applied microbiology research lab

We are very pleased to welcome Ana Gabriela from Colombia. Ana will spend a year in the lab to pursue her bachelor's thesis and internship, she will work heavily on the AMREvo project with Elisa.

We are very pleased to welcome our new lab technician Anna Diversi. We wish Anna all the best in her new role and a wonderful start in Zurich!!!

Hearty congratulations to Priya on her successful master's thesis defense on fungal genomics. We thank Priya for her efforts in establishing fungal genome sequencing with ONT and wish her all the best.

We congratulate Thiviya Punniyamoorthy for her excellent bachelor thesis on skin microbiome control. She has successfully defended her thesis during the exam at the Fachhochschule Nordwest Schweiz. Thank you for your engagement and hard work for the group. We wish you all the best for your future endeavors.

We are pleased to welcome Joy Scherrer, who will do her one-year apprenticeship in our lab. We wish her a wonderful and interesting time with lots of new techniques to learn.

Helena has been a core member of AMR for many years, bringing her expertise, passion, and friendliness to the table. She is now launching a new phase with her own research group. Her focus is on obtaining genomes from clinical samples without culture. For more information on Enriching Microbiology, be sure to check her website: https://enrichingmicrobiology.net/.

She is very grateful for the opportunities, interactions and support over the years within AMR. We look forward to future exchanges and continued collaborations. Here’s to many more years of groundbreaking research and enriching the world of microbiology!

The AMR group had a wonderful 2-day retreat in the beautiful Walensee, Even though the weather was in low spirits, the group was in high spirits enjoying the swim and cruise in Walensee. We also had a range of scientific sessions on publishing, pitching, and the role of ChatGPT in research. We are already looking forward to the 2025 retreat!!!.

We have some significant updates to share about our research group. As we continue to evolve and grow, we must also acknowledge the contributions and departures of key team members who have been instrumental in our success.

Elena bids adieu to the group. We thank Elena for her excellent assistance in developing new PCR assays for studying nasal microbes and wish her good luck in her future endeavors.

We are very pleased to welcome Ashley Rooney to our research group. Ashley has joined our group as a  Post-Doc, where she will be working on metagenomics with ONT. We wish Ashley a great start.

We are very pleased to welcome Mariella Greutmann to our group. Mariella will work on bacterial evolution in patients with prolonged antibiotic treatment. We wish her a great start.

With great pleasure Prof.Dr.Dr. Adrian Egli gave his inauguration lecture on the topic "Why do bacteria make us sick?". Many thanks to all the people who attended in person and online for this personal and very special moment. Please find the link for the talk here.

A warm welcome to our three (!) new students!

Thiviya does her BSc at the FHNW and will do an internship for 6 months, supervised by Tim. 

Priya, an MSc student at the VU Amsterdam, will do her Master's project for 6 months, supervised by Fanny and Adrian. 

Laze does his MSc at ETH and will do a 12-week internship, supervised by Diana.

We wish you all a good start!

Marco leaves us for pastures new. We thank Marco for his contributions to 16s metagenomics sequencing and analysis. We wish him all the best in his future endeavors. 

We extend a very warm welcome to Eline Meijer. Eline has joined the group as a PhD candidate in the Data science program. We wish her a great start.

We are delighted to welcome our new research assistant Désirée Tischli to our group. We wish Désirée a wonderful start in the lab.

We are very pleased to welcome our new research assistant Elena Melgarejo Ros to our lab. We wish Elena a very great start.

We are very pleased to welcome our new intern Vera Bregy to the group. Vera will have hands-on experience in extracting DNA from Chlamydia species using Agilent Sureselect probes. We wish Vera a good start to her internship.

We are very delighted to welcome Klara Haldimann to the group as our new lab technician. We wish her a great start in the lab.

We congratulate Vanni on successfully defending his Master's Thesis! Of course, this called for a spontaneous lab trip to the pub. 
After some well-deserved holidays, Vanni will return to our lab as a Software engineer and Bioinformatician. Cheers to you, Vanni! 🍻🎓

Through great teamwork, we successfully completed our relocation from Basel to Zurich, and have now our complete sample collection united, stored and inventoried in Zurich. 

We had an amazing two-day lab retreat in Kandersteg packed with speed networking, data management workshops, and a hike down to Oeschinensee.

Christina leaves us for pastures new. We thank Christina for her contributions to the group and wish her good luck!!!

Viviane has successfully finished her internship with us. We thank Vivi for helping us to optimize the nanopore 16s ribosomal operon sequencing and wish her good luck.

Ashim has successfully completed his rotation in UZH and moving to Biozentrum in Basel to continue his Ph.D. journey. We wish him all the best in his future endeavors.

We are very happy to welcome our new lab technician Ana Maria to our group. We wish Ana a very good start in the lab.

Last week, we trained colleagues Veronica Misana and Nasoro Lilolime from the Ifakara Health Institute as well as Venessa Trefzer from the Swiss Tropical and Public Health Institute in Illumina library prep and sequencing of TB isolates on the MiSeq. We wish them good luck in setting up a sequencing workflow in their respective labs!

We warmly welcome Karina, a PhD student from Buenos Aires, joining us for 6 months! She will be analysing genomes of Chlamydia trachomatis.

Nine months after arriving in Zurich, we are officially all settled in the (wet) lab. Time for an apéro! Here are some pictures. 

A warm welcome to Claudia, our new lab technician, to Karl, an intern in his gap year between high school and university, and to Noel, who is doing part of his BSc thesis in our lab! We are delighted to see our group growing with so many new faces. 

We are very happy to welcome our new intern Viviane to the group. Viviane will be working in 16s ribosomal operon sequencing using the long read nanopore sequencing platform. Have a great start Viviane.

We are very delighted to welcome Christina to our research group. Christina will be working as a lab technician and we wish her a great start.

We are very happy to welcome Zoey to our group for her Phd. Zoey will work on Capnocytophaga canimorsus. We wish her a great start for the Phd.

We are very delighted to welcome back Aline Cuénod. Aline has joined the group as a Post-Doc to setup the MALDI-TOF pipeline. We wish Aline a great start.

We are pleased to welcome Elisa to our group. Elisa will spend some time with our group as an intern learning the sequencing techniques. We wish Elisa a great start.

We are pleased to welcome Ashim to our group. As a part of his NCCR Antiresist Phd program, Ashim will spend some time with our group in learning whole genome sequencing of E.coli isolates. We wish Ashim a great start.

The Applied Microbiology Research lab starts its next adventure at the Institute of Medical Microbiology, University of Zurich (www.uzh.ch). Our research focus will remain on host-pathogen interaction and risk profiling of bacterial pathogens. Please check out the Institute website: www.imm.uzh.ch to learn more about the Institute – its diagnostic and research focuses.We look forward to meet and collaborate with new colleagues!

We had a lovely lab retreat at the Engelberg filled with science, brainstorming sessions in boats, glacier walk and beautiful views.

We thank Michéle for the great master thesis work and the following two months in developing bioinformatics pipeline. Your help to develop a new AMR tool and to transfer this into routine applications was very important. It was great to work with you and thank you for all the great moments!. Wish you all the best for your future endeavours.

Michèle has successfully submitted her Master's thesis. Her thesis work was focussed on benchmarking bioinformatics pipeline for resistance gene prediction from whole genome sequencing data.

Hearty congratulations to Aline for her very successful PhD thesis defence with high impact publications. We celebrated it with an amazing pizza dinner at the Vito's.

After 9 years in Basel, Adrian Egli was elected as Professor of Medical Microbiology and new Director of the Institute of Medical Microbiology at the University of Zurich.

In August 2022, our research team will move from the “Zentrum für Lehre und Forschung” in Basel to our new home on Gloriastrasse in Zurich (https://www.imm.uzh.ch/de.html). We want to thank all our many wonderful collaboration partners both in and outside Basel – these interactions are very important to us. Thank you and more details of our move will follow.

Denise Waelchli has joined our group for her Bachelor's thesis. We extend a warm welcome and wish her good luck for the project.

We would like to wish all our team, collaborators, readers, families and all and sundry a HAPPY NEW YEAR! Hoping for further interesting projects, successful collaborations, accepted manuscripts, and great team interactions this year!

Who says you can't have fun on zoom?! With a lovely Gourmet dinner each, partly to prepare at home, good chats and a VERY special guest star, we whiled away some fun hours and felt the season's spirit! HAPPY CHRISTMAS!!

We had an amazing lab retreat at Creux du van. A day filled with an exhilarating hike, cheese, fine food and fascinating views, including steinbock!!!

We are very pleased to welcome Yukino. She has joined our group as a Lab technician. We wish Yukino a great start.

Michèle has joined our group to carry out her Master's thesis. We extend a warm welcome to Michèle and wish her a great start.

We are very pleased to welcome Alexander to the group, as our Laboratory Technician and wish him a great start.

Laurent has joined our group for his observership program. We extend a warm welcome to Laurent and wish him a great start.

Michael also leaves us this week, having completed his project. We enjoyed your time with us and we wish you the best for the future!

We are sorry to say goodbye to Myrta. She has brought fantastic geographic insights to our lab and we wish her well in her next role.

Many thanks to Madlen for her valuable work and contributions to the SARS-CoV-2 analysis efforts in the lab. We wish you very well in your future role!

Dr. Janina Linnik is leaving our group for pastures new, after a successful PhD. It's been an absolute pleasure to work with her, and the learning was definitely on both sides. We are thrilled that she has landed her dream job, and we wish her all the best for her future!

We are pleased that Dr Giovanni Ghielmetti is joining our team for 6 months as a visiting scientist. He will be analysing Campylobacter genomes and we look forward to sharing expertise with him!

Our team is ever expanding!

And is reflected now up-to-date in our new group picture, courtesy of Stefan Auf der Maur.

Dr Marco Meola joined our group as a Post Doc. We are very pleased to welcome him and wish him a great start.  

Dr Veronika Muigg brings her expertise in family medicine and tropical medicine to the group, as she starts at the Division of Clinical Bacteriology and Mycology with her FAMH training. Welcome!

We are excited and grateful that Dr Michael Biggel from the Institute for Food Safety and Hygiene at the University of Zurich is taking on a couple of small projects for us. We look forward to exploiting your expertise!

We are pleased to add another member to the group. Dr Fanny Wegner has joined us as a PostDoc continuing our research into SARS-CoV-2. Welcome!

We are pleased that Vanni Benvenga has joined the AMR team for his Bachelor's thesis. We welcomed him with a small, distanced event.

We are happy that Danica Nogarth is joining the lab team from today. Welcome to the AMR group!

We are very pleased to welcome Srinithi Purushothaman to the AMR group for her PhD. In normal times we'd celebrate better than with just a zoom coffee...

We are pleased to welcome Stefanie Heller to the lab, as our latest Laboratory Technician. Sorry we can't hang out much at the moment, Stefanie, but we're very happy you've joined us!

A sad farewell to Ann Kathrin after her 11 week internship with us. Good luck with the bachelors. We hope to see you again!

After his very successful years in the AMR team, Yaseen has finished his PhD and numerous publications, and is moving to fresher fields. We will miss him greatly. As important as anything else, he can give a great party!

Dr Madlen Stange in our team has been awarded a Leibniz Professorship at the Zoological Research Museum Alexander Koenig (ZFMK) - Leibniz Institute for Animal Biodiversity. We hope that she has enjoyed her distraction with viral genomes, we look forward to the next few months working with her, and wish her the best for her professorship!

Our farewell to Alex was our first event in months, and also an opportunity to celebrate Josi's time with us. Still under COVID-19 restrictions, but very nice to have a social interaction with the group!

We are pleased that Ann-Kathrin Schlotterbeck is joining us for a two month internship. We hope you learn lots!

We are pleased that Myrta Brunner is joining our group 20% as a student research assistant. Following her BA in religious studies and geography, she is now studying the interdisciplinary MA religion – economics – politics.

We warmly welcome Dr. Kirstine Kobberoee Soegaard in our research group. Kirstine moved to Basel from Denmark, where she did a training in clinical microbiology and has a PhD in clinical statistics. Here in Basel, Kirstine who works parts in clinical microbiology routine diagnostics but also parts in research projects. She currently helps with a few SARS-CoV-2 related projects. Welcome and have a good start!

The new coronavirus SARS-CoV-2 has a tremendous impact on individual life - especially for the elderly. The public health measures were necessary to control the ongoing viral transmission and protect high risk groups. The University of Basel and our Department contributed to these measures - research activities slowed down for most of us. My research team helped in the routine diagnostics of the University Hospital Basel to manage the large amount of samples from COVID-19 patients. In addition, my team rapidly established a protocol to sequence SARS-CoV-2! The sequences have been shared via Nextstrain. Thereby we contribute to molecular epidemiology to better understand the transmission. Finally, we help with data structuring and analysis from the Hospitals Clinical Data Warehouse. We also help to build various biobanks and submited ethical and research proposals. This would not be possible with such a great team and the hard work of all members of my research group! It is a difficult time for all of us, but you all make the best of it and help with your dedication and enthusiasm! Thank you for this!

We are pleased that Dr Madlen Stange will be joining us to help with bioinformatic analysis. Welcome, Madlen!

Josiane Reist, who completed a very successful Masters with us and stayed as a lab technician, made a further leap in social distancing and will be moving on to pastures new. We thank her very much for all her hard work and wish her the best for her new position.

We are very pleased to welcome Diana Albertos Torres and Michael Schweitzer to the group. Given the current situation, we have yet to all meet in the flesh, but we are looking forward to lots of exciting research when we are let back in the lab!

Many thanks and a fond farewell to Daniela Lang, and best wishes for the future!

We thank Olivia Grüninger for her work in our team (and cake!), and wish her the best for the future!

Wishing all our readers, collaborators and fellow scientists a very happy and successful 2020.

Adrian Egli was promoted to Professor in Experimental Medicine on the 22^nd of November. Thanks to all the supporters and collaborators!

UniNews

Today was our last day working with Dr Daniel Wüthrich, who is moving to a different position in Bern. We have made great progress, and it has been a pleasure!

A hearty welcome to Dr Tim Roloff, coming with experience at the FMI and Idorsia, who will advance our NGS facility even further!

We are thrilled that Dr Alfredo Mari has joined us from the University of Tuebingen, to work on projects related to Personalised Health Basel.

We are very happy to welcome Olivia Grüningen to the Applied Microbiology Research team. She will be helping the project to move smoothly, as a Research Assistant. We look forward to working together!

Today we bid a sad farewell to Dr Ferdinando Bonfiglio, who is moving to a position in Lugano. It won't stop us collaborating in the future though! All the best for your future!

Exciting science on Interferon lambda with Dr. Marc Bienias from Dresden, followed by great art and food - Marc, was a pleasure to host you in Basel!

Thanks to Anne and Josiane for arranging a lovely evening with the research teams from the AMR group and Prof. Dr. Nina Khanna's group. Topically, we learnt how to play Krobs!

As if a slap up meal weren't enough for Christmas team building, we also were challenged to Room Escape Basel, solving puzzles to reach the goal and escape the room. Super fun!

We would like to congratulate Josiane Reist on the very successful conclusion of her Master of Science in Life Sciences from the University of Applied Science and Arts Northwestern Switzerland. Her thesis is on "Chicken meat as a potential source of campylobacteriosis: a three year comparative study in the area of Basel, using Whole Genome Sequencing (WGS)"

We are pleased to announce that she will be staying on with the group as a research assistant, and will be extending her Campylobacter study.

Inspired by top-of-the-league team work, we had a great day sharing our work and brainstorming.

We enjoyed great science and fabulous views at Pilatus, brainstorming on projects and enjoying each others' company! Lots of ideas to follow up on...