Survival of Salmonella enterica serovar Heidelberg in pine shavings used as broiler litter
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Wood shavings is the most common bedding material used around the world to raise broiler. Therefore, wood shavings can be a vehicle for the transmission of pathogens to live birds. In this study, we performed an in-depth genomic characterization of three <em>Salmonella enterica </em>serovar Heidelberg (<em>S</em>. Heidelberg) strains recovered after their inoculation into fresh pine shaving. The three strains used for the microcosm study were previously isolated from broiler feces (SH-AAFC), broiler carcass (SH-ARS) and chicken thigh (SH-FSIS) and differed one from another by 46 - 94 single nucleotide variants. The SH-AAFC strain harbored an antimicrobial resistant gene (ARG) (<em>bla</em><sub>CMY-2</sub>) on an IncI1 plasmid while the SH-FSIS strain harbored multiple ARGs (<em>floR, cmlA1, tet(A), bla</em><sub>TEM-1B</sub><em>, ant(2'')-Ia, aph(6)-Id, aph(3'')-Ib </em>and<em> sul2</em>) on an IncC plasmid. The SH-ARS isolate was pan susceptible to several antibiotics evaluated. We determined the abundance of <em>Salmonella </em>at days 0, 1, 7, 14 and 21 and performed antibiotic susceptibility testing and whole genome sequencing (on 77 randomly selected <em>S</em>. Heidelberg isolates. After 21 days of incubation, <em>Salmonella </em>abundance decreased by 4.4 logs. <em>Salmonella</em> with high minimum inhibitory concentrations (MICs) against ampicillin showed a significantly higher abundance and survival rate compared to <em>Salmonella</em> with high MIC against gentamicin (<em>P</em>< 0.05). Clonal SH-AAFC was the most prevalent strain in the microcosms (48/77), followed by the strain SH-ARS (25/77). Only 4/77 isolates were determined to be clones of SH-FSIS. We identified recombination events and plasmid copy number changes that were associated with the fitness of <em>S</em>. Heidelberg strain carrying IncI1 and Col plasmids. Lastly, we found that litter physicochemical variables including water activity could explain up to 85% of the variability in our data.
