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[Muruleedhara Byappanahalli <byappan@usgs.gov>]

fyi...

Environmental Microbiology
Volume 10 Issue 10, Pages 2598 - 2608

Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics

G. H. Reischer, ¹ J. M. Haider, ¹ R. Sommer, ² H. Stadler, ³ K. M. Keiblinger, ¹ R. Hornek, ⁴ W. Zerobin, ⁵ R. L. Mach ¹ and A. H. Farnleitner ¹ *

  ¹ Institute of Chemical Engineering, Gene Technology Group, Vienna University of Technology, Getreidemarkt 9/166-5-2, A-1060 Vienna, Austria.
  ² Clinical Institute of Hygiene and Medical Microbiology, Medical University Vienna, Kinderspitalgasse 15, A-1090 Vienna, Austria.
  ³ Institute of Water Resources Management, Hydrogeology and Geophysics, Joanneum Research, Elisabethstraße 16/II, A-8010 Graz, Austria.
  ⁴ Institute for Water Quality and Waste Management, Department for Chemistry and Biology of Water, Vienna University of Technology, Karlsplatz 13, A-1040 Vienna, Austria.
  ⁵ Vienna Waterworks, Grabnergasse 4-6, A-1060 Vienna, Austria.
Correspondence to   *E-mail a.farnleitner@aon.at; Tel. (+43) 1 58801 17251; Fax (+43) 1 588801 17299.
Copyright Journal compilation © 2008 Society for Applied Microbiology and Blackwell Publishing Ltd

ABSTRACT
The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.

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Environmental Microbiology
Volume 10 Issue 10, Pages 2484 - 2496

Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method

David M. Gordon, ¹ Olivier Clermont, ² Heather Tolley ¹ and Erick Denamur ²

  ¹ School of Botany and Zoology, Australian National University, Canberra ACT 0200, Australia.
  ² Institut National de la Santé et de la Recherche Médicale (INSERM) U722 and Faculté de Médecine Xavier Bichat, Université Paris 7 Denis Diderot, 75018 Paris, France.
Correspondence to   *E-mail David.Gordon@anu.edu.au; Tel. (+61) 26125 3552; Fax (+61) 26125 5573.
Copyright Journal compilation © 2008 Society for Applied Microbiology and Blackwell Publishing Ltd
ABSTRACT
It is well recognized that Escherichia coli consists of a number of distinct phylo-groups and that strains of the different phylo-groups vary in their ecological niches, life-history characteristics and propensity to cause disease. Consequently, much can be learnt by assigning a strain of E. coli to one of the recognized phylo-groups. A triplex PCR-based method that enables strains of E. coli to be assigned to a phylo-group using a dichotomous key approach based on the presence or absence of two genes (chuA and yjaA) and an anonymous DNA fragment (TSPE4.C2) has been developed. However, the accuracy with which this method assigns strains to their correct phylo-group has not been adequately evaluated. Consequently, 662 strains of E. coli were characterized using a multi-locus sequence typing approach. Unsupervised population assignment algorithms were used to assign strains to phylo-groups based on the multi-locus sequence typing data. The analyses revealed that 85–90% of E. coli strains can be assigned to a phylo-group and that 80–85% of the phylo-group memberships assigned using the Clermont method are correct. However, the accuracy with which strains are assigned to the correct phylo-group depends on their Clermont genotype. For example, strains yielding a Clermont genotype consistent with phylo-groups B1 and B2 are assigned correctly 95% of the time. Strains failing to yield any PCR products using the Clermont method are seldom members of phylo-group A and strains with such a genotype should not be assigned to a phylo-group.

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