Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in Two Cohorts of High-Risk Military Trainees

Background. MRSA skin and soft tissue infection (SSTI) is a significant cause of morbidity in military trainees. To guide interventions, it is critical we understand the epidemiology of MRSA in this population. Methods. Two cohorts (‘companies’) of US Army Infantry trainees (N=343) at Fort Benning, GA, USA, were followed during their training cycles (Jun.-Dec. 2015). Trainees had nares, oropharynx, perianal and inguinal areas swabbed for MRSA colonization at five ~2-4 week intervals, and monitored for SSTI throughout training. Epidemiological data were collected. Isolates were sequenced using Illumina HiSeq and NovaSeq. Single-nucleotide polymorphisms and clusters were identified. Multi-locus sequence type (MLST) and antimicrobial resistance genes were predicted from de novo assemblies. Results. 87 trainees were positive at least once for MRSA (12 had SSTI, 2 without any colonization). Excluding those positive at baseline, 43.7% were colonized within the first month of training. 244/254 samples were successfully sequenced (including all SSTI). ST8 (n=135, 100% of SSTI), ST5 (n=81) and ST87 (n=21) were the most represented. Three main Clusters were identified, largely corresponding to these STs. Sub-analyses within Clusters showed multiple importations of MRSA, with transmission subsequently predominantly within, rather than between, platoons in each company. Over 50% of trainees were colonized only at other anatomical sites; restricting analyses to nares missed substantial transmission. Conclusions. Serial importations of MRSA into this high-risk setting likely contribute to the ongoing burden of MRSA colonization and infection among military trainees. Sampling multiple anatomical sites is critical for comprehensive characterization of MRSA transmission.