Kiiru Susan, Kasiano Purity, Maina John, Mwaniki John Njeru, Songoro Edinah, Kariuki Samuel
Center for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya.
Jomo Kenyatta University of Agriculture and Technology, JKUAT, Nairobi, Kenya.
Microbiol Spectr. 2025 Jun 3;13(6):e0142024. doi: 10.1128/spectrum.01420-24. Epub 2025 May 15.
High genomic plasticity within enables it to acquire and accumulate genetic material through horizontal gene transfer. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes, plasmid replicons, multilocus sequence types (MLST), and core genome MLST of multidrug-resistant recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement in Nairobi, Kenya. A total of 39 multidrug-resistant (MDR) strains had their DNA extracted, and whole-genome sequencing was done using the Illumina HiSeq 2000 platform. Twenty-six assemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology and EnteroBase. The isolates were categorized into four main phylogroups, where 10/26 (38.5%) belonged to the B2 phylogroup, 4/26 (15.4%) belonged to D, 3/26 (11.5%) belonged to A, 1/26 (3.8%) belonged to B1, while 8/26 (30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and sequence type (ST) 131. The most common beta-lactam resistance genes were and , followed by three fluoroquinolone resistance genes [ 6/26 (23.1%), 2/26 (7.7%), and , 8/26 (30.8%)]. Of 26 isolates, 15 had at least one amino acid substitution in the housekeeping genes (), (), (), (), (), and (), associated with resistance to fluoroquinolones. A total of 40 diverse virulence genes were detected among the isolates. Thirteen different STs were isolated from the genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46, and ST 1722. Only two isolates (2/26, 7.7%) from the Municipal City Council clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107), in particular, followed by the Col family. The study highlighted the first ST46 to harbor the gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR associated with diarrhea in an endemic setting in Kenya.
This study investigated the molecular characterization of multidrug-resistant isolated from diarrheagenic children under 5 years of age in Mukuru Informal Settlement in Nairobi, Kenya. This is an important addition to the genomic analysis data of multi-drug resistant diarrheal in Kenya. The use of whole-genome sequencing to identify and characterize these isolates is valuable and provides valuable insights into the molecular epidemiology of in the region.
其高度的基因组可塑性使其能够通过水平基因转移获取和积累遗传物质。在本研究中，我们试图调查从肯尼亚内罗毕穆库鲁非正式定居点5岁以下腹泻儿童中分离出的多重耐药性大肠杆菌的毒力基因、系统发育群、抗生素抗性基因、质粒复制子、多位点序列类型（MLST）和核心基因组MLST。总共提取了39株多重耐药（MDR）菌株的DNA，并使用Illumina HiSeq 2000平台进行全基因组测序。使用基因组流行病学中心和肠杆菌数据库提供的基于网络的生物信息学工具对26个组装体进行了分析。分离株被分为四个主要系统发育群，其中10/26（38.5%）属于B2系统发育群，4/26（15.4%）属于D群，3/26（11.5%）属于A群，1/26（3.8%）属于B1群，而8/26（30.8%）未确定。FimH30主要存在于最常见的B2系统发育群和序列类型（ST）131中。最常见的β-内酰胺抗性基因是blaCTX-M和blaTEM，其次是三种氟喹诺酮抗性基因[qnrS 6/26（23.1%）、qnrB 2/26（7.7%）和oqxB，8/26（30.8%）]。在26株分离株中，15株在管家基因gyrA、gyrB parC、parE、acrA和acrB中至少有一个氨基酸替换，与对氟喹诺酮的抗性相关。在分离株中总共检测到40种不同的毒力基因。从基因组中分离出13种不同的ST，包括ST 131、ST 3036、ST 38、ST 10、ST 12569、ST 15271 ST 2076、ST 311、ST 3572、ST 394、ST 453 ST 46和ST 1722。市议会诊所仅分离出的两株（2/26，7.7%）具有遗传相关性。此外，鉴定出的最丰富的质粒复制子属于IncF家族，特别是IncFII（pRSB107），其次是Col家族。该研究突出了肯尼亚首例携带编码在Col（BS512）、IncFII（pRSB107）和IncFIB（AP001918）质粒复制子中的blaCTX-M-15基因的ST型46。我们进一步证明了肯尼亚地方性环境中与腹泻相关的多重耐药性大肠杆菌的多样性。
本研究调查了从肯尼亚内罗毕穆库鲁非正式定居点5岁以下腹泻儿童中分离出的多重耐药性大肠杆菌的分子特征。这是肯尼亚多重耐药性腹泻大肠杆菌基因组分析数据的重要补充。使用全基因组测序来鉴定和表征这些分离株很有价值，并为该地区大肠杆菌的分子流行病学提供了有价值的见解。
