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Prompt water monitoring and quality control are essential for public health protection and risk regulation. Consequently, the rapid, specific and sensitive detection of microbial indicators and waterborne pathogens represent a key challenge in modern water quality monitoring. In the last years the application of monitoring concepts and technologies was expedited at the TZW as well as at the CSIRO and Griffith University. Both the Australian and German collaborators have developed new methods in these specific areas, which enables deep collaboration and exchange possibilities with great benefits and synergistic effects.

Overarching objectives of the German-Australian collaboration are to optimize and extent monitoring methods of water quality:

  • PCR detection of hygienically relevant microorganisms in different waters
  • Microbial Source Tracking with culture-independent methods
  • Detection of relevant antibiotic resistant bacteria and antibiotic resistance genes
  • Improved methodology for the concentration and detection of viruses from water environments
  • PCR-based live-dead differentiation
  • Application of microarray technology in water monitoring
  • Elimination of hygienic relevant microorganisms during ground water recharge and wastewater reuse
  • Microbiological Risk Assessment


gabi Partners

Australian Partners
Dr. Simon Toze
Simon Toze
CSIRO Land and Water, Brisbane
Simon Toze obtained his PhD in Environmental Microbiology from the University of Queensland in 1992 and has been working with CSIRO since 1994 on a range of water based topics. He is also an honorary Associate Professor with the UQ School of Population Health.
He has a range of research interests which include studying the fate and behaviour of microbial pathogens in the environment; the influence of groundwater microorganisms on the biogeochemistry of aquifers; and the development of rapid and accurate molecular based methods for the tracking, detection and enumeration of viable microbial pathogens in environmental water samples.

Dr. Jatinder Sidhu
Jatinder Sidhu
CSIRO Oceans and Atmosphere, Brisbane
Dr. Jatinder Sidhu is a Senior Research Scientist in CSIRO’s Oceans and Atmosphere Business Unit, and team leader Coastal Microbiology and Biogeochemistry within the Coasts program. Dr. Sidhu’s research focuses on public health and environmental microbiology with an emphasis on the quantification, fate, and transport of pathogenic microorganisms in the environment (stormwater, surface water, marine and coastal water, groundwater, recycled water, wastewater, and biosolids). His research work is also focused on the use of high-throughput genomic technologies for surveillance of pathogens and antibiotic resistance determinants in the environment.
His work includes extensive laboratory-based research to develop and evaluate methods for concentration and quantitation (molecular methods) of enteric pathogens in the laboratory with subsequent application in field-based investigations. The gathered data from the field-based studies is then used for human health risk assessments and development of risk mitigation strategies. The goal of his research is to deliver high-quality science to achieve sustainable use of water resources which meets health and environmental needs at both national and international level. He is a member of Australian Strategic and Technical Advisory Group on Antimicrobial Resistance (ASTAG).

Anne Roiko
Anne Roiko
Environmental Health, Griffith University
Associate Professor Anne Roiko is the Discipline Lead for Environmental Health in the School of Medicine, Griffith University. Anne has over 30 years of professional experience in the field of environmental health, predominantly in academia. She has worked overseas as a researcher in the National Public Health Institute in Finland, the Chinese University of Hong Kong and within the water policy unit of the Environmental Protection Department in Hong Kong. She has an extensive background in transdisciplinary, team-based research, with expertise in quantitative microbial risk assessment, risk communication, health and environment data linkage and systems modelling. Her current research focuses on systems-based modelling of water-related health risks, the transfer of risk-based evidence into policy and predicting and managing the health impacts of climate change.

Declan Page
Declan Page
CSIRO Land and Water, Adelaide
Declan Page holds a PhD in chemistry from the University of South Australia specializing in drinking water quality and management and an MBA from Monash University specialising in research management. He worked for several years in water utilities across Australia in catchment management, source water protection, and supply of water to rural and remote communities before he joined CSIRO in 2005. He has had a significant influence on Australian national guidance and on the science of natural and engineered water treatment and reuse systems with a particular emphasis on Managed Aquifer Recharge. He has published extensively and is a sought after national and international collaborator. He currently leads a high performing research group, delivering water reuse options to meet Australia’s urban water demands. In this work, he advocated consolidation of the assessment and planning stages of such schemes into a single nationally accepted framework and it remains the only national framework consistent with the WHO Drinking Water Guidelines. This work has been further developed by collaboration with international research projects such as the European RECLAIM WATER project where he led the international risk assessment case studies across Europe, China, Mexico, South Africa and Australia. His work in risk assessment and problem solving has contributed to the development of a full-scale follow-on project, SAPH PANI in India.

German Partners
Prof. Andreas Thiem, TZW Karlsruhe
Andreas Tiehm
TZW | Technologiezentrum Wasser
Prof. A. Tiehm, the head of the department Microbiology and Molecular Biology at TZW with experience of health related water microbiology, environmental bioremediation and wide knowledge of water diagnostic. He is leader of international research projects and a leading expert for detection of different bacteria and bacterial groups in water assessment of biodegradation processes, microbiological detection of antibiotic resistance bacteria and application of molecular biological techniques for the evidence of antibiotic resistance genes in water. Furthermore, he has extensive experiences with the elimination of chemical substances and microbial degradation in field applications.

Dr. Johannes Ho
Johannes Ho
TZW | Technologiezentrum Wasser
Johannes Ho obtained his PhD in molecular biology and focused on ecology, evolution and bioinformatics at his Master of Science. He is working on the development of modern detection methods for waterborne viruses and bacteria at TZW since 2010. His current research is focused on molecular detection via qPCR, flow cytometry, live/dead differentation and the concentration of large water volumes.

Claudia Stange
Claudia Stange
TZW | Technologiezentrum Wasser
Claudia Stange graduated with diploma in engineering (main field: biotechnology) at the University of Applied Sciences Mannheim, Germany, in 2005. Since that time she works in the department of environmental biotechnology at the TZW as project scientist. She is particularly experienced in the application of molecular biological analysis of microorganisms (e.g. pathogenic and indicator) organisms), antibiotic resistance genes and Microbial Source Tracking markers.

Lab | Equipment

Molecular Biology
Lab for the concentration, extraction and detection of bacteria, viruses and functional genes e.g. for antibiotic resistances and microbial degradation of various contaminants. Organisms are concentrated and their DNA and RNA is extracted with chemical or physical treatment and purified for post applications. Several approaches are available for quantification of specific DNA or RNA sequences following quality control and deeper analysis.

Pre PCR preparation
  • high volume ultrafiltration
  • membrane filter device for size or charge based concentration
  • automated DNA/RNA extraction
  • automated sample homogenizer
molecular detection
  • real time PCR systems
  • digital droplet PCR
  • gradient PCR
  • end point PCR
  • automated pipetting systems
  • PCR workstations
post PCR
  • automated capilary electrophoresis system
  • classical electrophoresis
  • DGGE (Denaturing gradient gel electrophoresis)
  • freeze-dryer
  • vaccum centrifuge
Lab for cultivation techniques around indicator bacteria and health related organisms like antibiotic resistant bacteria, bacteriophages and legionella. Additional analytical methods like AOC (assimilable organic carbon) or MALDI-TOF-MS can give a deeper view in bacterial communities.

  • classic cultivation methods (indicators, hygiene relevant bacteria, antibiotic resistant bacteria)
  • viral plaque assay
  • flow cytometer and cell sorter
  • fluorescence microscope
  • binoculare stereomicroscope
  • AOC-Systems (Assimilable organic carbon)


The GAbi project is one of 27 projects funded by the German Federal Ministry of Education and Research (BMBF) in the frame of the APRA program to establish joint research centres with partners in the Asia-Pacific Research Area (APRA).

News & Events

February 2022 Joint method development for the detection of antibiotic resistance genes (next phase)
For combined detection of antibiotic resistance genes, a list of nearly 200 gene targets including PCR primers was identified and ranked. This work was the final step before lab work can be initiated - moving from in-silico to in-vitro. The planned work will be divided to TZW and CSIRO labs as each partner has a different set of control DNA available. After establishment, both partners will combine their material.

August 2021 New postdoc at CSIRO
Dr. Heng Ku - a bioinformatics specialist - joined the team at CSIRO. With his expertise, he will enrich the Gabi project with regard to metagenome analyses and will cooperate closely with Dr.Johannes Ho at TZW.

March 2021 Joint method development for the detection of antibiotic resistance genes
Both CSIRO and TZW researchers started working on an array based assay for the parallel detection of multiple antibiotic resistance genes. In the initial steps, primer sequences combined of both institutes were reviewed and analyzed with bioinformatics. The first task was to optimize each primer to allow a combined detection on a single plate.

September 2020 Joint manuscript deaccepted for publication
A joint manuscript written by researchers from CSIRO and TZW was accepted for publication in the International Journal Water Research. The research focusses on understanding movement and prevalence of microbial communities carrying antibiotic resistance genes (ARGs) and virulence genes (VGs) in aquifers recharged with storm water. This investigation is essential to comprehend potential human health risks from reused water and improves the current understanding of groundwater recharge technologies.

August 2020 Joint method development and optimization for SARS-CoV-2
Both CSRIO and TZW research groups exchange information on concentration, extraction and detection methods for SARS-CoV-2 in wastewater. As initial step, published primers and probes for SARS-CoV-2 qPCR based detection were compared using bioinformatics and experiments in the labs. Additionally, the development process builds on past cooperative work in the GAbi project in the last years regarding virus detection from surface waters.

March - Juli 2020 Identification of a new joint research topic
Due to the COVID 19 pandemic, planned visits and experimental work in Australia unfortunately had to be cancelled. But the pandemic also offers a new opportunity for joint research activities. The gabi partners began to develop molecular biological methods for the detection of SARS-CoV-2 . The quantification of SARS-CoV-2 in wastewater affords the ability to monitor the prevalence of infections among the population via wastewater-based epidemiology (WBE).

9.-12. October 2019 The TZW could welcome Dr. Jatinder Sidhu in Karlsruhe
The long-standing cooperation partner Dr. Sidhu visited Germany. During intensive conversations, laboratory results were exchanged and further joint studies planned. Especially the procedure for metagenome analyses and a concept for investigating the occurrence and elimination of antibiotic resistance genes and antibiotic resistant bacteria in wastewater treatment at a special treatment plant was discussed.

15.-20. September 2019 Presentation of the GAbi project at an international conference
The 20th International Symposium on Health Related Water Microbiology covered all aspects of health related water microbiology in the whole water cycle, applied and basic research on water and microorganisms as it impacts human health. In the context of this event the participants were informed about the GAbi project. Stimulating discussions during the poster session showed the interest of the researchers in this project.

12. and 13. September 2019 Delegation of the Griffith University visits the TZW in Karlsruhe
The TZW was pleased to welcome Anne Roiko and Sonya Kozak from the School of Medicine at the Griffith University. Both gave an overview about a recent project on the comparison of microbial health risks associated with alternative approaches to managing sewer overflows using integrated modelling. Afterwards, Beate Hambsch, Johannes Ho and Claudia Stange from TZW showed current work on the quantitative microbial risk assessment (QMRA). The relevance of adenovirus and Cryptosporidium in Australian and German surface waters were discussed. Furthermore, considerations on the integration of antibiotic resistance into the QMRA were advanced.

19. August 2019 Strengthening the partnership with CSIRO Land and Water
Dr. Warish Ahmed, a senior research scientist of CSIRO Land and Water visited the TZW in Karlsruhe. He is expert on identifying the point and non-point sources of microbial contaminants in catchment and recreational waters. Together a small study on the elimination of microbial source tracking markers, antibiotic resistance genes and viruses during wastewater treatment has been designed.

February 2019 Joint Australian-German manuscript published
A joint manuscript written by researchers from CSIRO and TZW was accepted for publication in the International Journal of Hygiene and Environmental Health. The publication is entitled “Comparative removal of antibiotic resistance genes during chlorination, ozonation, and UV treatment”. In this study the removal of antibiotic resistant bacteria and antibiotic resistance genes by three disinfection processes (chlorination, ozonation, and UV treatment) was investigated on a laboratory scale.

Dezember 2018 Exchange | Australian study project in Germany
Within the framework of GAbi, a student from Griffith University could perform a study project in Germany. Katharina Gutjahr-Holland focused on the detection of antibiotic resistant bacteria, the genes and mobile genetic elements in raw water used for drinking water production. She successfully learned to use cultural methods and molecular biological techniques for the detection of antibiotic resistance in the environment. In a next step, evaluation of suitability of these methods for quantitative microbial risk assessment (QMRA) will be performed in cooperation with her supervisor Prof. Anne Roiko, Griffith University.

16. October 2018 Workshop with CSIRO Perth
To further strengthen the cooperation with CSIRO, a workshop with representatives of different departments was organized in Perth. In the meeting, Dr. Anna Kaksonen, group leader of Biotechnology and Synthetic Biology, introduced CSIRO work in the areas (1) biodegradation of environmental pollutants, (2) biological and chemical research into biotransformation processes and (3) monitoring of microbial communities in natural and engineered environments. The workshop helped to identify additional topics for the next 3 years cooperation research proposal.

15. October 2018 Meeting, Workshop and field survey with CSIRO Land and Water Adelaide
In Adelaide, the GAbi project partners met the group of Dr. Declan Page at CSIRO Adelaide. Dr Page is head of Groundwater Contamination and Remediation at CSIRO. His research focusses on water reuse and especially managed aquifer recharge. During the meeting, results from previous sampling campaigns were exchanged, discussed and prepared for joint paper to be published with Dr. Jatinder Sidhu and Dr. Simon Toze (CSIRO Brisbane). Additionally, CSIRO pilot test sites were visited and future joint research topics identified.

11. October 2018 Preparation of Cooperation Agreement with Griffith University, Brisbane
Prof. Anne Roiko organized a meeting at Griffith University. Dr. Simon Toze (CSIRO), Prof. Andreas Tiehm and Claudia Stange (TZW) attended the meeting and presented the GAbi project concept. Prof. Anne Roiko has over 30 year experience in environment and health topics. During the meeting, cooperation in the areas of risk assessment and risk communication, the share of heath related and environmental data as well as system modelling were discussed. The cooperation agreement between TZW and Griffith University was prepared, and officially signed afterwards. The research concept for visits of two Griffith University students to TZW in Germany was another successful outcome of this meeting.

October 2018 Workshop at the University of Queensland, Brisbane
At the first GAbi workshop in march 2018, TZW and CSIRO project members met Dr. Jianhua Guo, expert in microbiology and group leader at the Advanced Water Management Center (AWMC) of Queensland University. As result of shared research topics, a second GAbi workshop was organized at Queensland University. Scientific topics such as the spread of antibiotic resistance and biological pollutant degradation in contaminated groundwater were presented to a larger audience of about 50 students at Queensland University. Future cooperation is foreseen with joint research e.g. focusing on antibiotic resistance genes transfer and exchange of students.

October 2018 TZW Meeting with CSIRO Brisbane and Fiji National University
The October 2018 travel to Australia started at CSIRO Brisbane for a meeting with Dr. Simon Toze and Dr. Jatinder Sidhu to update latest research results. Future sampling campaigns and the proposal concept for next 3 years cooperation were developed. As important result of the first GAbi cooperation period, two manuscripts for international journals were prepared.
GAbi project partners Professor Andreas Tiehm and Claudia Stange (TZW) also met with Dr. Andy Steven, research director of CSIRO Ocean and Atmosphere, and Professor Paul Jagals from Fiji National University. The sanitation and monitoring concept on south pacific islands was discussed as well as suitable measures to assess microbiological water quality in this region as part of the GAbi project.

March 2018 GAbi Workshop - Workshop at CSIRO with speakers from science and industry
The first GAbi workshop focused on recent progress in water science, research needs, and opportunities for joint German-Australian studies. Beside presenters from CSIRO and TZW, speakers from the Australian waterworks, the University of Queensland and the Global Water Research Coalition (GWRC) gave an overview of current research needs. Therefore the workshop could cover broad topics from local to global interest. Additionally, detailed talks were hold focusing Microbial Source Tracking, detection methodologies, antibiotic resistances and issues with indicators. Finally, in a round table discussion, details of the future partnership and cooperation with universities were discussed. At this point we like to thank everyone for a very successful workshop with fruitful discussions.

Topics and speakers of the GAbi Workshop

GAbi PartnershipWelcome, Acknowledgement of Country, Introduction, HousekeepingSimon Toze, CSIRO
GABI Project – Inception and intentAndreas Tiehm, German Water Technology Center (TZW)
CSIRO Partnership – Engagement and purposeSimon Toze, CSIRO
Research NeedsLocalGreg Jackson, Brisbane Waterworks
EuropeAndreas Tiehm, TZW
South PacificPaul Jagals, University of Queensland
GlobalStephanie Rinck-Pfeiffer, Global Water Research Coalition
Research ToolsMicrobial Source TrackingWarish Ahmed, CSIRO
Detection methodologiesJohannes Ho, TZW
Antibiotic ResistancesClaudia Stange, TZW
Issues with indicatorsJatinder Sidhu, CSIRO

February - May 2018 Scientific exchange

Hygienic quality at bathing beaches
Five sites including bathing beaches were sampled in a dry period in the area around Brisbane. Multiple samples had already been taken by CSIRO staff in the previous wet season. Two liters of samples were each taken to the CSIRO lab and prepared for downstream analysis:

Human pathogen Viruses
Samples were concentrated using a multi-step ultrafiltration from one liter to 3 milliliters. After extraction of RNA and DNA, samples were prepared for the detection of viruses in Germany. Target organisms are human pathogenic viruses like norovirus or enteroviruses. The analysis will help understanding the distribution of RNA-Viruses in surface water during dry and wet periods.

Antibiotic resistance and indicator organisms
Due to the widespread use of antibiotics in human and veterinary medicine, resistances have spread in the environment during the last few years. However, knowledge with respect to antibiotic resistant bacteria and antibiotic resistance genes in raw water used for drinking water production is limited. To help understanding the distribution of antibiotic resistant bacteria at public beaches, selective agar plates were used to prove the presence of Vancomycin resistant enterococci (VRE), Methicillin resistant Staphylococcus aureus (MRSA) and Extended spectrum beta-lactamase (ESBL)-producing coliform bacteria. Since VRE, MRSA and ESBL can cause severe infections, these types of antibiotic resistant bacteria are highly relevant.

Training: Analysis of microarray data
Microarrays are a promissing tool to reveal the pathogenic potential of microbial communities. Highly parallel microarrays provide a culture-independent method that permits over 100.000 of assays to detect target genes – e.g. involved in antibiotic resistance - in a single run. Beside the preparation of nucleic acids for the analysis, the complex result data structure has to be analyzed and interpreted. During the scientific exchange, TZW researchers were trained in a data processing pipeline including analytical tools. In conclusion, current microarray data could be analyzed and displayed constructively to give information about antibiotic resistance and pathogen profiles.

November 2017 - February 2018 Preparation of CSIRO/TZW visit
The upcoming meeting of CSIRO and TZW in March 2018 is planned in frequent video conferences. The current scientific program includes field studies in the area around Brisbane, Lab analysis of antibiotic resistant bacteria and RNA viruses as well as a deep knowledge exchange focusing microarray technology.

02 October 2017 Kick-off workshop of the project in Brisbane
Exchange of information about running and planned projects Reports about the progress in the molecular analysis of water Planning of the joint work.


Sidhu J.P.S., Gupta V.V.S.R., Stange C., Ho J., Harris N., Barry K., Gonzalez D., Van Nostrand J.D., Zhou J., Page D., Tiehm A., Toze S.:
Prevalence of antibiotic resistance and virulence genes in the biofilms form an aquifer recharged with stormwater,
Water Research 185:116269. doi: 10.1016/j.watres.2020.116269 (2020 )

Stange C., Sidhu J.P.S., Toze S., Tiehm A.:
Comparative removal of antibiotic resistance genes during chlorination, ozonation, and UV treatment.
International journal of hygiene and environmental health 222, 3: 541–548 (2019). DOI: 10.1016/j.ijheh.2019.02.002

Sidhu J., Ho J., Stange C., Smith K., Ning D., Wu L., Zhou J.:
Microbial community structure and diversity of activated sludge in wastewater treatment plants located in different climate zones of Australia.
In: 20th Symposium on Health-Related Water Microbiology (HRWM), Wien, Österreich, 15.-20. September 2019. ISBN 978-3-9503828-3-9, Book of abstracts: 92 (2019)

Stange C., Sidhu J., Roiko A., Page D., Ho J., Toze S., Tiehm A.:
German-Australian Cooperation for Water Microbiology.
In: 20th Symposium on Health-Related Water Microbiology (HRWM), Wien, Österreich, 15.-20. September 2019. ISBN 978-3-9503828-3-9, Book of abstracts: 124 (2019)

Tiehm A., Stange C., Sidhu J., Toze S.:
Removal of antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) during drinking water treatment.
In: 20th Symposium on Health-Related Water Microbiology (HRWM), Wien, Österreich, 15.-20. September 2019. ISBN 978-3-9503828-3-9, Book of abstracts: 191 (2019)

Ho J., Sidhu J., Toze S., Tiehm A.:
Molecular biological live/dead differentiation in water treatment
In: Annual Conference of the Association for General and Applied Microbiology (VAAM), Wolfsburg 15.-18. April 2018, Book of abstracts: EMP156, 142 (2018)

Stange C., Sidhu J., Ho J., Toze S., Tiehm A.:
German-Australian Cooperation for Water Microbiology.
In: Annual Conference of the Association for General and Applied Microbiology (VAAM), Wolfsburg 15.-18. April 2018, Book of abstracts: EMP166, 146 (2018)

Stange C., Sidhu J., Toze S., Ho J., Tiehm A.:
German-Australian Joint Lab on Health-Related Water Microbiology.
In: One Health & Food Safety Congress, Bonn 18.-19. September 2018, Proceedings, 111 (2018)

Stange C., Sidhu J., Toze S., Ho J., Tiehm A.:
Occurrence of Antibiotic Resistant Bacteria and Resistance Genes in Surface and Ground Water.
In: Annual Conference of the Association for General and Applied Microbiology (VAAM), Wolfsburg 15.-18. April 2018, Book of Abstracts: EMP167, 146 (2018)

Stange C.,Sidhu J.P.S.,Tiehm A.,Toze S.:
Antibiotic resistance and virulence genes in coliform water isolates.
International Journal of Hygiene and Environmental Health 219: 823-831 (2016). 10.1016/j.ijheh.2016.07.015 

Schmidt N., Page D., Tiehm A.:
Biodegradation of pharmaceuticals and endocrine disruptors with oxygen, nitrate, menganes(IV), iron(III) and sulfate as electron acceptors.
Journal of Contaminant Hydrology: 203: 62-69 (2017)

Otto J., Sidhu J., Toze S., Tiehm A:
Comparing methods for virus and bacteria concentration from different water sources.
In: 17th International Symposium on Health Related Water Microbiology, IWA WaterMicro 2013, Florianopolis, Brazil, 15-20 September 2013, Proceedings: 2 pages (2013)

Tiehm A., Sidhu J., Toze S., Stoll C.:
Antibiotic resistance genes and virulence genes in surface water samples from Germany and Australia.
In: 17th International Symposium on Health Related Water Microbiology, IWA WaterMicro 2013, Florianopolis, Brazil, 15-20 September 2013, Proceedings: 3 pages (2013)

Stoll C., Sidhu J.P.S., Tiehm A., Toze S.:
Prevalence of clinically relevant antibiotic resistance genes in surface water samples collected from Germany and Australia.
Environmental Science & Technology 46: 9716-9726 (2012)


Aktueller Flyer des GAbi-Projektes.

Projektblatt für Projekte des BMBF-Förderprogramms zur Etablierung gemeinsamer Forschungspräsenzen mit Partnern im Asiatisch-Pazifischen Forschungsraum (APRA)

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