Multiple Staphylococcus species and modifiable production-related risk factors associated with bovine subclinical mastitis in Kenyan cattle systems

Bovine subclinical mastitis (SCM) remains a major constraint to dairy productivity and udder health in Kenya. However, most studies have not resolved non-aureus Staphylococcus (NAS) species beyond the genus level, limiting epidemiological understanding. We assessed Staphylococcus species diversity and modifiable production-related risk factors associated with SCM across heterogeneous cattle production systems. A cross-sectional study was conducted involving 436 composite milk samples collected from 436 lactating cows in 152 herds. SCM was defined using somatic cell count thresholds and bacterial isolates were characterized using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Risk factors were assessed using mixed-effects logistic regression models to account for herd-level clustering and unmeasured heterogeneity. SCM prevalence was 53.0% (229/436) at the cow-level and 73.0% (111/152) at the herd-level. Culture-positive samples were 58.0% (251/436), yielding 174 bacterial isolates. NAS species accounted for 44.3% of isolates, exceeding S. aureus (35.6%). S. chromogenes was the predominant NAS species (19.0%), followed by S. succinus (5.2%). Additional pathogens included E. coli (19.5%) and P. aeruginosa (0.6%). Mixed bacterial growth occurred in 8.8% of culture-positive samples, with NAS present in 5.0%. The odds of having SCM were significantly higher in indigenous cattle compared with exotic cattle (adjusted odds ratio [aOR] = 2.51, 95% CI: 1.16–5.57, p = 0.020), in cattle housed in temporary (aOR = 6.27, 95% CI:1.97–21.0, p = 0.002) or semi-permanent structures (aOR = 4.63, 95% CI: 1.91–11.8, p < 0.001) compared with permanent housing, and in medium-sized herds compared with small-sized herds (aOR = 2.43, 95% CI: 1.19–5.06, p = 0.016). SCM remains prevalent across Kenyan cattle systems and is characterized by substantial Staphylococcus species diversity, including S. aureus and multiple NAS species, with occasional mixed bacterial growth. In resource-limited settings, sustainable mastitis control strategies should prioritize system‑specific interventions integrating scalable diagnostic tools with species‑level pathogen surveillance and targeted improvements in modifiable production‑related risk factors, particularly housing quality and herd management.