The productivity of smallholder sheep and goat flocks is constrained by high morbidity and mortality of young stock due to helminthosis and coccidiosis. We hypothesized that gastrointestinal parasites are prevalent and may cause severe infections amongst small ruminants in Malaysia. A cross-sectional survey was conducted between March and December 2019 to investigate the prevalence, risk factors, and levels of infection with gastrointestinal strongyle and coccidia in selected smallholder goat flocks in Negeri Sembilan, Malaysia. A total of 257 blood and fecal samples and management data were collected from four farms in Negeri Sembilan. Gastrointestinal parasites were detected by routine sodium chloride floatation, and the McMaster technique was used to quantify the fecal eggs/oocysts per gram outputs (EPG/OPG). The severity of infection was classified as mild (50-799), moderate (800-1200), or severe (>1200). The packed cell volume (PCV) was determined by microhematocrit centrifugation and classified as anemic or non-anemic. Coprological examination revealed an overall prevalence of 78.6% (CI = 72.74-83.44) and 100% flock level prevalence of strongyle and coccidia infection among goats from Negeri Sembilan with a higher infection in flock A-Lenggeng (95.6%) than B-Senawang (87.3%), D-Mendom (80.6%), or C-Seremban (60.0%). The co-infections of strongyle + Eimeria (50.6; CI = 44.50 to 56.64) were more common than single infections of either strongyle (16.7%; CI = 12.66 to 21.78) or Eimeria (4.3%; CI = 2.41 to 7.50). Quantitative analysis has revealed different (p < 0.05) patterns of EPG/OPG in various categories of goats. In total, there were 49.8% mild, 8.6% moderate, and 13.6% severe infections of strongyle and 40.1% mild, 6.6% moderate, and 19.8% severe infections of coccidia among goats. The mean PCV of goats with severe strongyle infection (24.60 ± 0.85) was significantly (p < 0.05) lower than the moderate (26.90 ± 1.15), or mild (28.23 ± 0.50) infections and the uninfected (30.4 ± 0.71). There were increased odds of infection with strongyle and coccidia among female (OR = 3.2) and adult (OR = 11.0) goats from smallholder flocks in Negeri Sembilan. In conclusion, gastrointestinal strongyles and coccidia occur at high frequency among smallholder goats, and there is a higher risk of infection amongst the adult and female stock.

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