Journal Article

cfr and fexA genes in methicillin-resistant Staphylococcus aureus from humans and livestock in the Netherlands

Witteveen, Sandra, Brouwer, Michael S. M., Veldman, Kees, Dierikx, Cindy, Hengeveld, Paul, Schouls, Leo M., Rapallini, Michel, Hendrickx, Antoni P. A., van Duijkeren, Engeline, van Santen-Verheuvel, Marga, Wullings, Bart, Wit, Ben, Landman, Fabian

2022

Overview

Background Although the Netherlands is a country with a low endemic level of methicillin-resistant Staphylococcus aureus (MRSA), a national MRSA surveillance has been in place since 1989. In 2003 livestock emerged as a major reservoir of MRSA and currently livestock-associated MRSA (clonal complex CC398) make up 25% of all surveillance isolates. To assess possible transfer of resistant strains or resistance genes, MRSA obtained from humans and animals were characterized in detail. Methods The sequenced genomes of 6327 MRSA surveillance isolates from humans and from 332 CC398 isolates from livestock-related samples were analyzed and resistance genes were identified. Several isolates were subjected to long-read sequencing to reconstruct chromosomes and plasmids. Results Here we show the presence of the multi-resistance gene cfr in seven CC398 isolates obtained from humans and in one CC398 isolate from a pig-farm dust sample. Cfr induces resistance against five antibiotic classes, which is true for all but two isolates. The isolates are genetically unrelated, and in seven of the isolates cfr are located on distinct plasmids. The fexA gene is found in 3.9% surveillance isolates and in 7.5% of the samples from livestock. There is considerable sequence variation of fexA and geographic origin of the fexA alleles. Conclusions The rare cfr and fexA resistance genes are found in MRSA from humans and animals in the Netherlands, but there is no evidence for spread of resistant strains or resistance plasmids. The proportion of cfr -positive MRSA is low, but its presence is worrying and should be closely monitored. Plain language summary A group of bacteria that cause difficult-to-treat infections in humans is methicillin-resistant Staphylococcus aureus (MRSA). Monitoring the spread of MRSA strains and genes that cause antibiotic resistance is important for appropriate intervention. In the Netherlands, 25% of MRSA isolates from patients are MRSA types often found in livestock (LA-MRSA). In this study we have identified the cfr gene in a small number of LA-MRSA obtained from humans and animals. The cfr gene causes resistance to five antibiotic classes, including the last resort antibiotic linezolid. We also found that MRSA from humans and animals carried the antibiotic resistance gene fexA and these were often also LA-MRSA. The results suggest that these resistance genes originate from livestock and were transferred to humans. Large scale antibiotic treatment of livestock may lead to increased antibiotic resistance in MRSA found in humans. Schouls et al. characterize antimicrobial resistance genes in MRSA isolates from humans and livestock in the Netherlands. The multidrug resistance gene cfr and the phenicol resistance gene fexA are identified in both types of samples, including in samples taken from persons having professional contact with livestock.

• Publisher: Nature Publishing Group UK,Springer Nature B.V,Nature Portfolio
• Subject: 45/23 / 631/326/41/1470 / 692/308/174 / Antibiotics / Antimicrobial agents / Chromosomes / Drug resistance / Genes / Genomics / Laboratories / Livestock / Medicine / Medicine & Public Health / Plasmids / Questionnaires / Software / Staphylococcus infections / Surveillance