Detection of naturally occurring enteroviruses and hepatitis A virus in undigested and anaerobically digested sludge using the polymerase chain reaction

Comparing extraction buffers to identify optimal method to extract somatic coliphages from sewage sludges

Somatic coliphages are present in high numbers in sewage sludge. Since they are conservative indicators of viruses during wastewater treatment processes, they are being used to evaluate the effectiveness of sludge treatment processes. However, efficient methods to extract them from sludge are lacking. The objective was to compare different virus extraction procedures and develop a method to extract coliphages from sewage sludge. Twelve different extraction buffers and procedures varying in composition, pH, and sonication were compared in their ability to recover indigenous phages from sludges. The 3% buffered beef extract (BBE) (pH 9.0), the 10% BBE (pH 9.0), and the 10% BBE (pH 7.0) with sonication were short-listed and their recovery efficiency was determined using coliphage-spiked samples. The highest recovery was 16% for the extraction that involved 10% BBE at pH 9.0. There is a need to develop methods to extract somatic phages from sludges for monitoring sludge treatment processes.

Toward a consensus view on the infectious risks associated with land application of sewage sludge

The science linking processed sewage sludge (biosolids) land application with human health has improved in the last ten years. The goal of this review is to develop a consensus view on the human health impacts associated with land-applying biosolids. Pre-existing risk studies are integrated with recent advances in biosolids pathogen exposure science and risk analysis. Other than accidental direct ingestion, the highest public risks of infection from land application are associated with airborne exposure. Multiple, independent risk assessments for enteroviruses similarly estimate the yearly probabilities of infection near 10(-4). However, the inclusion of other emerging pathogens, specifically norovirus, increases this yearly infectious risk by over 2 orders of magnitude. Quantitative microbial risk assessment for biosolids exposure more effectively operates as a tool for analyzing how exposure can be reduced rather than being used to assess "safety". Such analysis demonstrates that the tradition of monitoring pathogen quality by Salmonella spp. and enterovirus content underestimates the infectious risk to the public, and that a rigorous biosolids pathogen treatment process, rather than extending community separation distances, is the most efficient method for reducing pathogen exposure and infectious risk.

Viral metagenome analysis to guide human pathogen monitoring in environmental samples

Aims:  The aim of this study was to develop and demonstrate an approach for describing the diversity of human pathogenic viruses in an environmentally isolated viral metagenome.

Methods and Results: In silico bioinformatic experiments were used to select an optimum annotation strategy for discovering human viruses in virome data sets and applied to annotate a class B biosolid virome. Results from the in silico study indicated that <1% errors in virus identification could be achieved when nucleotide‐based search programs (BLASTn or tBLASTx), viral genome only databases and sequence reads >200 nt were considered. Within the 51 925 annotated sequences, 94 DNA and 19 RNA sequences were identified as human viruses. Virus diversity included environmentally transmitted agents such as parechovirus, coronavirus, adenovirus and aichi virus, as well as viruses associated with chronic human infections such as human herpes and hepatitis C viruses.

Conclusions:  This study provided a bioinformatic approach for identifying pathogens in a virome data set and demonstrated the human virus diversity in a relevant environmental sample.

Significance and Impact of the Study:  As the costs of next‐generation sequencing decrease, the pathogen diversity described by virus metagenomes will provide an unbiased guide for subsequent cell culture and quantitative pathogen analyses and ensures that highly enriched and relevant pathogens are not neglected in exposure and risk assessments.

Sanitation composting process in different seasons. Ascaris suum as model

The influence of aerobic composting of organic wastes (straw, sawdust, wood brash and sludge from WWTP) on the viability of the model parasite eggs were studied in production conditions of the Industrial Composting Plant TOPVAR, Inc. in Topolcany, Slovak Republic. During summer and winter seasons (2005-2006), the survival of non-embryonated Ascaris suum eggs was evaluated with respect to aerobic composting processes and air temperature, which varied from -6 degrees C to +12 degrees C in winter and from 11 degrees C to 32 degrees C in summer. Our results revealed the induction of maximum temperature of the substrate (+65 degrees C) on day 6 of the composting irrespective of the low air temperature in winter. During the summer season, higher substrate temperature was observed (+71 degrees C). Due to a high temperature and chemical changes (pH, dry matter, inorganic and organic matter, NH(4)(+), total phosphorus, total nitrogen and the C:N ratio), which occur in substrate during composting process, the total devitalization of the A. suum eggs was observed between day 4-5 of the experiment in the winter season and on day 6 in the summer season. Thus we may conclude that the final product is suitable for agricultural purposes without a risk of transmitting the pathogenic germs into the environment.

Hepatitis A virus detection in oysters (Crassostrea gigas) in Santa Catarina State, Brazil, by reverse transcription-polymerase chain reaction

Shellfish are readily contaminated with viruses present in water containing sewage because of the concentration effect of filter feeding. Hepatitis A virus (HAV) is the main cause of acute hepatitis worldwide and may lead to severe illness or even death. It is transmitted through fecal and oral routes and causes widespread endemic and asymptomatic infections in young children. Here we describe a method for the detection of HAV RNA in shellfish involving the extraction of total RNA from oyster meat followed by reverse transcription-polymerase chain reaction (RT-PCR). Virus recovery from oyster extracts artificially seeded with HAV strain HM 175 was examined by RT-PCR. The minimum detection limit was 3.3 focus-forming units of HAV, and the recovery rate was 75.7%. This method was used to assess the viral contamination of four shellfish beds in Santa Catarina State, Brazil, over a 1-year period. Six (22%) of 27 samples collected in autumn and winter from one shellfish bed tested positive for HAV.

Evaluation of integrated cell culture-PCR (C-PCR) for virological analysis of environmental samples

AIMS

The aims of this study were to establish an integrated culture-polymerase chain reaction (C-PCR) method for detection of enteric viruses in environmental samples, and to evaluate it for sensitivity, speed and provision of virus infectivity data.

METHODS AND RESULTS

C-PCR, direct reverse transcription (RT)-PCR, PCR and plaque assay methods were used to detect enteroviruses and adenoviruses in seeded and naturally contaminated environmental samples. Using C-PCR, infectious enterovirus presence was confirmed in 3 d and adenovirus presence in 5 d, compared with up to 10 d required by conventional cell culture methods.

CONCLUSIONS

C-PCR was the preferred method for detection of enteric viruses in environmental samples containing high viral concentrations. It was less successful for samples with low viral concentrations or containing toxic materials or inhibitors.

SIGNIFICANCE AND IMPACT OF THE STUDY

C-PCR provides sensitive, specific results within 2-5 d and is useful as a rapid screen for environmental samples of low toxicity.

Microbial quality of wastewater: detection of hepatitis A virus by reverse transcriptase-polymerase chain reaction

AIMS

The persistent circulation of hepatitis A virus (HAV) in the Mediterranean area suggests the need for monitoring its presence in the environment. A reverse transcriptase-polymerase chain reaction (RT-PCR) was used to detect the presence of HAV in several consecutive raw sewage and final effluent samples, collected over an 8-month period from an activated sludge treatment plant in southern Italy.

METHODS AND RESULTS

Two distinct purification protocols, either based on antigen-capture with monoclonal antibody (AC) or RNA extraction, were compared. The possible influence of the antibody used in the AC phase was evaluated in preliminary experiments on HAV-spiked samples, using two different monoclonal antibodies. Hepatitis A virus RNA was detected in all but one sewage environmental sample examined. The contemporary presence of enteroviruses, reoviruses and phages was observed, while HAV growth in cell culture was hampered.

CONCLUSIONS

The RT-PCR technique was confirmed to be a valuable tool for the rapid monitoring of HAV in sewage samples. In addition, this study demonstrated that application of different sample purification methods can result in different levels of sensitivity of the assay and that, in the antigen-capture method, the choice of antibody can have a crucial role.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work underlines the need for technical uniformity in environmental studies from different laboratories for a correct and useful comparison of the results.

Microbiological quality of sewage sludge in Greece disposed for agricultural use

For the disposal of sewage, sludge landfill is currently the practice adopted in Greece. Thirteen wastewater treatment plants located throughout Greece (islands excluded) were investigated over a period of 1 year in order to determine sludge microbiological quality. The time of exposure of the samples to environmental conditions and stress varied considerably, from a few hours to several months. The mean values for total coliforms were 4 to > 2400/100 ml and for faecal coliforms < 3 to > 2400/100. Salmonellae were isolated from all plants with the exception of two. Parasites were isolated from five treatment plants. There was no difference in the bacterial indicator counts of faecal pollution or the presence of salmonellae and parasites according to the time of disposal of the sludge to the fields. The samples taken from the soil, or from flowers and vegetables which grow in the area of the sludge disposal were mostly negative for faecal pollution bacteria indicators. Salmonellae and parasites were not recovered from any samples. Five of the 16 serotypes reported from the National Salmonella Reference Center were present in the sludge samples.

Occurrence and levels of phages proposed as surrogate indicators of enteric viruses in different types of sludges

A method based on the treatment of sludge with beef extract recovered, with similar efficiency, the three groups of bacteriophages studied from different kinds of sludges. The three groups of bacteriophages were found in high numbers in the different sludge types, the highest value being that of somatic coliphages in primary sludge of a biological treatment plant (1.1 x 10(5) pfu g-1) and the lowest being that of Bacteroides fragilis phages (110 pfu g-1) in de-watered, anaerobically, mesophilically-digested sludge. All phages studied accumulated in the sludges. In primary and activated sludges, all three types accumulated similarly but in lime-treated sludge and de-watered, anaerobically, mesophilically-digested sludge, the relative proportion of F-specific bacteriophages decreased significantly with respect to somatic coliphages and bacteriophages infecting B. fragilis. All phages survived successfully in stored sludge, depending on the temperature, and again, F-specific bacteriophages survived less successfully than the others.

Comparison of seven RNA extraction methods on stool and shellfish samples prior to hepatitis A virus amplification

When choosing an extraction method, two parameters have to be considered: recovery of the viral material and elimination or inactivation of inhibitory substances. Seven techniques for extracting hepatitis A virus (HAV) from stool and shellfish samples were compared, in order to identify the protocol most suited to both types of sample and with the best extraction yield. The protocols tested were either techniques for the recovery and purification of total RNA, such as RNAzol, PEG-CETAB, GTC-silica and Chelex, or techniques for isolating specifically HAV using a nucleotide probe or a monoclonal antibody. For stool samples, RNAzol, PEG-CETAB, and magnetic beads with antibody allowed detection of the virus in 11/12 and 12/12 of samples. For shellfish samples, three protocols allowed RNA to be extracted in 90% of cases, RNAzol, PEG-CETAB, and GTC-silica. Their rapidity and low cost make RNAzol and GTC-silica the most suitable for routine diagnostic testing. reserved.

Incidence of enteroviruses in Mamala Bay, Hawaii using cell culture and direct polymerase chain reaction methodologies

The consequence of point and nonpoint pollution sources, discharged into marine waters, on public recreational beaches in Mamala Bay, Hawaii was evaluated using virus cell culture and direct reverse transcriptase - polymerase chain reaction (RT-PCR). Twelve sites, nine marine, two freshwater (one stream and one canal), and one sewage, were assessed either quarterly or monthly for 1 year to detect the presence of human enteric viruses. Water samples were concentrated from initial volumes of 400 L to final volumes of 30 mL using Filterite electronegative cartridge filters and a modified beef extract elution procedure. Cell culture was applied using the Buffalo Green Monkey kidney cell line to analyze samples for enteroviruses. Positive samples were also evaluated by RT-PCR, using enterovirus-specific primers. Levels of RT-PCR inhibition varied with each concentrated sample. Resin column purification increased PCR detection sensitivity by at least one order of magnitude in a variety of sewage outfall and recreational marine water samples but not in the freshwater canal samples. Using cell culture, viable enteroviruses were found in 50 and 17% of all outfall and canal samples, respectively. Samples were positive at beaches 8% of the time. These data illustrate the potential public health hazard associated with recreational waters. Using direct PCR, viruses were detected at the outfall but were not found in any beach or canal samples, in part, owing to substances that inhibit PCR. Therefore, conventional cell culture is the most effective means of detecting low levels of infectious enteroviruses in environmental waters, whereas direct RT-PCR is rendered less effective by inhibitory compounds and low equivalent reaction volumes.Key words: enteroviruses, RT-PCR, cell culture, marine waters.

Detection of low levels of enteric viruses in metropolitan and airplane sewage

To detect less prevalent viruses, such as wild-type polioviruses in sewage from a highly immunized community, a method was developed to efficiently recover viruses and remove PCR inhibitors. The method consisted of initial separation of solids from liquid, followed by solvent extractions, polyethylene glycol precipitations, Sephadex G-200 chromatography, and guanidinium isothiocyanate (GIT) extraction. To elute viruses from the separated solids, 0.5 M threonine (pH 7.5) was as efficient as 3% beef extract but conferred no PCR inhibition. In samples that were concentrated approximately 1,000-fold, 21% of the initially seeded viruses were recovered. When poliovirus type 3 (PV3) Sabin strain at low levels and PV1 LSc strain at high levels were seeded in raw sewage, PV3 was specifically detected in the final sample concentrates at sensitivities of 14 PFU by direct PCR and 0.7 PFU by GIT extraction-PCR. While applying the method to international airplane sewage, which contains high levels of solids as well as commercial sanitizers, 44% (7 of 16) of the samples were found to harbor enteroviruses by both cell culture infectivity and pan-enterovirus PCR analyses. Nucleotide sequencing of the PCR products revealed that multiple enterovirus genotypes were amplified from each final sewage concentrate, whereas the fewer virus genotypes detected by cell culture infectivity were probably the better growing strains. By this method, we demonstrated that air travel may contribute to the intercontinental dissemination of enteric pathogens.

Three-step isolation method for sensitive detection of enterovirus, rotavirus, hepatitis A virus, and small round structured viruses in water samples

Control of drinking or bathing water quality in respect to viral contamination remains an unsolved problem. A highly sensitive isolation protocol was developed for concentration and detection of different enteric viruses from water samples. The three-step isolation procedure combines filtration with a positively charged nylon membrane, ultrafiltration and clean-up of the viral RNA with a silica based membrane. Detection of the viral RNA is accomplished by reverse-transcription polymerase chain reaction (RT-PCR). Detection limits were determined to be one 50% tissue culture infective dose (TCID50) of seeded coxsackievirus B2 or hepatitis A Virus per litre of tap water by RT-PCR compared to two orders of magnitude lower sensitivity for culture in the case of coxsackievirus B2. The isolation procedure is highly sensitive, easy to perform and allows the detection of different human pathogenic virus groups in one water sample. The application of the isolation procedure to six river water samples and subsequent detection with nested or semi-nested PCR revealed enterovirus in 6/6 (100%), rotavirus in 6/6 (100%), hepatitis A virus in 0/6 (0%), small round structured virus genotype I in 6/6 (100%) and small round structured virus genotype II in 2/6 (33%) of the samples. These findings suggest that first, we have developed a very sensitive detection procedure and second, that river water in Switzerland-where most of the wastewater is handled by sewage treatment plants-shows a high contamination rate with enteric viruses.