Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil.
Eur J Clin Microbiol Infect Dis. 2022 Apr;41(4):547-558. doi: 10.1007/s10096-022-04413-8. Epub 2022 Feb 15.
Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.e., Phytobacter spp., that have so far gone unrecognised due to unsatisfactory identification procedures in clinical diagnostics. Here, we present a genomics and literature-based approach to establish the importance of the genus Phytobacter as a clinically relevant member of the Enterobacteriaceae family.
尽管许多具有临床重要意义的肠杆菌科菌株属于少数几个属和种，但仍有相当数量的分离株无法归入这一分类，其正确鉴定仍然具有挑战性。随着基因组学领域的当前进展，不仅可以生成高质量的数据来准确鉴定医院内分离株的种水平，并了解其致病潜力，还可以回顾性地分析基因组序列数据库，以鉴定特定生物体的过去复发情况，特别是那些最初根据错误或过时的分类法发表的生物体。我们建议一般使用这种方法来进一步分类临床上相关的分类单元，即迄今为止由于临床诊断中鉴定程序不完善而未被识别的 Phytobacter 属。在这里，我们提出了一种基于基因组学和文献的方法来确定 Phytobacter 属作为肠杆菌科家族中具有临床相关性的成员的重要性。
