Antimicrobial resistance, molecular epidemiology and farmer dynamics associated with salmonella infections in indigenous poultry in North Central Nigeria

Abstract

Salmonella serovars are globally known to cause diseases in animals and humans. This study sought to evaluate farmers’ perceptions and practices about Salmonella infections, identify and characterize the serovars circulating in indigenous poultry and their drinking water sources in North Central Nigeria. aimed at having targeted control measures. A total of 1,208 samples comprising of poultry faeces (n=1,108) and water (n=100) from 15 markets were collected and processed using ISO 6579:2002 protocols. Using the disk diffusion method, thirteen antimicrobials were used in antimicrobial susceptibility testing. Whole genome sequencing, traditional and molecular serotyping methods were used to characterize the isolates. Across 54 villages in North Central Nigeria, 419 farmer interviews were conducted using a structured e-questionnaire and data was analysed and associations were made between variables. About 6.5% (78/1,208) of the samples were positive for Salmonella, with 60.3% (47/78) susceptibility to all the antimicrobials used and 14.1% (11/78) being multi-drug-resistant phenotypes. Serotyping and whole genome sequencing carried out on 56.4% (44/78) of the isolates identified 23 serovars and 21 antimicrobial resistance genes. Multilocus sequence typing using 7 housekeeping gene loci identified 12 novel sequence types. Cluster analysis from 3255 loci using INNUENDO cgMLST showed close relatedness among isolates from different sources in the same location. Farmer interviews revealed 89.3% (p-value =0.001) of farmers were not aware of Salmonella infections in poultry while 94.5%, (p-value= 0.01) were unaware that Salmonella infections are zoonotic. This study has revealed diverse, pansusceptible and rare Salmonella serovars in indigenous poultry and the water they drink, highlighted farmers’ low awareness of Salmonella, and identified AMR genes, novel sequence types, and genetic relatedness among the isolates. This study calls for improved surveillance and farmer education regarding Salmonella infections so as to enhance poultry health and productivity, as well as reduce public health threats.