尼日利亚西南部侵袭性伤寒和非伤寒沙门氏菌的基因组特征。

Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria.

机构信息

Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.

Department of Medical Microbiology and Parasitology, University of Ilorin, Ilorin, Kwara State, Nigeria.

出版信息

PLoS Negl Trop Dis. 2022 Aug 26;16(8):e0010716. doi: 10.1371/journal.pntd.0010716. eCollection 2022 Aug.

BACKGROUND

Salmonellosis causes significant morbidity and mortality in Africa. Information on lineages of invasive Salmonella circulating in Nigeria is sparse.

METHODS

Salmonella enterica isolated from blood (n = 60) and cerebrospinal fluid (CSF, n = 3) between 2016 and 2020 from five tertiary hospitals in southwest Nigeria were antimicrobial susceptibility-tested and Illumina-sequenced. Genomes were analysed using publicly-available bioinformatic tools.

RESULTS

Isolates and sequence types (STs) from blood were S. Typhi [ST1, n = 1 and ST2, n = 43] and invasive non-typhoidal Salmonella (iNTS) (S. Enteritidis [ST11, n = 7], S. Durham [ST10, n = 2], S. Rissen [ST8756, n = 2], S. Chester [ST2063, n = 1], S. Dublin [ST10, n = 1], S. Infantis [ST603, n = 1], S. Telelkebir [ST8757, n = 1] and S. Typhimurium [ST313, n = 1]). S. Typhi ST2 (n = 2) and S. Adabraka ST8757 (n = 1) were recovered from CSF. Most S. Typhi belonged to genotype 3.1.1 (n = 44), carried an IncY plasmid, had several antibiotic resistance genes (ARGs) including blaTEM-1 (n = 38), aph(6)-Id (n = 32), tet(A) (n = 33), sul2 (n = 32), dfrA14 (n = 30) as well as quinolone resistance-conferring gyrA_S83Y single-nucleotide polymorphisms (n = 37). All S. Enteritidis harboured aph(3")-Ib, blaTEM-1, catA1, dfrA7, sul1, sul2, tet(B) genes, and a single ARG, qnrB19, was detected in S. Telelkebir. Typhoidal toxins cdtB, pltA and pltB were detected in S. Typhi, Rissen, Chester, and Telelkebir.

CONCLUSION

Most invasive salmonelloses in southwest Nigeria are vaccine-preventable infections due to multidrug-resistant, West African dominant S. Typhi lineage 3.1.1. Invasive NTS serovars, including some harbouring typhoidal toxin or resistance genes, represented a third of the isolates emphasizing the need for better diagnosis and surveillance.

背景

沙门氏菌病在非洲造成了很大的发病率和死亡率。关于在尼日利亚流行的侵袭性沙门氏菌谱系的信息很少。

方法

2016 年至 2020 年间，从尼日利亚西南部的五家三级医院采集血液（n=60）和脑脊液（CSF，n=3）中的沙门氏菌 enterica 进行抗生素敏感性试验和 Illumina 测序。使用公开的生物信息学工具对基因组进行分析。

结果

血液分离株和序列型（ST）为伤寒沙门氏菌[ST1，n=1 和 ST2，n=43]和侵袭性非伤寒沙门氏菌（iNTS）（肠炎沙门氏菌[ST11，n=7]、都柏林沙门氏菌[ST10，n=1]、杜伦沙门氏菌[ST10，n=2]、里森沙门氏菌[ST8756，n=2]、切斯特沙门氏菌[ST2063，n=1]、都柏林沙门氏菌[ST10，n=1]、婴儿沙门氏菌[ST603，n=1]、泰莱基尔沙门氏菌[ST8757，n=1]和鼠伤寒沙门氏菌[ST313，n=1]）。从 CSF 中分离出伤寒沙门氏菌 ST2（n=2）和 Adabraka ST8757（n=1）。大多数伤寒沙门氏菌属于基因型 3.1.1（n=44），携带 IncY 质粒，具有多种抗生素耐药基因（ARGs），包括 blaTEM-1（n=38）、aph（6）-Id（n=32）、tet（A）（n=33）、sul2（n=32）、dfrA14（n=30）以及喹诺酮耐药相关的 gyrA_S83Y 单核苷酸多态性（n=37）。所有肠炎沙门氏菌均携带 aph（3"）-Ib、blaTEM-1、catA1、dfrA7、sul1、sul2、tet（B）基因，在 Telelkebir 中检测到一个单一的 ARG，qnrB19。伤寒毒素 cdtB、pltA 和 pltB 在伤寒沙门氏菌、里森沙门氏菌、切斯特沙门氏菌和 Telelkebir 中均有检出。