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Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades.

Youngblut ND, Reischer GH, Walters W, Schuster N, Walzer C, Stalder G, Ley RE, Farnleitner AH.

Nat Commun. 2019 May 16;10(1):2200. doi: 10.1038/s41467-019-10191-3.


Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community.

Savio D, Stadler P, Reischer GH, Demeter K, Linke RB, Blaschke AP, Mach RL, Kirschner AKT, Stadler H, Farnleitner AH.

Front Microbiol. 2019 Feb 15;10:28. doi: 10.3389/fmicb.2019.00028. eCollection 2019.


Event-transport of beta-d-glucuronidase in an agricultural headwater stream: Assessment of seasonal patterns by on-line enzymatic activity measurements and environmental isotopes.

Stadler P, Blöschl G, Nemeth L, Oismüller M, Kumpan M, Krampe J, Farnleitner AH, Zessner M.

Sci Total Environ. 2019 Apr 20;662:236-245. doi: 10.1016/j.scitotenv.2019.01.143. Epub 2019 Jan 15.


Detection of a microbial source tracking marker by isothermal helicase-dependent amplification and a nucleic acid lateral-flow strip test.

Kolm C, Martzy R, Führer M, Mach RL, Krska R, Baumgartner S, Farnleitner AH, Reischer GH.

Sci Rep. 2019 Jan 23;9(1):393. doi: 10.1038/s41598-018-36749-7.


Challenges and perspectives in the application of isothermal DNA amplification methods for food and water analysis.

Martzy R, Kolm C, Krska R, Mach RL, Farnleitner AH, Reischer GH.

Anal Bioanal Chem. 2019 Mar;411(9):1695-1702. doi: 10.1007/s00216-018-1553-1. Epub 2019 Jan 8.


Spatial patterns of enzymatic activity in large water bodies: Ship-borne measurements of beta-D-glucuronidase activity as a rapid indicator of microbial water quality.

Stadler P, Loken LC, Crawford JT, Schramm PJ, Sorsa K, Kuhn C, Savio D, Striegl RG, Butman D, Stanley EH, Farnleitner AH, Zessner M.

Sci Total Environ. 2019 Feb 15;651(Pt 2):1742-1752. doi: 10.1016/j.scitotenv.2018.10.084. Epub 2018 Oct 8.


Spatiotemporal resolved sampling for the interpretation of micropollutant removal during riverbank filtration.

van Driezum IH, Derx J, Oudega TJ, Zessner M, Naus FL, Saracevic E, Kirschner AKT, Sommer R, Farnleitner AH, Blaschke AP.

Sci Total Environ. 2019 Feb 1;649:212-223. doi: 10.1016/j.scitotenv.2018.08.300. Epub 2018 Aug 24.


Hotspots and main drivers of fecal pollution in Neusiedler See, a large shallow lake in Central Europe.

Hatvani IG, Kirschner AKT, Farnleitner AH, Tanos P, Herzig A.

Environ Sci Pollut Res Int. 2018 Oct;25(29):28884-28898. doi: 10.1007/s11356-018-2783-7. Epub 2018 Aug 13.


Poikilothermic Animals as a Previously Unrecognized Source of Fecal Indicator Bacteria in a Backwater Ecosystem of a Large River.

Frick C, Vierheilig J, Linke R, Savio D, Zornig H, Antensteiner R, Baumgartner C, Bucher C, Blaschke AP, Derx J, Kirschner AKT, Ryzinska-Paier G, Mayer R, Seidl D, Nadiotis-Tsaka T, Sommer R, Farnleitner AH.

Appl Environ Microbiol. 2018 Aug 1;84(16). pii: e00715-18. doi: 10.1128/AEM.00715-18. Print 2018 Aug 15.


Application of three different methods to determine the prevalence, the abundance and the environmental drivers of culturable Vibrio cholerae in fresh and brackish bathing waters.

Kirschner AKT, Pleininger S, Jakwerth S, Rehak S, Farnleitner AH, Huhulescu S, Indra A.

J Appl Microbiol. 2018 Oct;125(4):1186-1198. doi: 10.1111/jam.13940. Epub 2018 Aug 13.


Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management.

Savio D, Stadler P, Reischer GH, Kirschner AKT, Demeter K, Linke R, Blaschke AP, Sommer R, Szewzyk U, Wilhartitz IC, Mach RL, Stadler H, Farnleitner AH.

WIREs Water. 2018 May-Jun;5(3):e1282. doi: 10.1002/wat2.1282. Epub 2018 Mar 9. Review.


Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents.

Mayer RE, Reischer GH, Ixenmaier SK, Derx J, Blaschke AP, Ebdon JE, Linke R, Egle L, Ahmed W, Blanch AR, Byamukama D, Savill M, Mushi D, Cristóbal HA, Edge TA, Schade MA, Aslan A, Brooks YM, Sommer R, Masago Y, Sato MI, Taylor HD, Rose JB, Wuertz S, Shanks OC, Piringer H, Mach RL, Savio D, Zessner M, Farnleitner AH.

Environ Sci Technol. 2018 May 1;52(9):5076-5084. doi: 10.1021/acs.est.7b04438. Epub 2018 Apr 16.


Spatiotemporal analysis of bacterial biomass and activity to understand surface and groundwater interactions in a highly dynamic riverbank filtration system.

van Driezum IH, Chik AHS, Jakwerth S, Lindner G, Farnleitner AH, Sommer R, Blaschke AP, Kirschner AKT.

Sci Total Environ. 2018 Jun 15;627:450-461. doi: 10.1016/j.scitotenv.2018.01.226. Epub 2018 Feb 3.


Antibiotic Resistance of Acinetobacter spp. Isolates from the River Danube: Susceptibility Stays High.

Kittinger C, Kirschner A, Lipp M, Baumert R, Mascher F, Farnleitner AH, Zarfel GE.

Int J Environ Res Public Health. 2017 Dec 30;15(1). pii: E52. doi: 10.3390/ijerph15010052.


Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River.

Kirschner AKT, Reischer GH, Jakwerth S, Savio D, Ixenmaier S, Toth E, Sommer R, Mach RL, Linke R, Eiler A, Kolarevic S, Farnleitner AH.

Water Res. 2017 Nov 1;124:543-555. doi: 10.1016/j.watres.2017.07.052. Epub 2017 Jul 22.


A loop-mediated isothermal amplification (LAMP) assay for the rapid detection of Enterococcus spp. in water.

Martzy R, Kolm C, Brunner K, Mach RL, Krska R, Šinkovec H, Sommer R, Farnleitner AH, Reischer GH.

Water Res. 2017 Oct 1;122:62-69. doi: 10.1016/j.watres.2017.05.023. Epub 2017 May 13.


A Complementary Isothermal Amplification Method to the U.S. EPA Quantitative Polymerase Chain Reaction Approach for the Detection of Enterococci in Environmental Waters.

Kolm C, Martzy R, Brunner K, Mach RL, Krska R, Heinze G, Sommer R, Reischer GH, Farnleitner AH.

Environ Sci Technol. 2017 Jun 20;51(12):7028-7035. doi: 10.1021/acs.est.7b01074. Epub 2017 Jun 9.


High genetic diversity of Vibrio cholerae in the European lake Neusiedler See is associated with intensive recombination in the reed habitat and the long-distance transfer of strains.

Pretzer C, Druzhinina IS, Amaro C, Benediktsdóttir E, Hedenström I, Hervio-Heath D, Huhulescu S, Schets FM, Farnleitner AH, Kirschner AK.

Environ Microbiol. 2017 Jan;19(1):328-344. doi: 10.1111/1462-2920.13612. Epub 2017 Jan 18.


Development and evaluation of a self-cleaning custom-built auto sampler controlled by a low-cost RaspberryPi microcomputer for online enzymatic activity measurements.

Stadler P, Farnleitner AH, Zessner M.

Talanta. 2017 Jan 1;162:390-397. doi: 10.1016/j.talanta.2016.10.031. Epub 2016 Oct 12.


Enterobacteriaceae Isolated from the River Danube: Antibiotic Resistances, with a Focus on the Presence of ESBL and Carbapenemases.

Kittinger C, Lipp M, Folli B, Kirschner A, Baumert R, Galler H, Grisold AJ, Luxner J, Weissenbacher M, Farnleitner AH, Zarfel G.

PLoS One. 2016 Nov 3;11(11):e0165820. doi: 10.1371/journal.pone.0165820. eCollection 2016.


Setback distances between small biological wastewater treatment systems and drinking water wells against virus contamination in alluvial aquifers.

Blaschke AP, Derx J, Zessner M, Kirnbauer R, Kavka G, Strelec H, Farnleitner AH, Pang L.

Sci Total Environ. 2016 Dec 15;573:278-289. doi: 10.1016/j.scitotenv.2016.08.075. Epub 2016 Aug 26.


QMRAcatch: Human-Associated Fecal Pollution and Infection Risk Modeling for a River/Floodplain Environment.

Derx J, Schijven J, Sommer R, Zoufal-Hruza CM, van Driezum IH, Reischer G, Ixenmaier S, Kirschner A, Frick C, de Roda Husman AM, Farnleitner AH, Blaschke AP.

J Environ Qual. 2016 Jul;45(4):1205-14. doi: 10.2134/jeq2015.11.0560.


Real-time monitoring of beta-d-glucuronidase activity in sediment laden streams: A comparison of prototypes.

Stadler P, Blöschl G, Vogl W, Koschelnik J, Epp M, Lackner M, Oismüller M, Kumpan M, Nemeth L, Strauss P, Sommer R, Ryzinska-Paier G, Farnleitner AH, Zessner M.

Water Res. 2016 Sep 15;101:252-261. doi: 10.1016/j.watres.2016.05.072. Epub 2016 May 27.


Antibiotic Resistance Patterns of Pseudomonas spp. Isolated from the River Danube.

Kittinger C, Lipp M, Baumert R, Folli B, Koraimann G, Toplitsch D, Liebmann A, Grisold AJ, Farnleitner AH, Kirschner A, Zarfel G.

Front Microbiol. 2016 May 3;7:586. doi: 10.3389/fmicb.2016.00586. eCollection 2016.


Occurrence of human-associated Bacteroidetes genetic source tracking markers in raw and treated wastewater of municipal and domestic origin and comparison to standard and alternative indicators of faecal pollution.

Mayer RE, Bofill-Mas S, Egle L, Reischer GH, Schade M, Fernandez-Cassi X, Fuchs W, Mach RL, Lindner G, Kirschner A, Gaisbauer M, Piringer H, Blaschke AP, Girones R, Zessner M, Sommer R, Farnleitner AH.

Water Res. 2016 Mar 1;90:265-276. doi: 10.1016/j.watres.2015.12.031. Epub 2015 Dec 19.


Potential applications of next generation DNA sequencing of 16S rRNA gene amplicons in microbial water quality monitoring.

Vierheilig J, Savio D, Ley RE, Mach RL, Farnleitner AH, Reischer GH.

Water Sci Technol. 2015;72(11):1962-72. doi: 10.2166/wst.2015.407. Erratum in: Water Sci Technol. 2016;73(7):1768.


QMRAcatch: Microbial Quality Simulation of Water Resources including Infection Risk Assessment.

Schijven J, Derx J, de Roda Husman AM, Blaschke AP, Farnleitner AH.

J Environ Qual. 2015 Sep;44(5):1491-502. doi: 10.2134/jeq2015.01.0048.


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

Stevenson ME, Sommer R, Lindner G, Farnleitner AH, Toze S, Kirschner AK, Blaschke AP, Sidhu JP.

J Environ Qual. 2015 Sep;44(5):1392-401. doi: 10.2134/jeq2015.01.0052.


Automated Sampling Procedures Supported by High Persistence of Bacterial Fecal Indicators and Bacteroidetes Genetic Microbial Source Tracking Markers in Municipal Wastewater during Short-Term Storage at 5°C.

Mayer RE, Vierheilig J, Egle L, Reischer GH, Saracevic E, Mach RL, Kirschner AK, Zessner M, Sommer R, Farnleitner AH.

Appl Environ Microbiol. 2015 Aug;81(15):5134-43. doi: 10.1128/AEM.00998-15. Epub 2015 May 22.


Bacterial diversity along a 2600 km river continuum.

Savio D, Sinclair L, Ijaz UZ, Parajka J, Reischer GH, Stadler P, Blaschke AP, Blöschl G, Mach RL, Kirschner AK, Farnleitner AH, Eiler A.

Environ Microbiol. 2015 Dec;17(12):4994-5007. doi: 10.1111/1462-2920.12886. Epub 2015 Jun 11.


Biotin- and Glycoprotein-Coated Microspheres as Surrogates for Studying Filtration Removal of Cryptosporidium parvum in a Granular Limestone Aquifer Medium.

Stevenson ME, Blaschke AP, Toze S, Sidhu JP, Ahmed W, van Driezum IH, Sommer R, Kirschner AK, Cervero-Aragó S, Farnleitner AH, Pang L.

Appl Environ Microbiol. 2015 Jul;81(13):4277-83. doi: 10.1128/AEM.00885-15. Epub 2015 Apr 17.


Dynamics of Vibrio cholerae abundance in Austrian saline lakes, assessed with quantitative solid-phase cytometry.

Schauer S, Jakwerth S, Bliem R, Baudart J, Lebaron P, Huhulescu S, Kundi M, Herzig A, Farnleitner AH, Sommer R, Kirschner A.

Environ Microbiol. 2015 Nov;17(11):4366-78. doi: 10.1111/1462-2920.12861. Epub 2015 May 18.


A novel triplex quantitative PCR strategy for quantification of toxigenic and nontoxigenic Vibrio cholerae in aquatic environments.

Bliem R, Schauer S, Plicka H, Obwaller A, Sommer R, Steinrigl A, Alam M, Reischer GH, Farnleitner AH, Kirschner A.

Appl Environ Microbiol. 2015 May 1;81(9):3077-85. doi: 10.1128/AEM.03516-14. Epub 2015 Feb 27.


Response to letter to the editor regarding "detection of the 35S promoter in transgenic maize via various isothermal amplification techniques: a practical approach".

Zahradnik C, Kolm C, Martzy R, Mach RL, Krska R, Farnleitner AH, Brunner K.

Anal Bioanal Chem. 2014 Dec;406(30):8061-2. doi: 10.1007/s00216-014-8183-z. Epub 2014 Oct 30. No abstract available.


Detection of the 35S promoter in transgenic maize via various isothermal amplification techniques: a practical approach.

Zahradnik C, Kolm C, Martzy R, Mach RL, Krska R, Farnleitner AH, Brunner K.

Anal Bioanal Chem. 2014 Nov;406(27):6835-42. doi: 10.1007/s00216-014-7889-2. Epub 2014 Jun 1.


Detection of the food allergen celery via loop-mediated isothermal amplification technique.

Zahradnik C, Martzy R, Mach RL, Krska R, Farnleitner AH, Brunner K.

Anal Bioanal Chem. 2014 Nov;406(27):6827-33. doi: 10.1007/s00216-014-7873-x. Epub 2014 Jun 1.


A sensitive and robust method for automated on-line monitoring of enzymatic activities in water and water resources.

Ryzinska-Paier G, Lendenfeld T, Correa K, Stadler P, Blaschke AP, Mach RL, Stadler H, Kirschner AK, Farnleitner AH.

Water Sci Technol. 2014;69(6):1349-58. doi: 10.2166/wst.2014.032.


Enumerating Microorganism Surrogates for Groundwater Transport Studies Using Solid-Phase Cytometry.

Stevenson ME, Blaschke AP, Schauer S, Zessner M, Sommer R, Farnleitner AH, Kirschner AK.

Water Air Soil Pollut. 2014;225:1827. Epub 2014 Jan 3.


Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study.

Layton BA, Cao Y, Ebentier DL, Hanley K, Ballesté E, Brandão J, Byappanahalli M, Converse R, Farnleitner AH, Gentry-Shields J, Gidley ML, Gourmelon M, Lee CS, Lee J, Lozach S, Madi T, Meijer WG, Noble R, Peed L, Reischer GH, Rodrigues R, Rose JB, Schriewer A, Sinigalliano C, Srinivasan S, Stewart J, Van De Werfhorst LC, Wang D, Whitman R, Wuertz S, Jay J, Holden PA, Boehm AB, Shanks O, Griffith JF.

Water Res. 2013 Nov 15;47(18):6897-908. doi: 10.1016/j.watres.2013.05.060. Epub 2013 Jul 5.


Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers--is it feasible?

Wang D, Farnleitner AH, Field KG, Green HC, Shanks OC, Boehm AB.

Water Res. 2013 Nov 15;47(18):6849-61. doi: 10.1016/j.watres.2013.02.058. Epub 2013 Jul 11.


Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources.

Raith MR, Kelty CA, Griffith JF, Schriewer A, Wuertz S, Mieszkin S, Gourmelon M, Reischer GH, Farnleitner AH, Ervin JS, Holden PA, Ebentier DL, Jay JA, Wang D, Boehm AB, Aw TG, Rose JB, Balleste E, Meijer WG, Sivaganesan M, Shanks OC.

Water Res. 2013 Nov 15;47(18):6921-8. doi: 10.1016/j.watres.2013.03.061. Epub 2013 Jul 5.


Dynamics of natural prokaryotes, viruses, and heterotrophic nanoflagellates in alpine karstic groundwater.

Wilhartitz IC, Kirschner AK, Brussaard CP, Fischer UR, Wieltschnig C, Stadler H, Farnleitner AH.

Microbiologyopen. 2013 Aug;2(4):633-43. doi: 10.1002/mbo3.98. Epub 2013 Jul 4.


Performance characteristics of qPCR assays targeting human- and ruminant-associated bacteroidetes for microbial source tracking across sixteen countries on six continents.

Reischer GH, Ebdon JE, Bauer JM, Schuster N, Ahmed W, Aström J, Blanch AR, Blöschl G, Byamukama D, Coakley T, Ferguson C, Goshu G, Ko G, de Roda Husman AM, Mushi D, Poma R, Pradhan B, Rajal V, Schade MA, Sommer R, Taylor H, Toth EM, Vrajmasu V, Wuertz S, Mach RL, Farnleitner AH.

Environ Sci Technol. 2013 Aug 6;47(15):8548-56. doi: 10.1021/es304367t. Epub 2013 Jul 10.


Clostridium perfringens is not suitable for the indication of fecal pollution from ruminant wildlife but is associated with excreta from nonherbivorous animals and human sewage.

Vierheilig J, Frick C, Mayer RE, Kirschner AK, Reischer GH, Derx J, Mach RL, Sommer R, Farnleitner AH.

Appl Environ Microbiol. 2013 Aug;79(16):5089-92. doi: 10.1128/AEM.01396-13. Epub 2013 Jun 7.


Effects of fluctuations in river water level on virus removal by bank filtration and aquifer passage--a scenario analysis.

Derx J, Blaschke AP, Farnleitner AH, Pang L, Blöschl G, Schijven JF.

J Contam Hydrol. 2013 Apr;147:34-44. doi: 10.1016/j.jconhyd.2013.01.001. Epub 2013 Jan 11.


Holy springs and holy water: underestimated sources of illness?

Kirschner AK, Atteneder M, Schmidhuber A, Knetsch S, Farnleitner AH, Sommer R.

J Water Health. 2012 Sep;10(3):349-57. doi: 10.2166/wh.2012.005.


Development of a new CARD-FISH protocol for quantification of Legionella pneumophila and its application in two hospital cooling towers.

Kirschner AK, Rameder A, Schrammel B, Indra A, Farnleitner AH, Sommer R.

J Appl Microbiol. 2012 Jun;112(6):1244-56. doi: 10.1111/j.1365-2672.2012.05289.x. Epub 2012 Apr 30.


High abundance of genetic Bacteroidetes markers for total fecal pollution in pristine alpine soils suggests lack in specificity for feces.

Vierheilig J, Farnleitner AH, Kollanur D, Blöschl G, Reischer GH.

J Microbiol Methods. 2012 Mar;88(3):433-5. doi: 10.1016/j.mimet.2012.01.009. Epub 2012 Jan 20.

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