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Scientific Program
Course Venue


University Hospital Basel, Clinical Microbiology

Course Organizator

Adrian Egli, University Hospital Basel, Switzerland


Whole genome sequencing offers the opportunity to understand pathogen evolution within and between hosts with highest resolution. This technology becomes increasingly important also for routine diagnostics. The workshop summarizes key aspects of phylogeny analysis in outbreak management and detection of resistance and virulence genes.

University of Cambridge, UK

What the public health specialist can expect from NGS…

Claudio Köser, University of Cambridge, UK



Over the past few years, numerous proof of principle studies have demonstrated the advantages of NGS over traditional genotypic techniques. Yet despite these advances, the clinical utility of NGS for routine diagnostic testing has been overstated by many researchers and sequencing companies. The objective of this talk is to provide an overview of a modern diagnostic microbiology laboratory to analyse at a practical level where NGS might be cost-effective and to highlight were current techniques will remain the standard in the foreseeable future. 

University Hospital Basel, Switzerland

What the Hospital Epidemiologist needs to know about NGS…

Sarah Tschudin-Sutter, University Hospital Basel, Switzerland



In contrast to conventional typing methodologies, next generation sequencing enables to track outbreaks and transmission chains at much higher resolution, facilitating the identification of sources and reservoirs across institutions, countries and continents. Possible identification of mobile genetic elements, such as plasmids, may reveal additional transmission events, which may have been missed previously, thus leading to the detection of additional transmission pathways. The increasing availability and abundance of next generation sequencing data, however, underlines  the need to link this data with relevant epidemiological observations to derive meaningful conclusions

Molecular and Experimental Mycobacteriology

Mycobacteria tuberculosis epidemiology and resistance detection by using NGS

Stefan Niemann, German Tuberculosis Reference Center, Germany



Next Generation Sequencing (NGS) allows for rapid analysis of nearly complete genomes of clinical Mycobacterium tuberculosis complex (MTBC) isolates. NGS based whole genome sequencing (WGS) analysis goes far beyond conventional molecular tests e.g. for drug susceptibility testing by detection of variants in virtually all target genes involved in resistance development (resistome analysis). Simultaneously, it allows for high-resolution strain comparison e.g. for outbreak analysis or even longitudinal genome based molecular epidemiological studies. The application of WGS for diagnostics and strains comparison has become realistic due to the development on so-called bench top NGS systems that can be integrated into a normal laboratory workflow, and allow for WGS of clinical isolates few days and at low costs.

University of Basel, Switzerland

Chlamydia trachomatis evolution and epidemiology

Helena Seth-Smith, University of Basel, Switzerland



Chlamydia trachomatis is a major cause of infectious blindness and sexually transmitted infection, with numbers of cases within Switzerland currently increasing. It is a bacterium with a complex lifecycle, requiring host cells for growth, which makes growth and manipulation in the laboratory non-trivial. Due to this, several novel techniques have had to be developed to allow access to the genomic information within clinical samples. Analysis of large, global collections of chlamydial genomes shows that the small, compact genome is subject to widespread recombination. This appears to be both an ancestral and ongoing phenomenon, with new genotypic combinations found recently in circulating populations throughout Europe and globally.

ETH Zurich, Switzerland

Typing: Taming the beast

Veronika Boskova, ETH Zurich, Switzerland



With the advent of sequencing, phylogenetic and phylodynamic methods
proved to be invaluable in estimating key epidemiological parameters such as
the basic reproductive number and the duration of the infectious period.
Furthermore, these methods provide an estimate of the total infected
population size, a quantity not easily measurable using classic epidemiological
approaches. These methods were in particular applied to sequence data of the
recent West Africa Ebola outbreak and the ongoing Zika epidemic in South
America. Besides between-host dynamics, the tools are also capable of revealing
within-host dynamics of chronic infections such as HIV or HCV. In my research I
focus on development of phylodynamic methods capable of handling large
datasets resulting from next-generation sequencing efforts, which contain
many biological sequence duplicates, and evaluating which methods are most
appropriate for sequence data being collected during epidemic spread.

Biozentrum, Switzerland

WGS and real-time analysis to track and predict pathogen spread

Richard Neher, Biozentrum, Switzerland



Whole genome sequencing is essential to resolve the evolutionary relationships between closely related isolates. WGS data requires substantially more processing and analysis before it can inform public health response. I will discuss recent work on real time phylogenetic analysis and data exploration tools that allow users to interrogate spread and evolution at multiple levels.

University Medical Center, Groningen

Typing: Molecular surveillance of MDR in Europe – call for action

Corinna Glasner, University Medical Center Groningen, Netherlands



Antimicrobial resistance has been declared the largest threat to humans worldwide, with an estimation of 10 Million deaths by 2050 (WHO, 2014). Multidrug resistance (MDR) bacteria, mostly species that are healthcare-associated and part of the human microbiota, are challenging healthcare institutions in many different ways. The occurrences of carbapenemase-producing Enterobacteriaceae (CPE) are the most emerging threat, especially since they are also frequently resistant to many other antibiotics than carbapenems leaving few treatment options. The extent, to which healthcare systems have already been affected, however, differs substantially from country to country. The objective of this talk is to introduce the European Survey of Carbapenemase-Producing Enterobacteriaceae (EuSCAPE) project and elaborate on the specific steps taken to establish a network of laboratories for active molecular surveillance in 36 countries in Europe. The exection and final results of the prospective multinational structured survey on the occurrence of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli in European hospitals will be presented with focus on the molecular surveillance aspect to prevent and control the spread of CPE in Europe.

SIB Swiss Institute of Bioinformatics, Switzerland

Does NGS occur faster with a catalyst? A Swiss perspective

Aitana Lebrand, SIB Swiss Institute of Bioinformatics, Switzerland



According to Wikipedia, “catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst, which is not consumed in the catalyzed reaction and can continue to act repeatedly. Often only tiny amounts of catalyst are required in principle.” During this talk, we will explore the added-value of having a non-medical catalyst within the Swiss NGS clinical microbiology community.

University Medical Center, Groningen

Practical quality control for whole genome sequencing in clinical microbiology

John Rossen, University Medical Center Groningen, Netherlands



Bringing next generation sequencing into the routine clinical microbiology laboratory implies that one have to fulfill several quality criteria. 
In our lab NGS has been accredited conform the ISO 15189 norm. QC and EQA as implemented in our lab will be presented and discussed.


Department of Medical Microbiology & Infection Prevention, University of Groningen, Groningen, Netherlands 
 Dr. John W. A. Rossen has a 25-year history in molecular microbiology and more than 105 peer reviewed publications (> 60 in the last five years; H-index 28). He is Assistant Professor at the University of Groningen, PI in the research group “Genomics for Infection Prevention” of Prof. dr. Alexander W. Friedrich and head of the molecular unit which has recently implemented the use of next generation sequencing for routine clinical microbiology and infection prevention. The method is used to determine the genetic relationship between pathogens (used to guide infection prevention measures) and for the molecular detection and further characterization of (emerging) pathogens. This includes analyses for revealing (new) antibiotic resistance mechanisms and for determining the virulence of pathogens resulting in improved risk assessment and infection prevention. In addition, based on comparing whole genomes of bacteria, tailor-made diagnostic tests are developed used for specific detection of outbreak and or virulent bacterial strains. Nowadays his research is focused on implementing metagenomics into clinical microbiology. Several PhD students, Post-Docs and technicians work together to investigate not only patient samples but also samples taken from animals, food and water - thereby realizing the one health principle in microbiology. Currently, Dr. Rossen is involved in the supervision of 9 PhD students. He is secretary of the ESCMID study group for genomic and molecular diagnostics (ESGMD) and treasurer of the Dutch Society of Medical Microbiology. Disclosure of Interest: None Declared

ETH Zurich, Switzerland

Emerging NGS technologies

Christian Beisel, ETH Zurich, Switzerland

Medical Faculty Lisboa, Portugal

Software pipelines: the good, the bad, and the ugly

Joao André Carrico, Medical Faculty Lisboa, Portugal



It is now clear the impact that the revolution started by High Throughput Sequencing (HTS) had in Clinical Microbiology. These novel technologies allow us to create draft genomes in a matter of days for the approximate same cost of sequencing a dozen of genes using Sanger technology. However,  in order to create those draft genomes or extract the data from the millions of reads created by HTS, researchers are confronted with a plethora of software pipelines. The choice of the pipeline to use can have significant impact on the results since from the reads to actionable results such as determination of antibiotic resistance profiles, strain lineage or presence of virulence factors, are always dependent on the software parameters and databases used. In this talk some software pipelines will be presented and their advantages and caveats discussed.