Emergence of Cfr-Mediated Linezolid Resistance among Livestock-Associated Methicillin-Resistant Staphylococcus aureus (LA-MRSA) from Healthy Pigs in Portugal

Abstract

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) ST398 is mainly found in Europe and North America, colonizing the nasal cavity of pigs. This study characterized the MRSA isolates recovered from pig nasal swabs (n = 171) by evaluating the antimicrobial susceptibility profile by broth microdilution and characterizing the genetic lineages by spa-typing. Three linezolid-resistant isolates were subjected to Whole-Genome Sequencing (WGS). All strains harbored the mecA gene and were resistant to tetracycline and susceptible to vancomycin. A high frequency of multidrug resistance (97.6%) was evidenced, with 55 different multidrug resistance profiles identified. The MRSA strains were found to belong to 17 spa-types, three being novel. The linezolid-resistant strains appeared to belong to the ST398 type, spa-type t011, and SCCmec_type_Vc and to harbor the cfr, fexA, blaZ, mecA, tetM, and tetK genes. The cfr gene was predicted to be carried in the plasmid, flanked by ISSau9 and the transposon TnpR. MRSA from Portuguese fattening pigs present a high diversity of genetic lineages. The presence of cfr-positive LA-MRSA may represent a risk of transmission to humans, mainly to those in contact with livestock.

First Isolation of Methicillin-Resistant Livestock-Associated Staphylococcus aureus CC398 and CC1 in Intensive Pig Production Farms in Argentina

“…This is consistent with recent studies reporting high level of multi-drug resistance in LA-MRSA isolated from pigs [28], which originated from the acquisition of genes encoding resistance to several antibiotic families by horizontal gene transfer from other staphylococci and bacteria of human and animal origin [29]. Macrolides, lincosamides, β-lactams, tetracyclines and sulfonamides are frequently used in pig production as curative, prophylactic or metaphylactic treatments [30].…”

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

“…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 ].…”

“…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 ].…”

Genetic Diversity of Salmonella enterica subsp. enterica Serovar Enteritidis from Human and Non-Human Sources in Portugal

“…Raw reads were deposited at ENA under project accession number PRJEB44445. Sequencing raw data quality was assessed, and reads were pre-processed and assembled according to Leão et al, 2022 [ 15 ].…”