Genetic characterization of Salmonella Infantis from South Africa, 2004-2016.
Genetic characterization of Salmonella Infantis from South Africa, 2004-2016.
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DOI：
10.1099/acmi.0.000371
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发表时间：
2022-08
影响因子：
--
通讯作者：
Langridge, Gemma C
中科院分区：
文献类型：
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作者：
Mattock, Jennifer;Smith, Anthony M;Keddy, Karen H;Manners, Emma J;Duze, Sanelisiwe T;Smouse, Shannon;Tau, Nomsa;Baker, David;Chattaway, Marie Anne;Mather, Alison E;Wain, John;Langridge, Gemma C
沙门 婴儿对公共卫生的风险越来越大。特别值得关注的是pESI的报告，多药耐药（MDR）编码megaplasma，在分离自多个国家，但很少有人知道它的存在或在南非的多样性。387株S.分析了南非（2004-2020年）婴儿分离株的遗传多态性、重组频率、抗菌素耐药性（AMR）决定因素、质粒存在和总体基因含量。对南非南苏丹的种群结构进行了分析。Infantis与S.其他地方报道的婴儿;只有三分之二的分离物属于eBG 31，而其余的被鉴定为eBG 297，这是全球罕见得多的组。在eBG 297分离株中观察到显著更高水平的重组，这与前噬菌体的存在相关。大多数分离株对抗菌剂敏感（335/387），并且缺乏任何质粒（311/387）;仅在1株分离株中存在大质粒pESI。与2%（3/124）的eBG 297相比，更大比例的eBG 31分离株（19%（49/263））含有至少一个AMR决定簇。通过比较来自两种eBG的分离株的全基因组，确定了943个与eBG显著相关的基因，其中43个仅在eBG 31分离株中发现，34个在eBG 297分离株中发现。沿着单核苷酸多态性距离和耐药谱的差异，表明eBG 31和eBG 297分离株在南非占据不同的生态位。如果S.婴儿出现在南非，可能是通过pESI质粒的传播，这种感染的治疗将受到影响。
Salmonella Infantis is presenting an increasing risk to public health. Of particular concern are the reports of pESI, a multidrug resistance (MDR) encoding megaplasmid, in isolates from multiple countries, but little is known about its presence or diversity in South Africa. Whole genome sequences of 387 S. Infantis isolates from South Africa (2004–2020) were analysed for genetic phylogeny, recombination frequency, antimicrobial resistance (AMR) determinants, plasmid presence and overall gene content. The population structure of South African S. Infantis was substantially different to S. Infantis reported elsewhere; only two thirds of isolates belonged to eBG31, while the remainder were identified as eBG297, a much rarer group globally. Significantly higher levels of recombination were observed in the eBG297 isolates, which was associated with the presence of prophages. The majority of isolates were putatively susceptible to antimicrobials (335/387) and lacked any plasmids (311/387); the megaplasmid pESI was present in just one isolate. A larger proportion of eBG31 isolates, 19% (49/263), contained at least one AMR determinant, compared to eBG297 at 2% (3/124). Comparison of the pan-genomes of isolates from either eBG identified 943 genes significantly associated with eBG, with 43 found exclusively in eBG31 isolates and 34 in eBG297 isolates. This, along with the single nucleotide polymorphism distance and difference in resistance profiles, suggests that eBG31 and eBG297 isolates occupy different niches within South Africa. If antibiotic-resistant S. Infantis emerges in South Africa, probably through the spread of the pESI plasmid, treatment of this infection would be compromised.