Livestock-associated methicillin-resistant Staphylococcus aureus along the pork food chain: a study of four commercial pig fattening farms in north-east Germany and survival in processed meat products

Introduction Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) of Sequence Type (ST) 398 is widespread in European pig farming, yet molecular evidence linking specific farm strains to finished pork products remains limited. Methods Four commercial pig fattening farms in northeastern Germany were sampled for MRSA across the full pork production chain, from nasal swabs collected from pigs and environmental samples taken on farms, through slaughter, to four processed meat products representing a gradient of processing intensity ( Hackepeter , Frische Zwiebelmettwurst , cervelat-type sliceable raw sausage , and Lyoner ). MRSA isolation followed two-step selective enrichment culture with confirmation by multiplex Real-Time PCR; all isolates were characterized by spa - and SCC mec -typing and subjected to whole-genome sequencing with Core Genome Multilocus Sequence Typing (cgMLST)-based cluster analysis using a 1,861-locus Staphylococcus aureus scheme. Results MRSA was detected on 3/4 farms (75%); all pooled nasal swab samples from positive farms were positive at both the farm (7/7 pools) and slaughterhouse (8/8 pools) levels. cgMLST revealed that pest flies carried ST398 strains genomically nearly identical (as few as 1 allele) to those colonizing farm pigs, identifying farm-associated pests as potential carriers of LA-MRSA. Among finished products, MRSA was not detected in seasoned raw minced meat ( Hackepeter ; 0/9) and heat-treated cooked sausage ( Lyoner ; 0/12). In contrast, LA-MRSA ST398 (t034/SCC mec V) survived in spreadable raw sausage ( Frische Zwiebelmettwurst ; 6/12 positive) through the full seven-day shelf life; a single ST398 MRSA (t011/SCC mec V) was detected in cervelat-type sliceable raw sausage after fermentation. Discussion Whole-genome sequencing and cgMLST confirmed the recent common ancestry of ST398 isolates recovered from pig nasal swabs, farm environments, slaughter stages, and final meat products, including raw fermented sausages, providing genomic evidence of LA-MRSA transmission along the farm-to-fork chain. Human-associated MRSA (ST39, t007/SCC mec II) was detected exclusively at the slaughterhouse and the meat processing stage and carried the human-associated immune evasion and egc enterotoxin gene clusters, absent from all ST398 isolates, implicating that the slaughterhouse may be an entry point for a non-livestock MRSA lineage into the pork food chain.