LIN-RES: Investigation of the molecular basis, origin, transferability and risk factors associated with linezolid-resistance emergence in Gram-positive bacteria of human and animal origin

Start: 1 January 2019
Duration: 3 Years
Domain: Antimicrobial Resistance
Members: Sciensano- Belgium, ANSES- France, BfR- Germany
Contact: Cecile Boland (Sciensano), Thierry van den Berg (Sciensano)

The Project

Linezolid belongs to the oxazolidinone family of antimicrobials and is one of the last resort drug used to fight human infections caused by multi-resistant Gram-positive bacteria such as Streptococci, Staphylococci and Enterococci. It is commercially available since 2000 and has not been licensed for use in animals. In 2008, the first instance of transferable resistance to Linezolid caused by the 23SrRNA methylase Cfr (for Chloramphenicol Florfenicol Resistance) was reported in US Staphylococcal isolates recovered from human infection cases. optrA is another gene conferring resistance to Linezolid and Phenicols whose sequence was first reported in 2015. It consists in an ABC-type of membrane transporter and works as an efflux pump. After its initial finding in China, it recently emerged in animal and human Enterococci / Staphylococci on both the American and European continents.

Cfr not only confers resistance to oxazolidinones but also to pleuromutilins, streptogramins, lincosamids and phenicols. EU Staphylococcus isolates harboring cfr were described from 2011 onwards, mainly in intensive care units. In China, the cfr gene was first detected in a Bacillus sp. of animal origin in 2010 and soon after in Enterococci and Staphylococci.

Cfr emerged in EU livestock first in coagulase-negative Staphylococci and very recently in Methicillin Resistant Staphylococcus aureus (LA-MRSA) strains isolated from healthy pigs. Surprisingly, the cfr gene found in LA-MRSA was born on plasmids carrying a Tn558::cfr variant identical to the one found on a plasmid hosted in a hospital-acquired coagulase-negative Staphylococcus in Germany and hosting another resistance gene, fexA involved in resistance to fenicols. Plasmids and bacterial species hosting this Tn558::cfr variant are thus different, but the recombinant transposon-like elements are 100% identical at nucleotide level.

Acquisition of transferable resistance to Linezolid by Staphylococci hence seems to follow a reproducible scenario. The hallmark is a cfr- or optrA-embedded transposon variant carried on a plasmid roughly 40-kb in size and hosted in a Staphylococcus species under selective pressure in a given ecological system. The selective pressure is obviously the use of Linezolid itself in Hospitals / Intensive Care Units, but must be different when it comes to animals raised for food production. Though currently limited in terms of frequency, emergence of cfr in European LA-MRSA is most probably attributable to a selection mechanism driven by the veterinary use of antimicrobial molecules unrelated to Linezolid but acting in a similar way on the bacterial ribosome. The usual suspects are Florfenicol and Lincomycine, which are used to treat common bacterial infections in pigs including pneumonia and diarrhea. If raising continuously, the horizontal spread of cfr – or optrA-carrying transposons could on the long term compromize the success of (human) antimicrobial therapies aimed at fighting infections caused by Gram-positive organisms with last-resort molecules such oxazolidinones or last-generation pleuromutilins. The presence of optrA in livestock-associated gram-positive bacteria has mainly been reported in China (Guangdong province) so far but its emergence on other continents is just a matter of time.

This raises important questions that we want to tackle through the present PhD proposal: Are optrA– and cfr-carrying transposons horizontally transferred from humans to animals or the other way around, from animals to humans? Are peculiar transposon variants such as Tn558:cfr the unique source of cfr transmission or are there other genetic carriers of concern? What is the prevalence of these genes in Gram-positive indicator bacteria isolated from healthy animals in the EU? What are the risk factors favoring their dissemination?

We propose to investigate the molecular basis, origin, transferability and risk factors associated with Linezolid-resistance emergence in Gram-positive bacteria of both human and animal origin.

Michaël Timmermans

About me: I was born in 1991. I like to know how the things and life work. I like to be connected with people and give help if it’s possible. Sciences is the field where this is possible and I’m very motivated to have the possibility to do a PhD. I was graduated in Biochemistry and Molecular and Cellular Biology in 2017. My masters thesis was in bacteriology and I started a PhD in the same field and more precisely in antimicrobial resistance in 2017. 

What motivated me to do a PhD: Sciences have interested me since my childhood. After my masters graduationI wanted to start a PhD. In 2017 I started my PhD on antimicrobial resistance. I think it’s a very important topic right now as antimicrobial resistance is a problem for humans and animals. We need to understand how the resistances are spreading among bacteria for better use of antibiotics. I’m really excited to work on this topic for my PhD and I’m feel lucky to have to possibility to work on this OHEJP project.


D2.1- Genetic resistance profiles and subtypes of strains sequenced during M13-M24.

D2.3- Genetic resistance profiles and subtypes of strains sequenced until M36.

D2.4- Results of in silico analysis of genetic scars of horizontal transfer or recombination events.

D3.1- Results of in silico analysis of transferability.

D3.3- Results of laboratory experiments to demonstrate transferability of linezolid resistance genes


Timmermans, M., Bogaerts, B., Vanneste, K., De Keersmaecker, S. C. J., Roosens, N. H., Kowalewicz, C., Simon, G., Argudin, M. A., Deplano, A., Hallin, M., Wattiau, P., Fretin, D., Denis, O., & Boland, C. (2021). LIN-RES project: Genomic analysis of linezolid resistance in strains isolated from healthy animals and human patients. Poster presentation at One Health EJP ASM 2021, Copenhagen, Denmark. 9-11th June 2021. DOI:

Timmermans, M., Wattiau, P., Fretin, D., Grobbel, M., Granier, S., Broens, E., Denis, O., & Boland, C. (2020). LDZ-R project: Linezolid selective monitoring during 2019 in Belgium: a linezolid resistance study. Poster presentation at One Health EJP ASM 2020, Online. 27-29th May 2020. DOI:

Timmermans, M., Wattiau, P., Fretin, D., Grobbel, M., Granier, S., Broens, E., Argudin M. A., Denis, O., & Boland, C. (2019). Project “LIN-RES” Molecular basis, origin, transferability, and risk factors associated with linezolid-resistance in Gram-positive bacteria of human and animal origin. Poster presentation at One Health EJP ASM 2019, Dublin, Ireland. 22-24 May 2019. DOI:


12-Month PhD Report 2021 LIN-RES. DOI:

Timmermans M, Bogaerts B, Vanneste K, De Keersmaecker S C J, Roosens N H C, Kowalewicz C, Simon G, Argudín M A, Deplano A, Hallin M, Wattiau P, Fretin D, Denis O and Boland C. (2021) Large diversity of linezolid-resistant isolates discovered in food-producing animals through linezolid selective monitoring in Belgium in 2019. Journal of Antimicrobial Chemotherapy, dkab376. DOI:



Log in with your credentials


Forgot your details?

Create Account