Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia.
Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia.
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DOI：
10.1099/mgen.0.000785
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发表时间：
2022-03
影响因子：
3.9
通讯作者：
Antonio, Martin
中科院分区：
文献类型：
--
作者：
Darboe, Saffiatou;Bradbury, Richard S.;Phelan, Jody;Kanteh, Abdoulie;Muhammad, Abdul-Khalie;Worwui, Archibald;Yang, Shangxin;Nwakanma, Davis;Perez-Sepulveda, Blanca;Kariuki, Samuel;Kwambana-Adams, Brenda;Antonio, Martin
关键词：
非伤寒 沙门 与多药耐药性相关的病毒导致撒哈拉以南非洲的侵袭性疾病。血清型鼠伤寒和肠杆菌的特定谱系已被牵连。在这里，我们描述了100个临床非伤寒的基因组多样性， 沙门 分别于2001年和2006 - 2018年从冈比亚东部地区和西部地区的93名患者中收集。使用Kirby-Bauer纸片扩散技术对代表单一感染事件的共93株分离株（64株侵袭性，23株胃肠炎和6个其他部位）进行了抗菌药物敏感性表型检测。使用Illumina进行100个分离株的全基因组测序，并使用SPAdes组装和分析读数。使用计算机沙门氏菌分型资源（SISTR）进行血清分型。使用Roary确定93个分离株之间的SNP差异，并在欧洲核苷酸档案的495个非洲菌株的背景下进行系统发育分析。 沙门 鼠伤寒血清型（26/64; 30.6%）和肠炎血清型（13/64; 20.3%）与侵袭性疾病相关，而其它血清型主要引起胃肠炎（17/23; 73.9%）。 确认了三个主要血清型肠杆菌进化枝的存在，包括入侵性西非进化枝，其占基因组的一半以上（11/16; 68.8%）。 多药耐药性仅限于血清型肠杆菌西非分支。这种流行性毒性进化枝的存在具有传播耐药性的潜力，因此对系统的患者管理具有重要意义。需要进行监测和流行病学调查以提供控制信息。
Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006–2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby–Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6 %) and Enteritidis (13/64; 20.3 %) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9 %). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8 %) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted.
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影响因子：
168.9
作者：
Feasey, Nicholas A.;Dougan, Gordon;Kingsley, Robert A.;Heyderman, Robert S.;Gordon, Melita A.
通讯作者：
Gordon, Melita A.
影响因子：
3.8
作者：
Aldrich, Cassandra;Hartman, Hassan;Eibach, Daniel
通讯作者：
Eibach, Daniel
影响因子：
3.7
作者：
Ceesay, Serign J.;Casals-Pascual, Climent;Conway, David J.
通讯作者：
Conway, David J.
影响因子：
11.8
作者：
Darboe, Saffiatou;Okomo, Uduak;Roca, Anna
通讯作者：
Roca, Anna
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.