Occurrence, Multidrug Resistance, SCCmec Typing of Methicillin-Resistant Staphylococcus aureus from Farmed Eggs and Environment

A comparative cross-sectional study was conducted on farmed eggs (n: 480) and environmental samples (n: 72; feed, water, and poultry droppings) from twenty-four deep litter and caged poultry layer farms across Punjab, India. The study noted a significantly higher occurrence of Staphylococcus aureus (31.67%; 95% CI 26.37-36.96%) and methicillin-resistant S. aureus (MRSA) (32.5%, 95% CI 23-43.3%) in deep litter farms (P < 0.05). The logistic regression analysis revealed while the odds of presumptive MRSA from egg isolates were high (Odds ratio: 2.714; 95% CI 1.172, 6.284) in deep litter, conversely, resistance against ceftriaxone (0.279; 95% CI 0.129, 0.605), tetracycline (0.227; 95% CI 0.104, 0.497), and erythromycin (0.46; 95% CI 0.218, 0.973) was low. The multi-drug resistance was high and nearly equal; 68.53%, and 72.22% in deep litter and cage systems respectively. Additionally, around 89.65% and 77.7% of MRSA from deep litter and cage systems had multiple antibiotic resistance index > 0.2 respectively. Among the resistance genes under study, the odds of mecA and tetL were 2.417 and 8.029 times higher in deep litter. The hierarchical clustering of MRSA isolates based on the antibiogram profile depicted the formation of a large number of cluster solutions with a mix of isolates from both systems. The SCCmec typing revealed a predominance of type V in both the systems (34.4%; deep litter and 33.3%; cage), with a scarce distribution of other types and subtypes viz., deep litter: types III; 13.7%, IVc; 6.8%, II; 6.8%, IVa, and IVb; 3.4% and cage system: types III and IVc; 11.1%. To, the best of our knowledge current study is the first-ever comprehensive study on comparative occurrence, AMR profile, molecular characterization, and typing of MRSA from farmed eggs and environment from India.