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
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 (Antimicrob Agents Chemother 2008; 52:2244-2246). optrA is another gene conferring resistance to Linezolid and Phenicols whose sequence was first reported in 2015 (J Antimicrob Chemother 2015; 70: 2182–2190). 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 (Antimicrob. Agents Chemother. 2010 54:3953–3955) and soon after in Enterococci and Staphylococci (Antimicrob Agents Chemother. 2012 56: 1650–16).
Cfr emerged in EU livestock first in coagulase-negative Staphylococci (J Antimicrob Chemother. 2013 68:300-7) and very recently in Methicillin Resistant Staphylococcus aureus (LA-MRSA) strains isolated from healthy pigs (Wattiau, unpublished). 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.