Research Groups

Bioinformatics / Biostatistics – Dr. sc. nat. A. Ramette


Ramette A, Kronenberg A, Burnens A, Cherkaoui A, Dubuis O, Egli A, Gaia V, Koch D, Leib SL, Nordmann P, Perreten V, Piffaretti J-C, Prod'hom G, Schrenzel J, Widmer AF, Zanetti G, Zbinden R (2018) Prevalence of carbapenem-resistant Acinetobacter baumannii from 2005 to 2016 in Switzerland. BMC Infectious Diseases 18(1).  DOI: 10.1186/s12879-018-3061-5


Background: We describe the prevalence of invasive carbapenem-resistant Acinetobacter spp. isolated from 2005 to 2016 in different regions of Switzerland.

Methods: Using the Swiss Antibiotic Resistance Centre (anresis) database that includes data from 70% of all hospitalized patients and one third of all ambulatory practitioners in Switzerland, we analysed the number of carbapenem-susceptible and resistant Acinetobacter spp. isolated from blood or cerebrospinal fluid, and further described their temporal and regional fluctuations.

Results: From 2005 to 2016, 58 cases of resistant or intermediate strains to carbapenem were observed among 632 cases of invasive Acinetobacter. Multivariable analyses indicated that the number of carbapenem-resistant isolates (mean 4.8 ± sd 2.12) and carbapenem resistance rates per region per annum (8.4% ± 13.9%) were low and stable over the studied period. Large fluctuations were observed at the regional level, with e.g. the North East region displaying resistance rates twice as high as that found in other regions.

Conclusion: Despite a relatively stable number of carbapenem-resistant Acinetobacter isolates in Switzerland, our results suggest the existence of a diverse pool of A. baumannii species in hospital settings, and confirm the implication of carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex in the vast majority of clinical infections and nosocomial outbreaks with notable regional fluctuations.


Ramette A, Spycher BD, Wang J, Goutaki M, Beardsmore CS, Kuehni CE (2018) Longitudinal associations between respiratory infections and asthma in young children. Am J Epidemiol. doi: 10.1093/aje/kwy053.


We examined temporal dependencies between repeated assessments of respiratory infections and asthma in children in the Leicester Respiratory Cohort, Leicestershire, UK. Asthma (doctor diagnosis, health care visits, wheeze frequency) and respiratory infections (cold duration and frequency, cough with colds, ear infections) in the previous 12 months were assessed repeatedly at ages 1, 4, and 6 years for children born between April 1996 and April 1997. We determined associations between contemporaneous and lagged measures of asthma and respiratory infections using structural equation modelling. In 1995 children, asthma was positively associated with contemporaneous infections. Asthma at age 6 was positively associated with asthma at age 4 (regression coefficient = 0.87; 95% CI 0.76, 0.97), but not with asthma at age 1 (-0.01; -0.14, 0.11). We found no evidence for direct protective effect of infections at age 1 on asthma either at age 4 (-0.20; -0.51, 0.10) or 6 (0.24; -0.04, 0.52). Adjusting for potential confounders did not qualitatively change those relationships. Our findings suggest that asthma at age 6 is directly influenced by asthma history and only indirectly if, at all, by earlier infection episodes. We found little support for a protective effect of preschool infections on asthma at early school age.

Kraemer JG, Ramette A, Aebi S, Oppliger A, Hilty M (2018) Influence of pig farming on the human's nasal microbiota: The key role of the airborne microbial communities. Applied and environmental microbiology, AEM. 02470-17


It has been hypothesized that the environment can influence the composition of the nasal microbiota. However, the direct influence of pig farming on the anterior and posterior nasal microbiota is unknown. Using a cross-sectional design, pig farms (n=28) were visited in 2014-2015 and nasal swabs from 43 pig farmers and 56 pigs as well as 27 air samples taken in the vicinity of pig enclosure were collected. As controls, nasal swabs from 17 cow farmers and 26 non-animal exposed individuals were also included. Analyses of the microbiota were performed based on 16S rRNA amplicon sequencing and the DADA2 pipeline to define sequence variants (SVs). We found that pig farming is strongly associated with specific microbial signatures (including alpha- and beta-diversity), which are reflected in the microbiota of the human nose. Furthermore, the microbial communities were more similar within the same farm as compared to between the different farms, indicating a specific microbiota pattern for each pig farm. In total, there were 82 SVs that occurred significantly more abundantly in samples from pig farms than from cow farmers and non-exposed (i.e. the core pig farm microbiota). Of those, nine SVs were significantly associated with the posterior part of the humans' nose. The results strongly indicate that pig farming is associated with a distinct human nose microbiota. Finally, the community structures derived by the DADA2 pipeline showed an excellent agreement with the outputs of the mothur pipeline which was revealed by procrustes analyses.

Molari M, Guilini K, Lott C, Weber M, de Beer D, Meyer S, Ramette A, Wegener G, Wenzhöfer F, Martin D, Cibic T, De Vittor C, Vanreusel V, Boetius A (2018) CO2 leakage alters biogeochemical and ecological functions of submarine sands.  Science Advances. vol. 4, no. 2, eaao2040 DOI: 10.1126/sciadv.aao2040


Subseabed CO2 storage is considered a future climate change mitigation technology. We investigated the ecological consequences of CO2 leakage for a marine benthic ecosystem. For the first time with a multidisciplinary integrated study, we tested hypotheses derived from a meta-analysis of previous experimental and in situ high-CO2 impact studies. For this, we compared ecological functions of naturally CO2-vented seafloor off the Mediterranean island Panarea (Tyrrhenian Sea, Italy) to those of nonvented sands, with a focus on biogeochemical processes and microbial and faunal community composition. High CO2 fluxes (up to 4 to 7 mol CO2 m−2 hour−1) dissolved all sedimentary carbonate, and comigration of silicate and iron led to local increases of microphytobenthos productivity (+450%) and standing stocks (+300%). Despite the higher food availability, faunal biomass (−80%) and trophic diversity were substantially lower compared to those at the reference site. Bacterial communities were also structurally and functionally affected, most notably in the composition of heterotrophs and microbial sulfate reduction rates (−90%). The observed ecological effects of CO2 leakage on submarine sands were reproduced with medium-term transplant experiments. This study assesses indicators of environmental impact by CO2 leakage and finds that community compositions and important ecological functions are permanently altered under high CO2.