Analysis of somatic cell count, bacteria distribution and antimicrobial susceptibility in lactating dairy cows from small holder dairy farms in Kenya

Subclinical mastitis is a major cause of economic loss and antimicrobial use in dairy cattle globally. In Kenyan smallholder systems, limited evidence on somatic cell counts (SCC), mastitis pathogens, and antimicrobial resistance patterns constrains effective control strategies. We conducted a cross-sectional study of 320 lactating cows from 119 smallholder farms in a peri-urban Kenyan county. Quarter milk samples ( n = 1261) were cultured for Escherichia coli , Klebsiella spp., Staphylococcus aureus , and Streptococcus spp. and confirmed by MALDI TOF MS. SCC was measured in 863 samples. Antimicrobial susceptibility testing was performed, and regression models used to identify animal- and farm-level factors associated with SCC variation. Elevated SCCs were associated with reduced teat-end clearance (< 30 cm, β = 3.1, p = 0.04), mid-lactation (β = 1.56, p = 0.03) and late-lactation (β = 1.7, p = 0.02), and higher parity (≥ 4 lactations; β = 2.1, p = 0.005). At farm level, increased SCC was associated with wet or muddy floors (β = 2.16, p = 0.001) and routine antimicrobial dry-cow therapy (β = 1.59, p = 0.02). Of 1251 samples, 67.8% showed growth on blood agar and 1% on MacConkey agar. Streptococcus agalactiae predominated (72.1%), followed by Streptococcus uberis (10.0%), Staphylococcus aureus (2.1%), and Escherichia coli (4.2%). Streptococcus spp. were susceptible to penicillins (100%), while tetracycline resistance was widespread in Streptococcus spp. (89.8%), Staphylococcus aureus (100%), and Escherichia coli (33.3%). Integrated control strategies targeting milking hygiene, environmental management, and antimicrobial stewardship are essential to reduce infection pressure and sustain productivity. • Udder health management was suboptimal on Kenyan smallholder dairy farms. • Somatic cell levels were influenced by host and farm-level factors. • Contagious and environmental pathogens co-dominated infections. • Most isolates remained susceptible to first-line antimicrobials.