Epidemiology of Clostridium chauvoei infections in southern Chile: Molecular prevalence, diagnostic gaps, and genetic characterization of cctA and nanA virulence genes

Background Blackleg, a mostly cattle disease caused by Clostridium chauvoei , represents a health challenge for the livestock industry. This study aimed to characterize the epidemiology of C. chauvoei infections in Southern Chile (Los Ríos and Los Lagos regions), where occasional outbreaks persist despite high perceived vaccination coverage. Methods A cross-sectional study was conducted on 100 cattle farms (50 beef and 50 dairy), combining a structured survey on management practices with molecular detection (PCR) of C. chauvoei in soil and fecal samples. Additionally, the virulence genes cctA and nanA were sequenced to assess local genetic diversity and evolutionary stability compared to international strains. Results A farm-level molecular prevalence of 30% (95% CI: 21.6–40.0) for C. chauvoei was estimated, with detection in 20% of soil and 19% of fecal samples. A diagnostic gap was identified: although 51% of farms reported a history of blackleg, 0% utilized laboratory confirmation, relying exclusively on presumptive clinical and/or pathologic diagnosis. Multivariable analysis identified a history of clinical cases (OR=7.13; 95% CI: 2.3–26.2), routine necropsy (OR=3.13; 95% CI: 1.05–10.1), alkaline soil pH (OR=0.19; 95% CI: 0.04–0.73, compared to acidic soils), and the combined use of chemical and organic fertilization (OR=0.03; 95% CI: 0.001–0.60) as significant independent predictors of farm positivity. Despite a 98% vaccination coverage, 70.4% of farms failed to administer a booster dose to calves during the primary vaccination series. Genetic characterization demonstrated 100% nucleotide identity between Chilean sequences and international reference strains for both cctA and nanA genes. Conclusions C. chauvoei is a ubiquitous and evolutionarily stable pathogen in Southern Chile. These findings suggest that persistent outbreaks in the region are attributable to improper immunization protocols and diagnostic deficiencies rather than vaccine strain mismatch.