Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi
Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi
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DOI：
10.1186/s12864-019-5916-6
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发表时间：
2019-06-28
期刊：
影响因子：
4.4
通讯作者：
Komurian-Pradel, Florence
中科院分区：
文献类型：
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作者：
Barroso Lima, Nicholas Costa;Tanmoy, Arif M.;Komurian-Pradel, Florence
伤寒是由伤寒沙门氏菌引起的一种主要的全球公共卫生问题，尤其是在孟加拉国这样的发展中国家，它通过粪便-口腔传播途径传播。越来越多的抗菌素耐药性(AMR)的出现是一个严重的问题；伤寒的治疗清单正在不断减少。除了IncHI1型质粒外，沙门氏菌基因组岛(SGI)11还被报道携带AMR基因。尽管最近有报道表明印度次大陆的多药耐药性(MDR)有所下降，但背景中相应的基因组变化尚不清楚。结果在这里，我们组装并注释了73S的完整闭合染色体和质粒。伤寒杆菌使用短长度光照读数进行分离。伤寒沙门氏菌有一个开放的泛基因组，核心基因组比以前报道的要小。结合AMR基因，我们鉴定了SGI11的五个变异体，包括先前报道的参考序列。共鉴定出5个质粒，包括新的pK91和pK43；pK43和pHCM2与AMR无关。PHCM1、pPRJEB21992和pK91质粒携带AMR基因，并与SGI11变异体一起决定耐药表型。PK91也含有qnr基因，具有较高的环丙沙星耐药性，并与表现相同表型的H58亚系Bdq相关。质粒(pHCM1和pK91)和SGI11的存在与两个H58谱系Ia和Bd连锁。Ia系分离物在基因组岛上的缺失和抗性基因的整合可能有助于Ia系的适合性优势。结论这类事件可能解释了为什么Ia系在全球范围内广泛分布，而Bd系在局部受到限制。需要进一步的研究来了解这些伤寒沙门氏菌AMR元件是如何传播和产生新的变种的。在流行国家也应考虑采取预防措施，如疫苗接种计划；此类举措可能会减少AMR的传播。
BackgroundTyphoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicrobial resistance (AMR) is a serious issue; the list of treatments for typhoid fever is ever-decreasing. In addition to IncHI1-type plasmids, Salmonella genomic island (SGI) 11 has been reported to carry AMR genes. Although reports suggest a recent reduction in multidrug resistance (MDR) in the Indian subcontinent, the corresponding genomic changes in the background are unknown.ResultsHere, we assembled and annotated complete closed chromosomes and plasmids for 73S. Typhi isolates using short-length Illumina reads. S. Typhi had an open pan-genome, and the core genome was smaller than previously reported. Considering AMR genes, we identified five variants of SGI11, including the previously reported reference sequence. Five plasmids were identified, including the new plasmids pK91 and pK43; pK43and pHCM2 were not related to AMR. The pHCM1, pPRJEB21992 and pK91 plasmids carried AMR genes and, along with the SGI11 variants, were responsible for resistance phenotypes. pK91 also contained qnr genes, conferred high ciprofloxacin resistance and was related to the H58-sublineage Bdq, which shows the same phenotype. The presence of plasmids (pHCM1 and pK91) and SGI11 were linked to two H58-lineages, Ia and Bd. Loss of plasmids and integration of resistance genes in genomic islands could contribute to the fitness advantage of lineage Ia isolates.ConclusionsSuch events may explain why lineage Ia is globally widespread, while the Bd lineage is locally restricted. Further studies are required to understand how these S. Typhi AMR elements spread and generate new variants. Preventive measures such as vaccination programs should also be considered in endemic countries; such initiatives could potentially reduce the spread of AMR.