Valley-Omar Ziyaad, Nindo Fredrick, Mudau Maanda, Hsiao Marvin, Martin Darren Patrick
Centre for Respiratory Diseases and Meningitis, Virology, National Institute for Communicable Diseases, Sandringham, Johannesburg, South Africa.
University of Cape Town, Faculty of Health Sciences, Department of Clinical Laboratory Sciences Medical Virology, Observatory, Cape Town, South Africa.
PLoS One. 2015 Nov 13;10(11):e0141744. doi: 10.1371/journal.pone.0141744. eCollection 2015.
Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events.
调查流感医院内传播的传统模式需要结合确证性分子诊断检测和流行病学调查。像流感这样常见的医院获得性感染需要具备敏锐的鉴别能力，以区分病毒分离株，从而准确识别患者传播链。我们评估了在南非开普敦一家儿童医院为期四个月的时间里，调查医院内传播程度时，流感血凝素序列系统发育分析是否可用于丰富流行病学数据。最初通过基本的患者入院数据，结合最大似然法和时间尺度贝叶斯系统发育分析来确定可能的传播链/途径。这些分析表明，大多数潜在的医院获得性感染病例是由甲型流感病毒多次传入医院所致，其中包括不同患者之间病毒血凝素序列相同的情况。此外，总体上无法建立患者/病毒分离株的流行病学传播联系，这意味着已鉴定的分离株可能源自无症状的住院患者、访客或医院工作人员。相比之下，一项未使用病毒系统发育分析的传统流行病学调查，基于特定时间段内患者共同入住特定病房的情况，表明多个医院获得性感染病例可能源于有限数量的可识别的指示病毒分离株/患者。这种传统的流行病学分析本身可能错误地暗示无关病例之间的联系，低估独特感染的数量，并且可能忽略医院传播可能具有的扩散性质，测序数据表明这是由甲型流感分离株多次独特传入各个医院病房所致。我们已经证明了病毒序列数据在医院内传播调查中的功能作用，即通过梳理可能的传播途径并更准确地计算可能的传播事件数量，丰富传统的非分子观察性流行病学调查。
