Bacterial carriage and invasive infections among people who inject drugs: clinical and molecular epidemiology in an Australian prospective cohort

Abstract Background People who inject drugs are at increased risk of invasive bacterial infections. We aimed to determine the prevalence and molecular epidemiology of Staphylococcus aureus and Streptococcus pyogenes carriage in this population. Methods We performed a cross-sectional survey of carriage among people who inject drugs in Melbourne, Australia. Participants provided a combined throat-anterior nares and an axillae swab for S. aureus and S. pyogenes culture. Univariable analysis identified factors associated with S. aureus and methicillin-resistant S. aureus (MRSA) carriage. Isolates underwent whole genome sequencing and were integrated in comparative genomic analysis with carriage and invasive disease isolates identified in three geo-temporally linked studies of persons who both do and do not inject drugs. Findings We enrolled 305 participants between June 2022 and March 2023. We identified carriage with S. aureus in 40% (122/305), MRSA in 3% (9/305), and S. pyogenes in 1% (3/305) of participants. Recent incarceration was associated with MRSA carriage (OR 6.05, 95% CI 1.55–25.20). Whole genome sequencing analysis identified multiple unrelated sequence types (STs), but S. aureus ST12 and ST398 were overrepresented in carriage and invasive disease isolates from people who inject drugs. We identified multiple clonal groupings (i.e., isolates whose core genomes differed by ≤25 single nucleotide polymorphisms) among carriage and invasive isolates. Interpretation S. aureus, but not S. pyogenes, carriage is common amongst people who inject drugs in Melbourne, with MRSA carriage associated with incarceration. While isolates from people who inject drugs in Melbourne were genetically diverse, the presence of clonal groupings and overrepresentation of specific lineages among people who inject drugs suggests that epidemiological dynamics may differ from those in the broader population.