背景:耐万古霉素肠球菌(VRE)是在全球耐抗生素细菌优先清单中被归类为高优先级细菌的重要病原体,以指导研究,发现,以及世界卫生组织发布的新抗生素的开发。这项研究的目的是确定风险因素,阻力,毒力,与在南非卫生系统后住院患者中循环的屎肠球菌和粪肠球菌的多药耐药和克隆谱系相关的动员体,使用全基因组测序(WGS)。
方法:对2017年住院患者进行了为期两个月的横断面研究。直肠拭子是从城市三级医院的内科和外科病房收治的患者中收集的,和uMgungundlovu区的一所农村地区医院,南非。在补充了6mg/L万古霉素的胆汁叠氮化琼脂上筛选肠球菌对万古霉素的耐药性,并使用ROSCO试剂盒进行VRE的确认。使用常规和实时PCR方法来确定VanA的存在,VanB,VanC-2/3和VanC-1基因。使用NexteraXTDNA样品制备试剂盒(Illumina,圣地亚哥,CA,美国)和基因组测序是使用IlluminaMiSeq仪器在国家传染病测序核心设施研究所进行的,覆盖率为100倍,南非。抗生素抗性基因,毒力因子,质粒,整合子和CRISPR使用RAST进行表征,ResFinder,VirulenceFinder,PlasmidFinder,分别为PHAST和ISFinder。
结果:测序分析表明,这些菌株具有许多对糖肽的抗性基因(vanC[100%],vex3[100%],vex2[83,33%]和vanG[16,66%]),大环内酯类,lincosamides,sterptogramineB(ermB[33,32%],伊萨[16,66%],地区和三级医院的emeA[16,66%])和四环素(tetM[33,32%])。多药外排泵,包括MATE,还鉴定了赋予对几类抗生素抗性的MFS和pmrA。观察到的主要转座因子在Tn3家族中,特别是TN1546。在地区医院的屎肠球菌中鉴定出四种单序列类型(STs),即ST822,ST636,ST97以及一个新的ST分配ST1386,而一个谱系,在三级医院检测到ST29。
结论:该研究揭示了住院患者中多药耐药粪肠球菌和屎肠球菌的遗传多样性和高致病性。它强调了对入院患者进行常规筛查以及感染控制程序的必要性,应加强抗菌药物管理和认识,以预防和/或遏制耐多药屎肠球菌和粪肠球菌在南非医院和社区的携带和传播。
BACKGROUND: Vancomycin-resistant enterococci (VRE) are important pathogens categorized as high-priority bacteria in the Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics published by the World Health Organization. The aim of this study was to determine the risk factors, resistance, virulence, mobilomes associated with multidrug-resistant and clonal lineages of Enterococcus faecium and faecalis circulating among hospitalized patients following the health system in South Africa, using whole genome sequencing (WGS).
METHODS: A cross-sectional study was conducted during a two-month periods among hospitalized patients in 2017. Rectal swabs were collected from patients admitted to medical and surgical wards in an urban tertiary hospital, and a rural district hospital in uMgungundlovu district, South Africa. Enterococci were screened for vancomycin resistance on bile esculin azide agar supplemented with 6 mg/L of vancomycin and confirmation of VRE was done using ROSCO kits. Conventional and real-time PCR methods were used to ascertain the presence of VanA, VanB, VanC-2/3 and VanC-1 genes. All six multidrug-resistant Enterococcus faecalis and faecium selected were identified using multiplexed paired-end libraries (2 × 300 bp) with the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA, USA) and genome sequencing was done using Illumina MiSeq instrument with 100× coverage at the National Institute of Communicable Diseases Sequencing Core Facility, South Africa. Antibiotic resistance genes, virulence factors, plasmids, integrons and CRISPR were characterized using RAST, ResFinder, VirulenceFinder, PlasmidFinder, PHAST and ISFinder respectively.
RESULTS: Sequencing analysis revealed that these strains harbouring numerous resistance genes to glycopeptides (vanC[100%], vex3[100%], vex2[83,33%] and vanG[16,66%]), macrolides, lincosamides, sterptogramine B (ermB[33,32%], Isa[16,66%], emeA[16,66%]) and tetracyclines (tetM[33,32%]) in both district and tertiary hospitals. Multidrug efflux pumps including MATE, MFS and pmrA conferring resistance to several classes of antibiotics were also identified. The main transposable elements observed were in the Tn3 family, specifically Tn1546. Four single sequence types (STs) were identified among E. faecium in the district hospital, namely ST822, ST636, ST97 along with a novel ST assigned ST1386, while one lineage, ST29 was detected in the tertiary hospital.
CONCLUSIONS: The study reveals the genetic diversity and high pathogenicity of multidrug-resistant Enterococcus faecalis and faecium circulating among hospitalized patients. It underlines the necessity to implement routine screening of admitted patients coupled with infection control procedures, antimicrobial stewardship and awareness should be strengthened to prevent and/or contain the carriage and spread of multidrug resistant E. faecium and E. faecalis in hospitals and communities in South Africa.