全基因组测序揭示了来自坦桑尼亚莫希一家三级保健医院患者的 中高度克隆多样性。
Whole genome sequencing reveals high clonal diversity of isolated from patients in a tertiary care hospital in Moshi, Tanzania.
机构信息
1Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre, Moshi, Tanzania.
2Kilimanjaro Christian Medical University College, Moshi, Tanzania.
出版信息
Antimicrob Resist Infect Control. 2018 Jun 8;7:72. doi: 10.1186/s13756-018-0361-x. eCollection 2018.
BACKGROUND
Limited information regarding the clonality of circulating strains in tertiary care hospitals in low and middle-income countries is available. The purpose of this study was to determine the serotypes, antimicrobial resistance and virulence genes. Further, we carried out a phylogenetic tree reconstruction to determine relatedness of isolated from patients in a tertiary care hospital in Tanzania.
METHODS
isolates from inpatients admitted at Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced at KCMC hospital. Sequence analysis was done for identification of resistance genes, Multi-Locus Sequence Typing, serotyping, and virulence genes. Phylogeny reconstruction using CSI Phylogeny was done to ascertain relatedness. Stata 13 (College Station, Texas 77,845 USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and whole genome sequence predicted antimicrobial resistance.
RESULTS
Out of 38 isolates, 21 different sequence types (ST) were observed. Eight (21.1%) isolates belonged to ST131; of which 7 (87.5.%) were serotype O25:H4. Ten (18.4%) isolates belonged to ST10 clonal complex; of these, four (40.0%) were ST617 with serotype O89:H10. Twenty-eight (73.7%) isolates carried genes encoding beta-lactam resistance enzymes On average, agreement across all drugs tested was 83.9%. Trimethoprim/sulphamethoxazole (co-trimoxazole) showed moderate agreement: 45.8%, kappa =15% and = 0.08. Amoxicillin-clavulanate showed strongest agreement: 87.5%, kappa = 74% and = 0.0001. Twenty-two (57.9%) isolates carried virulence factors for host cells adherence and 25 (65.7%) for factors that promote immune evasion by increasing survival in serum. The phylogeny analysis showed that ST131 clustering close together whereas ST10 clonal complex had a very clear segregation of the ST617 and a mix of the rest STs.
CONCLUSION
There is a high diversity of isolated from patients admitted to a tertiary care hospital in Tanzania. This underscores the necessity to routinely screen all bacterial isolates of clinical importance in tertiary health care facilities. WGS use for laboratory-based surveillance can be an effective early warning system for emerging pathogens and resistance mechanisms in LMICs.
背景
关于中低收入国家三级保健医院循环菌株的克隆性，信息有限。本研究的目的是确定血清型、抗菌药物耐药性和毒力基因。此外，我们进行了系统发育树重建，以确定从坦桑尼亚一家三级保健医院的患者中分离出的 的相关性。
方法
2013 年 8 月至 2015 年 8 月期间，在乞力马扎罗基督教医学中心住院的患者中分离出的 ，在 KCMC 医院进行全基因组测序。通过序列分析鉴定耐药基因、多位点序列分型、血清分型和毒力基因。使用 CSI 系统发育进行系统发育重建以确定 的相关性。使用 Stata 13（美国德克萨斯州立大学 77845 号，学院站）确定表型检测和全基因组序列预测的抗菌药物耐药性之间的 Cohen's kappa 系数一致性。
结果
在 38 株 中，观察到 21 种不同的序列类型（ST）。8 株（21.1%）属于 ST131；其中 7 株（87.5%）为血清型 O25：H4。10 株（18.4%）属于 ST10 克隆复合体；其中 4 株（40.0%）为 ST617，血清型为 O89：H10。28 株（73.7%）携带编码β-内酰胺类药物耐药酶的基因。平均而言，所有测试药物的一致性为 83.9%。甲氧苄啶/磺胺甲恶唑（复方新诺明）显示出中等程度的一致性：45.8%，kappa=15%， = 0.08。阿莫西林-克拉维酸显示出最强的一致性：87.5%，kappa=74%， = 0.0001。22 株（57.9%）携带宿主细胞黏附的毒力因子，25 株（65.7%）携带促进免疫逃避的因子，从而增加血清中的存活率。系统发育分析表明，ST131 聚类紧密，而 ST10 克隆复合体则清楚地分离出 ST617，并且混合了其余的 STs。
结论
从坦桑尼亚一家三级保健医院的患者中分离出的 具有高度多样性。这突显了在三级医疗机构中常规筛查所有具有临床重要性的细菌分离株的必要性。基于实验室的监测中使用 WGS 可以作为中低收入国家新兴病原体和耐药机制的有效早期预警系统。
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