Resistance after long term antibiotic treatment

Elodie Charvet from France has been in Oslo this summer, doing an internship with professor Fernanda Petersens research group. She has looked at samples from patients who have been treated with antibiotics for a whole of three months.

- I study biotechnological engineering at Polytech Clermont-Ferrand, and I heard about this opportunity from a friend who did her internship with the Microbiome and Antibiotic Resistance research group last year. My friend was very happy with everything: the lab, the team and the city, and since I wanted to go to a Nordic country it sounded perfect for me.

Image may contain: pharmacy technician, research, chemist, medical assistant, medicine.
Elodie Charvet has spent the summer in the lab in Institute for Oral Biology. Photo: Ingar Arnodd Storfjell, OD/UiO

Interdisciplinary research group

Professor Petersen and her group have received students from abroad before. This winter, Leonardo from Brasil spent three months with the group. - Our experience with the students from Polytech Clermont-Ferrand has been excellent, says professor Petersen, and she is happy to hear that also Elodie enjoyed her stay in Oslo:

Professor Fernanda Petersen
Professor Fernanda Petersen

- It is important for us that students participating in ERASMUS programs have a good experience at our faculty. The students participate in ongoing projects, but with a plan that they help designing together with other members of the group. The group is interdisciplinary, and this helps the students to immerse into the dynamics of working with professionals with different backgrounds. For us, receiving students from other countries exposes the group to new cultures and new forms of communication. It also gives young researchers in the group the opportunity to acquire experience in research supervision.

Patients with back pain on long term antibiotics

Elodie is part a project studying the effects of long-term antibiotic treatment on patients. Some studies have shown that long-term antibiotic treatment, up to three months, is beneficial for patients with chronic lower back pain, and the project examines samples from one of these studies.

- For our purposes, it is interesting to see what such a long treatment with antibiotics does with the antibiotic resistance levels in the patients’ microbiota, says Elodie.

- I have studied samples from the saliva of 7 patients who received the antibiotic amoxicillin, and 9 patients who got a placebo. We have three different samples from each patient: before they started the antibiotic treatment, right after the treatment was over, and one year after the treatment. We have some first results, but it’s hard to make any interpretation yet.

Image may contain: circle, glass.
Patients' samples - from left to right: Control plate, baseline test (day 0 of the antibiotics treatment), 100 days after the treatment started, 1 year after the treatment started. - We saw that many patients had resistant genes also before the treatment, Elodie says. - But it is exciting to see if the genes that show resistance after the treatment are the same as the resistant genes at day zero. Photo: Elodie Charvet

Preparing the samples for DNA sequencing

Elodie's work focuses on functional metagenomics - a method by which DNA fragments from a community of microbes are inserted into a bacterial host, with the aim of identifying the function of specific genes. If a DNA fragment carries for instance an antibiotic resistance gene, this will enable the bacterial host to grow in the presence of the antibiotic. In this methodology, fragments are ligated to specific markers that allow the easy identification of the antibiotic resistance genes by DNA sequencing

In this project, the bacterial host Escherichia coli is used. It is itself sensitive to antibiotics, but becomes resistant when it receives DNA from the microbial community that confers antibiotic resistance.

- What I have been doing is to prepare this material so that it is ready to be sequenced. We need to make sure that we are only using the cells with the right DNA fragments. When we have made sure we have only the right cells, we put them on plates containing different antibiotics. If they start forming colonies, it is very likely that they are resistant to the antibiotic on the plate. Once the DNA sequencing results are obtained, we will know the identity of the resistant genes.

Image may contain: text, line.
Illustration of the functional metagenomics process: Step 1-8 shows the process of selecting and preparing the cells to be tested for antibiotic resistance and sent to sequencing. 9. The selected cells are put on plates with antibiotic. If they start making colonies, they are probably resistant to antibiotics. 10, 11, 12. The cells are sent to sequencing: After the sequencing Elodie and the researchers will know which genes cause antibiotic resistence. Illustration: Elodie Charvet

Which genes are resistant?

- In the last years we have focused our attention into the challenges posed by the dramatic increase in antibiotic resistance, says professor Fernanda Petersen. - Functional metagenomics, which is the focus of Elodie’s project, enables the identification of resistance genes from bacteria that we can not culture in the laboratory. In addition, it has the potential to reveal mechanisms of resistance that remain undiscovered. These are important in providing information that can be used in surveillance and in the development of new antimicrobial strategies.

Elodie Charvet in lab with lab tools and white lab coat
Elodie in the lab. Photo: Ingar Arnodd Storfjell, OD/UiO

Elodie is going back to Clermont-Ferrand in the start of August, to finish her master's degree. But she will not forget the samples just yet:

- I am already looking forward to seeing the results of the DNA sequencing, and fortunately the group have promised to send me the results. I am especially excited to see if new resistance genes have developed during the course of antibiotic treatment.

Published Aug. 6, 2019 12:15 PM - Last modified Sep. 3, 2019 11:37 AM