Azarian Taj, Cook Robert L, Johnson Judith A, Guzman Nilmarie, McCarter Yvette S, Gomez Noel, Rathore Mobeen H, Morris J Glenn, Salemi Marco
1College of Public Health and Health Professions and College of Medicine,Department of Epidemiology,University of Florida,Gainesville,Florida.
3Department of Pathology,Immunology and Laboratory Medicine,University of Florida,Gainesville,Florida.
Infect Control Hosp Epidemiol. 2015 Jul;36(7):777-85. doi: 10.1017/ice.2015.73. Epub 2015 May 8.
BACKGROUND Infants in the neonatal intensive care unit (NICU) are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) acquisition. Outbreaks may be difficult to identify due in part to limitations in current molecular genotyping available in clinical practice. Comparison of genome-wide single nucleotide polymorphisms (SNPs) may identify epidemiologically distinct isolates among a population sample that appears homogenous when evaluated using conventional typing methods. OBJECTIVE To investigate a putative MRSA outbreak in a NICU utilizing whole-genome sequencing and phylogenetic analysis to identify recent transmission events. DESIGN Clinical and surveillance specimens collected during clinical care and outbreak investigation. PATIENTS A total of 17 neonates hospitalized in a 43-bed level III NICU in northeastern Florida from December 2010 to October 2011 were included in this study. METHODS We assessed epidemiological data in conjunction with 4 typing methods: antibiograms, PFGE, spa types, and phylogenetic analysis of genome-wide SNPs. RESULTS Among the 17 type USA300 isolates, 4 different spa types were identified using pulsed-field gel electrophoresis. Phylogenetic analysis identified 5 infants as belonging to 2 clusters of epidemiologically linked cases and excluded 10 unlinked cases from putative transmission events. The availability of these results during the initial investigation would have improved infection control interventions. CONCLUSION Whole-genome sequencing and phylogenetic analysis are invaluable tools for epidemic investigation; they identify transmission events and exclude cases mistakenly implicated by traditional typing methods. When routinely applied to surveillance and investigation in the clinical setting, this approach may provide actionable intelligence for measured, appropriate, and effective interventions.
新生儿重症监护病房（NICU）中的婴儿感染耐甲氧西林金黄色葡萄球菌（MRSA）的风险增加。由于临床实践中现有分子基因分型存在局限性，疫情爆发可能难以识别。全基因组单核苷酸多态性（SNP）的比较可能会在使用传统分型方法评估时看似同质的人群样本中识别出流行病学上不同的分离株。目的：利用全基因组测序和系统发育分析调查NICU中疑似的MRSA疫情，以识别近期的传播事件。设计：在临床护理和疫情调查期间收集的临床和监测标本。患者：2010年12月至2011年10月在佛罗里达州东北部一家拥有43张床位的三级NICU住院的17名新生儿纳入本研究。方法：我们结合4种分型方法评估流行病学数据：抗菌谱、脉冲场凝胶电泳（PFGE）、spa分型以及全基因组SNP的系统发育分析。结果：在17株USA300型分离株中，使用脉冲场凝胶电泳鉴定出4种不同的spa分型。系统发育分析确定5名婴儿属于2组具有流行病学关联的病例，并排除了10例与疑似传播事件无关的病例。在初步调查期间获得这些结果将改善感染控制干预措施。结论：全基因组测序和系统发育分析是疫情调查的宝贵工具；它们可识别传播事件，并排除被传统分型方法错误牵连的病例。当常规应用于临床环境中的监测和调查时，这种方法可能为有针对性、适当且有效的干预措施提供可操作的情报。
