Table_4_Prevalence and genomic characterization of Salmonella isolates from commercial chicken eggs retailed in traditional markets in Ghana.XLSX

Salmonella enterica are important foodborne bacterial pathogens globally associated with poultry. Exposure to Salmonella-contaminated eggs and egg-related products is a major risk for human salmonellosis. Presently, there is a huge data gap regarding the prevalence and circulating serovars of Salmonella in chicken eggs sold in Ghana. In this study, 2,304 eggs (pools of six per sample unit) collected from informal markets in Accra, Kumasi and Tamale, representing the three ecological belts across Ghana, were tested for Salmonella. Antimicrobial susceptibility testing and Whole Genome Sequencing (WGS) of the isolates were performed using standard microdilution protocols and the Illumina NextSeq platform, respectively. The total prevalence of Salmonella was 5.5% with a higher rate of contamination in eggshell (4.9%) over egg content (1.8%). The serovars identified were S. Ajiobo (n = 1), S. Chester (n = 6), S. Hader (n = 7), S. enteritidis (n = 2); and S. I 4:b:- (n = 8). WGS analysis revealed varied sequence types (STs) that were serovar specific. The S. I 4:b:- isolates had a novel ST (ST8938), suggesting a local origin. The two S. enteritidis isolates belonged to ST11 and were identified with an invasive lineage of a global epidemic clade. All isolates were susceptible to ampicillin, azithromycin, cefotaxime, ceftazidime, gentamicin, meropenem, and tigecycline. The phenotypic resistance profiles to seven antimicrobials: chloramphenicol (13%), ciprofloxacin (94%), and nalidixic acid (94%), colistin (13%), trimethoprim (50%) sulfamethoxazole (50%) and tetracycline (50%) corresponded with the presence of antimicrobial resistance (AMR) determinants including quinolones (gyrA (D87N), qnrB81), aminoglycosides (aadA1), (aph(3“)-Ib aph(6)-Id), tetracyclines (tet(A)), phenicols (catA1), trimethoprim (dfrA14 and dfrA1). The S. enteritidis and S. Chester isolates were multidrug resistant (MDR). Several virulence factors were identified, notably cytolethal distending toxin (cdtB gene), rck, pef and spv that may promote host invasion and disease progression in humans. The findings from this study indicate the presence of multidrug resistant and virulent strains of Salmonella serovars in Ghanaian chicken eggs, with the potential to cause human infections. This is a critical baseline information that could be used for Salmonella risk assessment in the egg food chain to mitigate potential future outbreaks.

肠炎沙门氏菌（Salmonella enterica）是全球范围内与家禽密切相关的重要食源性细菌致病菌。人类暴露于沙门氏菌污染的鸡蛋及蛋相关制品，是感染沙门氏菌病的主要风险因素。目前，加纳在售鸡肉鸡蛋中沙门氏菌的流行率与流行血清型仍存在巨大数据缺口。本研究从覆盖加纳三大生态带的阿克拉、库马西及塔马利的非正规市场采集了2304枚鸡蛋（每个采样单元为6枚鸡蛋的混合样本），对其开展沙门氏菌检测。研究分别采用标准微量稀释方案与Illumina NextSeq测序平台，完成了分离株的抗菌药物敏感性试验与全基因组测序（Whole Genome Sequencing, WGS）。本次检测中沙门氏菌总检出率为5.5%，蛋壳污染率（4.9%）高于蛋内容物污染率（1.8%）。共鉴定出以下血清型：S. Ajiobo（n=1）、S. Chester（n=6）、S. Hader（n=7）、肠炎沙门氏菌（S. enteritidis，n=2）以及S. I 4:b:-（n=8）。全基因组测序分析显示，存在多种血清型特异性的序列型（Sequence Types, STs）。其中S. I 4:b:-分离株携带新型序列型ST8938，提示其为本地起源菌株。两株肠炎沙门氏菌属于ST11型，且被鉴定为全球流行克隆群的侵袭性谱系。所有分离株对氨苄西林、阿奇霉素、头孢噻肟、头孢他啶、庆大霉素、美罗培南及替加环素均表现为敏感。针对7种抗菌药物的表型耐药谱分别为：氯霉素（13%）、环丙沙星（94%）、萘啶酸（94%）、黏菌素（13%）、甲氧苄啶（50%）、磺胺甲恶唑（50%）与四环素（50%），该耐药表型与相应的抗菌药物耐药（Antimicrobial Resistance, AMR）基因决定簇相匹配，包括喹诺酮类耐药基因（gyrA(D87N)、qnrB81）、氨基糖苷类耐药基因（aadA1、aph(3")-Ib、aph(6)-Id）、四环素类耐药基因（tet(A)）、苯丙醇类耐药基因（catA1）以及甲氧苄啶耐药基因（dfrA14和dfrA1）。肠炎沙门氏菌与S. Chester分离株均为多重耐药（Multidrug Resistant, MDR）菌株。本研究还鉴定出多种毒力因子，其中尤以可促进人类宿主侵袭与疾病进展的细胞致死性肿胀毒素（cytolethal distending toxin, cdtB基因）、rck、pef及spv基因为显著。本研究结果表明，加纳市售鸡肉鸡蛋中存在多重耐药且携带毒力因子的沙门氏菌血清型菌株，具备引发人类感染的潜在风险。本研究所得的关键基线数据，可用于鸡蛋食物链中的沙门氏菌风险评估，以缓解未来潜在的暴发疫情。