHMED, J TUCKER, J HARPER, R NELLER, M KATOULI (2006)  Comparison of the Efficacy of an Existing Versus a Locally Developed Metabolic Fingerprint Database to Identify Non-point Sources of Faecal Contamination in a Coastal Lake   Water Research 40: 2339-2348 (ISI Impact Factor 4.865)  
Abstract: A comparison of the efficacy of an existing large metabolic fingerprint database of enterococci and Escherichia coli with a locally developed database was undertaken to identify the sources of faecal contamination in a coastal lake, in southeast Qld., Australia. The local database comprised of 776 enterococci and 780 E. coli isolates from six host groups. In all, 189 enterococci and 245 E. coli biochemical phenotypes (BPTs) were found, of which 118 and 137 BPTs were unique (UQ) to host groups. The existing database comprised of 295 enterococci UQ-BPTs and 273 E. coli UQ-BPTs from 10 host groups. The representativeness and the stability of the existing database were assessed by comparing with isolates that were external to the database. In all, 197 enterococci BPTs and 179 E. coli BPTs were found in water samples. The existing database was able to identify 62.4% of enterococci BPTs and 64.8% of E. coli BPTs as human and animal sources. The results indicated that a representative database developed from a catchment can be used to predict the sources of faecal contamination in another catchment with similar landuse features within the same geographical area. However, the representativeness and the stability of the database should be evaluated prior to its application in such investigation
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2005
W AHMED, R NELLER, M KATOULI (2005)  Host Species Specific Metabolic Fingerprint Database for Enterococci and Escherichia coli and its Application to Identify sources of Fecal Contamination in Surface Waters   Applied and Environmental Microbiology 71: 4461-4468 (ISI Impact Factor 3.829)  
Abstract: A metabolic fingerprint database of enterococci and Escherichia coli from 10 host groups of animals was developed to trace the sources of fecal contamination in surface waters. In all, 526 biochemical phenotypes (BPTs) of enterococci and 530 E. coli BPTs were obtained from 4,057 enterococci and 3,728 E. coli isolates tested. Of these, 231 Enterococcus BPTs and 257 E. coli BPTs were found in multiple host groups. The remaining 295 Enterococcus BPTs and 273 E. coli BPTs were unique to individual host groups. The database was used to trace the sources of fecal contamination in a local creek. The mean diversities (Di) of enterococci (Di = 0.76 +/- 0.05) and E. coli (Di = 0.88 +/- 0.04) were high (maximum 1) in water samples, indicating diverse sources of fecal contamination. Overall, 71% of BPTs of enterococci and 67% of E. coli BPTs from water samples were identified as human and animal sources. Altogether, 248 Enterococcus BPTs and 282 E. coli BPTs were found in water samples. Among enterococci, 26 (10%) BPTs were identical to those of humans and 152 BPTs (61%) were identical to those of animals (animal BPTs). Among E. coli isolates, 36 (13%) BPTs were identical to those of humans and 151 (54%) BPTs were identical to those of animals. Of the animal BPTs, 101 (66%) Enterococcus BPTs and 93 (62%) E. coli BPTs were also unique to individual animal groups. On the basis of these unique Enterococcus BPTs, chickens contributed 14% of contamination, followed by humans (10%), dogs (7%), and horses (6%). For E. coli, humans contributed 13% of contamination, followed by ducks (9%), cattle (7%), and chickens (6%). The developed metabolic fingerprint database was able to distinguish between human and animal sources as well as among animal species in the studied catchment.
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W AHMED, R NELLER, M KATOULI (2005)  Evidence of Septic System Failure Determined by a Biochemical Fingerprinting Method   Journal of Applied Microbiology 98: 910-920 (ISI Impact Factor 2.337)  
Abstract: AIMS: To provide evidence of septic system failure by comparing two faecal indicator bacteria, enterococci and Escherichia coli, from defective septic tanks and adjacent creeks. METHODS AND RESULTS: A biochemical fingerprinting method was used to type and compare enterococci and E. coli strains from 39 septic tanks with creek water samples. Phenotypic diversity of enterococci (0.5 +/- 0.3) and E. coli (0.5 +/- 0.3) in septic tanks were significantly lower than those found in water samples (0.8 +/- 0.1, P < 0.0001 for enterococci and 0.9 +/- 0.1, P < 0.0001 for E. coli). Among 1072 enterococci isolates tested from septic tanks, 203 biochemical phenotypes (BPTs) were found of which 98 BPTs from 33 septic tanks were identical to several water samples. Similarly, among 621 E. coli isolates tested from septic tanks, 159 BPTs were found of which 53 BPTs from 26 septic tanks were also identical to water samples. The number of the latter bacteria was significantly (P = 0.01) higher in water samples collected from downstream compared with that of upstream in the study area. A high similarity between the populations of both indicator bacteria was also found between defective septic tanks and downstream water samples further indicating the contamination of both creeks by defective septic systems. CONCLUSIONS: Biochemical fingerprinting of faecal indicator bacteria is a useful and rapid method to provide direct evidence for septic system failure. Combination of both faecal indicator bacteria (enterococci and E. coli) provides a better judgement of the performance of a septic system. SIGNIFICANCE AND IMPACT OF THE STUDY: This study is the first to provide direct evidence of septic system failure by identifying the presence of specific bacterial types in septic tanks and surface waters. Based on our findings, we suggest that the performance evaluation of a septic system should be accompanied by direct analysis of faecal indicator bacteria.
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Book chapters

2011

Other

2012
2011
2010
2009
2008
2007
2006
2005
2004

PhD theses

2005

Technical reports

2012
2007
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