Salmonella enterica subsp. enterica serovar Heidelberg strain:FT3-7B | isolate:FT3-7B Genome sequencing

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 Salmonella enterica serovar Heidelberg (S. 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 polymorphisms. The SH-AAFC strain harbored an antimicrobial resistant gene (ARG) (blaCMY-2) on an IncI1 plasmid while the SH-FSIS strain harbored multiple ARGs (floR, cmlA1, tet(A), blaTEM-1B, ant(2'')-Ia, aph(6)-Id, aph(3'')-Ib and sul2) on an IncC plasmid. The SH-ARS isolate was pan susceptible to several antibiotics evaluated. We determined the abundance of Salmonella at days 0, 1, 7, 14 and 21 and performed antibiotic susceptibility testing and whole genome sequencing (on 77 randomly selected S. Heidelberg isolates. After 21 days of incubation, Salmonella abundance decreased by 4.4 logs. Salmonella with high minimum inhibitory concentrations (MICs) against ampicillin showed a significantly higher abundance and survival rate compared to Salmonella with high MIC against gentamicin (P< 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 S. 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.

木屑是全球范围内用于肉鸡饲养的最常见垫料材料。因此，木屑可能成为病原体传播至活禽的媒介。在本研究中，我们对从新鲜松木屑中分离出的三种沙门氏菌属海德尔堡血清型（S. Heidelberg）菌株进行了深入的基因组特征分析。这三种用于微宇宙研究的菌株先前分别从肉鸡粪便（SH-AAFC）、肉鸡尸体（SH-ARS）和鸡大腿（SH-FSIS）中分离得到，彼此之间在46至94个单核苷酸多态性上存在差异。SH-AAFC菌株携带一个位于IncI1质粒上的抗生素耐药基因（ARG）（blaCMY-2），而SH-FSIS菌株携带多个ARGs（floR、cmlA1、tet(A)、blaTEM-1B、ant(2'')-Ia、aph(6)-Id、aph(3'')-Ib和sul2）位于IncC质粒上。SH-ARS分离株对所评估的多种抗生素表现出广谱敏感性。我们确定了0、1、7、14和21天时的沙门氏菌丰度，并进行了抗生素敏感性测试和全基因组测序（对77个随机选择的S. Heidelberg分离株）。经过21天的培养，沙门氏菌的丰度降低了4.4个对数级。对氨苄西林具有高最低抑菌浓度（MICs）的沙门氏菌与对庆大霉素具有高MICs的沙门氏菌相比，显示出显著更高的丰度和存活率（P< 0.05）。SH-AAFC克隆株在微宇宙中最为普遍（77个中的48个），其次是SH-ARS菌株（77个中的25个）。仅有4个分离株被确认为SH-FSIS的克隆株。我们识别了与携带IncI1和Col质粒的S. Heidelberg菌株的适应性相关的重组事件和质粒拷贝数变化。最后，我们发现垫料的物理化学变量，包括水分活性，可以解释数据中高达85%的变异性。