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

Abstract

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.

Genomics Insight into cfr-Mediated Linezolid-Resistant LA-MRSA in Italian Pig Holdings

“…However, this strain did not harbour the cfr gene. The BLAST best match (98.00% coverage and 99.72% identity) with cfr -positive MRSA was with the chromosome sequence of the LA-MRSA ST398 strain (RIVM_M047065; CP096539) isolated from a human nasal swab in the Netherlands in 2019 [ 11 ].…”

“…This isolate, together with the CC1 isolate ID 55864/23, presented a frameshift mutation caused by a single base-pair deletion in the cfr gene and, consequently, a truncated protein, corroborating their phenotypic susceptibility to linezolid (MIC value = 1 mg/L). Prior to our findings, linezolid-susceptible MSSA and MRSA associated with cfr variants with a single base-pair deletion or mutation were isolated from two human clinical cases (one in Brazil [ 21 ] and one in the Netherlands [ 11 ]), and also from two nasal swabs of porcine origin (one in Italy [ 18 ] and the other in Australia (CP029172)). All of them belonged to CC398.…”

“…In this study, we report the in-depth molecular characterisation of CC1 (two isolates) and CC398 (one isolate) cfr -positive MDR LA-MRSA isolates of porcine origin detected for the first time in Italian animal production in 2008–2011 [ 16 , 17 ] by using the combined approach of short- and long-read sequencing. Based on previous population studies (2008–2014) conducted on Italian animal production and according to other European-wide studies on cfr -positive MRSA isolated from pig holdings, the occurrence of cfr -positive LA-MSSA and -MRSA in animal production is emerging, but seems to be sporadic [ 8 , 9 , 10 , 11 ]. Accordingly, in a recent study (2019–2020) conducted on dairy cattle farms located in Italian regions representing around 80% of Italian milk production, 22 LA-MRSA samples isolated from 316 bulk tank milk samples and belonging to different CCs tested negative for the presence of cfr [ 20 ].…”

“…However, we could speculate that LA-MRSA of swine origin has had, so far, a mild attitude to acquire and maintain such resistance genes along the production cycles. This may reflect the low frequency of detection of cfr -positive MRSA observed so far in humans [ 11 ], even in case they may represent an important reservoir of exposure for animal production.…”

“…In livestock, cfr was first described in S. aureus of porcine origin in Germany in 2006 [ 7 ]. Since then, it has sporadically been detected in pig samples from Belgium [ 8 ], Spain [ 9 ], Portugal [ 10 ], the Netherlands [ 11 ], China [ 12 ], and South Korea [ 13 ], and in bovine samples from Egypt [ 14 ]. These genes are most frequently located on mobile genetic elements (MGEs), especially plasmids, which were proven to harbour cfr -carrying transposons and translocatable units (TUs), playing a crucial role in their dissemination [ 15 ].…”