Ziebell Kim, Chui Linda, King Robin, Johnson Suzanne, Boerlin Patrick, Johnson Roger P
National Microbiology Laboratory at Guelph, PHAC, Guelph, ON, Canada.
Alberta Provincial Laboratory for Public Health, Edmonton, AB, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada.
J Microbiol Methods. 2017 Aug;139:29-36. doi: 10.1016/j.mimet.2017.04.012. Epub 2017 Apr 26.
Salmonella enterica subspecies enterica serovar Enteritidis (SE) is one of the most common causes of human salmonellosis and in Canada currently accounts for over 40% of human cases. Reliable subtyping of isolates is required for outbreak detection and source attribution. However, Pulsed-Field Gel Electrophoresis (PFGE), the current standard subtyping method for Salmonella spp., is compromised by the high genetic homogeneity of SE. Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) was introduced to supplement PFGE, although there is a lack of data on the ability of MLVA to subtype Canadian isolates of SE. Three subtyping methods, PFGE, MLVA and phage typing were compared for their discriminatory power when applied to three panels of Canadian SE isolates: Panel 1: 70 isolates representing the diversity of phage types (PTs) and PFGE subtypes within these PTs; Panel 2: 214 apparently unrelated SE isolates of the most common PTs; and Panel 3: 27 isolates from 10 groups of epidemiologically related strains. For Panel 2 isolates, four MLVA subtypes were shared among 74% of unrelated isolates and in Panel 3 isolates, one MLVA subtype accounted for 62% of the isolates. For all panels, combining results from PFGE, MLVA and PT gave the best discrimination, except in Panel 1, where the combination of PT and PFGE was equally as high, due to the selection criteria for this panel. However, none of these methods is sufficiently discriminatory alone for reliable outbreak detection or source attribution, and must be applied together to achieve sufficient discrimination for practical purposes. Even then, some large clusters were not differentiated adequately. More discriminatory methods are required for reliable subtyping of this genetically highly homogeneous serovar. This need will likely be met by whole genome sequence analysis given the recent promising reports and as more laboratories implement this tool for outbreak response and surveillance.
肠炎沙门氏菌肠炎亚种肠炎血清型（SE）是人类沙门氏菌病最常见的病因之一，在加拿大目前占人类病例的40%以上。为了进行疫情检测和溯源，需要对分离株进行可靠的分型。然而，脉冲场凝胶电泳（PFGE）作为目前沙门氏菌属的标准分型方法，因SE的高遗传同质性而受到影响。多基因座可变数目串联重复分析（MLVA）被引入以补充PFGE，尽管缺乏关于MLVA对加拿大SE分离株进行分型能力的数据。比较了三种分型方法，即PFGE、MLVA和噬菌体分型，将它们应用于三组加拿大SE分离株时的鉴别力：第1组：70株分离株，代表噬菌体类型（PTs）及其内部PFGE亚型的多样性；第2组：214株显然不相关的最常见PTs的SE分离株；第3组：来自10组流行病学相关菌株的27株分离株。对于第2组分离株，74%的不相关分离株共享四种MLVA亚型，对于第3组分离株，一种MLVA亚型占分离株的62%。对于所有组，结合PFGE、MLVA和PT的结果可提供最佳鉴别力，但在第1组中除外，由于该组的选择标准，PT和PFGE的组合同样具有很高的鉴别力。然而，这些方法单独使用时，都没有足够的鉴别力用于可靠的疫情检测或溯源，必须一起应用才能达到实际所需的足够鉴别力。即便如此，一些大的聚类仍未得到充分区分。对于这种遗传高度同质的血清型进行可靠分型，需要更具鉴别力的方法。鉴于最近有前景的报告以及越来越多的实验室将此工具用于疫情应对和监测，全基因组序列分析可能会满足这一需求。
