Characterisation of nasopharyngeal colonisation by Staphylococcus aureus and the factors associated with colonisation in comorbid adults in a low- and middle-income country.

Introduction: Staphylococcus aureus is a major cause of pneumonia globally, with a particularly high burden in low- and middle-income countries (LMICs). Nasopharyngeal colonisation (NPC) by S. aureus plays a critical role in the pathogenesis of respiratory infections. However, existing research has predominantly focused on paediatric and immunocompromised populations. Data on general adult populations, especially in LMICs, are limited. This study aimed to determine the prevalence of S. aureus NPC in adults with chronic comorbidities and identify associated risk factors.

Methods: Participants with chronic comorbidities were recruited from community-based settings. Samples were processed using conventional culture techniques to isolate S. aureus. Bacterial identification was confirmed by matrix-assisted laser desorption ionisation-time of flight mass spectrometry. To characterise antimicrobial resistance profiles, cefoxitin disc diffusion and D-zone tests were performed in accordance with standardised clinical microbiology protocols. Participants were longitudinally followed and resampled at 6, 12 and 18 months postenrolment to evaluate colonisation dynamics over time.

Results: A total of 810 adults were enrolled. Baseline S. aureus NPC prevalence was 15.3% (124/810), with 11.2% (14/124) of isolates being methicillin-resistant S. aureus (MRSA) and 6.4% (8/124) showing clindamycin resistance. At 6-month follow-up, the cumulative incidence of S. aureus colonisation was 14.2%. In multivariable logistic regression, active smoking (OR 1.73, 95% CI 1.06 to 2.85, p=0.02) and rheumatoid arthritis (OR 3.03, 95% CI 1.38 to 6.67, p<0.01) were independently associated with colonisation. Influenza vaccination was associated with reduced risk (OR 0.60, 95% CI 0.38 to 0.94, p=0.02).

Conclusion: S. aureus NPC, including MRSA, was common among adults with chronic comorbidities. Active smoking and autoimmune diseases, particularly rheumatoid arthritis, were independently associated with increased colonisation risk. These findings have direct implications for community-acquired pneumonia management, supporting consideration of empiric anti-MRSA therapy in high-risk patients. Preventive strategies, including smoking cessation and targeted vaccination, should be prioritised in this population.