New articles from AEM

[Muruleedhara Byappanahali <byappan@usgs.gov>]

Please see below for abstracts.


Applied and Environmental Microbiology, December 2006,
p. 7438-7444, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01024-06
Copyright
© 2006, American
Society for Microbiology. All Rights Reserved.
Quantitative Detection of Hepatitis A Virus and Enteroviruses
Near the United States-Mexico Border and Correlation with Levels of Fecal
Indicator Bacteria

Richard M. Gersberg,1* Michael A. Rose,1
Refugio Robles-Sikisaka,2 and Arun K. Dhar2

Graduate School of Public Health, San Diego State University, San Diego, California 92182,¹ Department of Biology, San Diego State University, San Diego, California 92182²

Received 2 May 2006/ Accepted 4 September 2006

For decades, untreated sewage flowing northward from Tijuana, Mexico, via the Tijuana River has adversely affected the water quality of the recreational beaches of San Diego, California. We used quantitative reverse transcription-PCR to measure the levels of hepatitis A virus (HAV) and enteroviruses in coastal waters near the United States-Mexico border and compared these levels to those of the conventional fecal indicators, Escherichia coli and enterococci. Over a 2-year period from 2003 to 2005, a total of 20 samples were assayed at two sites during both wet and dry weather: the surfzone at the mouth of the Tijuana River and the surfzone near the pier at Imperial Beach (IB), California (about 2 km north of the mouth of the Tijuana River). HAV and enterovirus were detected in 79 and 93% of the wet-weather samples, respectively. HAV concentrations in these samples ranged from 105 to 30,771 viral particles/liter, and enterovirus levels ranged from 7 to 4,417 viral particles/liter. The concentrations of HAV and enterovirus were below the limit of detection for all dry weather samples collected at IB. Regression analyses showed a significant correlation between the densities of both fecal bacterial indicators and the levels of HAV (R² > 0.61, P < 0.0001) and enterovirus (R² > 0.70, P < 0.0001), a finding that supports the use of conventional bacterial indicators to predict the levels of these viruses in recreational marine waters.
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Applied and Environmental Microbiology, December 2006, p. 7548-7553, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01352-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Identification of Novel Cryptosporidium Genotypes from Avian Hosts
Josephine Ng,^1* Ivan Pavlasek,² and Una Ryan¹

Division of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia,¹ State Veterinary Institute Prague, Pathology and Parasitology Department, 165 03 Prague 6, Czech Republic²

Received 13 June 2006/ Accepted 25 September 2006

A total of 430 avian-derived fecal specimens were randomly collected from selected Western Australian commercial aviaries, poultry farms, hatcheries, wildlife parks, and the Perth Zoo and screened for the presence of Cryptosporidium by PCR. Of these, 27 Cryptosporidium-positive isolates were detected, characterized, and compared with 11 avian-derived isolates from the Czech Republic at the 18S rRNA and actin gene loci. Sequence and phylogenetic analysis identified four genetically distinct genotypes, avian genotypes I to IV, from various avian hosts. In addition, the host range for Cryptosporidium galli was extended. Cryptosporidium muris and Cryptosporidium andersoni were also identified in a tawny frogmouth and a quail-crested wood partridge, respectively.

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Applied and Environmental Microbiology, December 2006, p. 7567-7574, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01317-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Detection of Human-Derived Fecal Pollution in Environmental Waters by Use of a PCR-Based Human Polyomavirus Assay
Shannon M. McQuaig,¹ Troy M. Scott,² Valerie J. Harwood,^3* Samuel R. Farrah,¹ and Jerzy O. Lukasik²

Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 33611,¹ Biological Consulting Services of North Florida, Gainesville, Florida 32609,² Department of Biology, University of South Florida, Tampa, Florida 33620³

Received 8 June 2006/ Accepted 13 September 2006

Regulatory agencies mandate the use of fecal coliforms, Escherichia coli or Enterococcus spp., as microbial indicators of recreational water quality. These indicators of fecal pollution do not identify the specific sources of pollution and at times underestimate health risks associated with recreational water use. This study proposes the use of human polyomaviruses (HPyVs), which are widespread among human populations, as indicators of human fecal pollution. A method was developed to concentrate and extract HPyV DNA from environmental water samples and then to amplify it by nested PCR. HPyVs were detected in as little as 1 µl of sewage and were not amplified from dairy cow or pig wastes. Environmental water samples were screened for the presence of HPyVs and two additional markers of human fecal pollution: the Enterococcus faecium esp gene and the 16S rRNA gene of human-associated Bacteroides. The presence of human-specific indicators of fecal pollution was compared to fecal coliform and Enterococcus concentrations. HPyVs were detected in 19 of 20 (95%) samples containing the E. faecium esp gene and Bacteroides human markers. Weak or no correlation was observed between the presence/absence of human-associated indicators and counts of indicator bacteria. The sensitivity, specificity, and correlation with other human-associated markers suggest that the HPyV assay could be a useful predictor of human fecal pollution in environmental waters and an important component of the microbial-source-tracking "toolbox

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Applied and Environmental Microbiology, December 2006, p. 7575-7585, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01174-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Multilocus Sequence Typing Supports the Hypothesis that Cow- and Human-Associated Salmonella Isolates Represent Distinct and Overlapping Populations ^,
S. D. Alcaine,¹ Y. Soyer,¹ L. D. Warnick,² W.-L. Su,¹ S. Sukhnanand,¹ J. Richards,¹ E. D. Fortes,¹ P. McDonough,² T. P. Root,³ N. B. Dumas,³ Y. Gröhn,² and M. Wiedmann^1*

Department of Food Science,¹ Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York 14853,² Wadsworth Center, New York State Department of Health, Albany, New York³

Received 21 May 2006/ Accepted 25 September 2006

A collection of 179 human and 156 bovine clinical Salmonella isolates obtained from across New York state over the course of 1 year was characterized using serotyping and a multilocus sequence typing (MLST) scheme based on the sequencing of three genes (fimA, manB, and mdh). The 335 isolates were differentiated into 52 serotypes and 72 sequence types (STs). Analyses of bovine isolates collected on different farms over time indicated that specific subtypes can persist over time on a given farm; in particular, a number of farms showed evidence for the persistence of a specific Salmonella enterica serotype Newport sequence type. Serotypes and STs were not randomly distributed among human and bovine isolates, and selected serotypes and STs were associated exclusively with either human or bovine sources. A number of common STs were geographically widespread. For example, ST6, which includes isolates representing serotype Typhimurium as well as the emerging serotype 4,5,12:i:-, was found among human and bovine isolates in a number of counties in New York state. Phylogenetic analyses supported the possibility that serotype 4,5,12:i:- is closely related to Salmonella serotype Typhimurium. Salmonella serotype Newport was found to represent two distinct evolutionary lineages that differ in their frequencies among human and bovine isolates. A number of Salmonella isolates carried two copies of manB (33 isolates) or showed small deletion events in fimA (nine isolates); these duplication and deletion events may provide mechanisms for the rapid diversification of Salmonella surface molecules. We conclude that the combined use of an economical three-gene MLST scheme and serotyping can provide considerable new insights into the evolution and transmission of Salmonella.

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Applied and Environmental Microbiology, December 2006, p. 7671-7677, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01106-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Inactivation of Poliovirus 1 and F-Specific RNA Phages and Degradation of Their Genomes by UV Irradiation at 254 Nanometers
Julien Simonet and Christophe Gantzer^*

Laboratoire de Chimie Physique et Microbiologie pour l'Environnement (LCPME), UMR 7564 CNRS/Université Henri Poincaré Nancy I, Equipe Microbiologie et Physique, Faculté de Pharmacie, BP 80403, 54001 Nancy Cedex, France

Received 12 May 2006/ Accepted 28 September 2006

Several models (animal caliciviruses, poliovirus 1 [PV1], and F-specific RNA bacteriophages) are usually used to predict inactivation of nonculturable viruses. For the same UV fluence, viral inactivation observed in the literature varies from 0 to 5 logs according to the models and the methods (infectivity versus molecular biology). The lack of knowledge concerning the mechanisms of inactivation due to UV prevents us from selecting the best model. In this context, determining if viral genome degradation may explain the loss of infectivity under UV radiation becomes essential. Thus, four virus models (PV1 and three F-specific RNA phages: MS2, GA, and Qß) were exposed to UV radiation from 0 to 150 mJ · cm^–2. PV1 is the least-resistant virus, while MS2 and GA phages are the most resistant, with phage Qß having an intermediate sensitivity; respectively, 6-log, 2.3-log, 2.5-log, and 4-log decreases for 50 mJ · cm^–2. In parallel, analysis of RNA degradation demonstrated that this phenomenon depends on the fragment size for PV1 as well as for MS2. Long fragments (above 2,000 bases) for PV1 and MS2 fell rapidly to the background level (>1.3-log decrease) for 20 mJ · cm^–2 and 60 mJ · cm^{– 2}, respectively. Nevertheless, the size of the viral RNA is not the only factor affecting UV-induced RNA degradation, since viral RNA was more rapidly degraded in PV1 than in the MS2 phage with a similar size. Finally, extrapolation of inactivation and UV-induced RNA degradation kinetics highlights that genome degradation could fully explain UV-induced viral inactivation.

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Applied and Environmental Microbiology, December 2006, p. 7886-7893, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01090-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Identification of Human and Animal Adenoviruses and Polyomaviruses for Determination of Sources of Fecal Contamination in the Environment
Ayalkibet Hundesa, Carlos Maluquer de Motes, Silvia Bofill-Mas, Nestor Albinana-Gimenez, and Rosina Girones^*

Department of Microbiology, Faculty of Biology, University of Barcelona, Av. Diagonal 645, Barcelona 08028, Spain

Received 11 May 2006/ Accepted 28 September 2006

The Adenoviridae and Polyomaviridae families comprise a wide diversity of viruses which may be excreted for long periods in feces or urine. In this study, a preliminary analysis of the prevalence in the environment and the potential usefulness as source-tracking tools of human and animal adenoviruses and polyomaviruses has been developed. Molecular assays based on PCR specifically targeting human adenoviruses (HAdV), porcine adenoviruses (PAdV), bovine adenoviruses (BAdV), and bovine polyomaviruses (BPyV) were applied to environmental samples including urban sewage, slaughterhouse, and river water samples. PAdV and BPyV were detected in a very high percentage of samples potentially affected by either porcine or bovine fecal contamination, respectively. However, BAdV were detected in only one sample, showing a lower prevalence than BPyV in the wastewater samples analyzed. The 22 slaughterhouse samples with fecal contamination of animal origin showed negative results for the presence of HAdV. The river water samples analyzed were positive for the presence of both human and animal adenoviruses and polyomaviruses, indicating the existence of diverse sources of contamination. The identities of the viruses detected were confirmed by analyses of the amplified sequences. All BPyV isolates showed a 97% similarity in nucleotide sequences. This is the first time that PAdV5, BAdV6, and BPyV have been reported to occur in environmental samples. Human and porcine adenoviruses and human and bovine polyomaviruses are proposed as tools for evaluating the presence of viral contamination and for tracking the origin of fecal/urine contamination in environmental samples.

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Applied and Environmental Microbiology, December 2006, p. 7894-7896, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.00965-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

SHORT REPORT

Quantification and Stability of Human Adenoviruses and Polyomavirus JCPyV in Wastewater Matrices
Silvia Bofill-Mas,¹ Nestor Albinana-Gimenez,¹ Pilar Clemente-Casares,¹ Ayalkibet Hundesa,¹ Jesus Rodriguez-Manzano,¹ Annika Allard,³ Miquel Calvo,² and Rosina Girones^1*

Department of Microbiology,¹ Department of Statistics, Faculty of Biology, University of Barcelona, Av. Diagonal 645, Barcelona 08028, Spain,² Department of Clinical Virology, Umeå University Hospital, S-901 85 Umeå, Sweden³

Received 24 April 2006/ Accepted 2 October 2006

Human adenoviruses (HAdV) and human polyomavirus JCPyV have been previously proposed as indicators of fecal viral contamination in the environment. Different wastewater matrices have been analyzed by applying real-time quantitative PCR procedures for the presence, quantity, and stability of a wide diversity of excreted HAdV and JCPyV. High quantities of HAdV and JCPyV were detected in sewage, effluent wastewater, sludge, and biosolid samples. Both viruses showed high stability in urban sewage. These results confirm the suitability of both viruses as indicators of human fecal viral pollution.

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Applied and Environmental Microbiology, December 2006, p. 7916-7918, Vol. 72, No. 12
0099-2240/06/$08.00+0     doi:10.1128/AEM.01903-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

SHORT REPORT

Giardia Cysts and Cryptosporidium Oocysts in Membrane-Filtered Municipal Wastewater Used for Irrigation
A. Lonigro,¹ A. Pollice,² R. Spinelli,³ F. Berrilli,⁴ D. Di Cave,^4,5 C. D'Orazi,⁵ P. Cavallo,³ and O. Brandonisio^3*

Dipartimento di Scienze delle Produzioni Vegetali, University of Bari, Via Amendola 165/A, 70126 Bari, Italy,¹ CNR IRSA, Istituto di Ricerca sulle Acque, Viale De Blasio 5, 70123 Bari, Italy,² Dipartimento di Clinica Medica, Immunologia e Malattie Infettive, University of Bari, Policlinico, 70124 Bari, Italy,³ Dipartimento di Sanità Pubblica e Biologia Cellulare, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy,⁴ Dipartimento di Medicina di Laboratorio—PTV, University of Rome Tor Vergata, Viale Oxford 81, 00133 Rome, Italy⁵

Received 9 August 2006/ Accepted 9 October 2006

A wastewater tertiary treatment system based on membrane ultrafiltration and fed with secondary-treated municipal wastewater was evaluated for its Giardia cyst and Cryptosporidium oocyst removal efficiency. Giardia duodenalis (assemblages A and B) and Cryptosporidium parvum were identified in feed water but were found in filtered water only during occasional failure of the filtration system.

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Murulee Byappanahalli, Ph. D.
Research Microbiologist
U.S. Geological Survey, Great Lakes Science Center
Lake Michigan Ecological Research Station,
1100 N. Mineral Springs Road
Porter, Indiana 46304
Phone: (219) 926-8336 ext. 421
Fax:      (219) 929-5792
E-mail: byappan@usgs.gov