Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

Salmonellais an important human pathogen and poultry products constitute an important source of human infections. This study investigated prevalence; identified serotypes based on whole genome sequence, described spatial distribution ofSalmonellaserotypes and predicted risk factors that could influence the prevalence ofSalmonellainfection in commercial poultry farms in Nigeria. A cross sectional approach was employed to collect 558 pooled shoe socks and dust samples from 165 commercial poultry farms in North West Nigeria. On-farm visitation questionnaires were administered to obtain information on farm management practices in order to assess risk factors forSalmonellaprevalence.Salmonellawas identified by culture, biotyping, serology and polymerase chain reaction (PCR). PCR confirmed isolates were paired-end Illumina- sequenced. Followingde novogenome assembly, draft genomes were used to obtain serotypes by SeqSero2 and SISTR pipeline and sequence types by SISTR and Enterobase. Risk factor analysis was performed using the logit model. A farm prevalence of 47.9% (CI95[40.3-55.5]) forSalmonellawas observed, with a sample level prevalence of 15.9% (CI95[12.9-18.9]). Twenty-three different serotypes were identified, withS. Kentucky andS. Isangi as the most prevalent (32.9% and 11%). Serotypes showed some geographic variation.Salmonelladetection was strongly associated with disposal of poultry waste and with presence of other livestock on the farm.Salmonellawas commonly detected on commercial poultry farms in North West Nigeria andS. Kentucky was found to be ubiquitous in the farms.