基于全基因组序列的方法验证了多聚gyrB PCR 检测法对鲍曼不动杆菌的鉴定有效性。
Multiplex gyrB PCR Assay for Identification of Acinetobacter baumannii Is Validated by Whole Genome Sequence-Based Assays.
机构信息
Department of Microbiology, College of Medicine, Kuwait University, Kuwait City, Kuwait.
出版信息
Med Princ Pract. 2022;31(5):493-496. doi: 10.1159/000526402. Epub 2022 Aug 9.
OBJECTIVE
A multiplex gyrB PCR assay has been used to diagnose Acinetobacter baumannii. However, this assay has not been validated against the gold standard DNA-DNA hybridization assay, which is a laborious method. DNA-DNA hybridization assay is now replaced by whole genome sequence (WGS)-based methods. Two such methods are a k-mer-based search of sequence reads using the Kraken 2 program and average nucleotide identity (ANI). The objective was to validate the gyrB PCR assay with WGS-based methods.
SUBJECTS AND METHODS
We cultured 270 sequential A. baumannii isolates from the rectal swabs of 32 adult patients. The identity of the isolates was determined by gyrB PCR. The sequences of 269 isolates were determined by Illumina sequencing and the taxonomy was inferred by the Kraken 2 program and ANI.
RESULTS
All the 269 isolates were confirmed as A. baumannii by Kraken 2 and ANI.
CONCLUSION
The gyrB PCR assay is now validated for easy identification of A. baumannii in comparison with gold standard WGS-based assays.
目的
已使用多重gyrB PCR 检测法诊断鲍曼不动杆菌。然而，该检测法尚未针对金标准 DNA-DNA 杂交检测法进行验证，而后者是一种繁琐的方法。DNA-DNA 杂交检测法现已被基于全基因组序列（WGS）的方法所取代。其中两种方法是使用 Kraken 2 程序对序列读数进行基于 k-mer 的搜索和平均核苷酸同一性（ANI）。本研究旨在通过基于 WGS 的方法对 gyrB PCR 检测法进行验证。
对象和方法
我们培养了来自 32 名成年患者直肠拭子的 270 株连续鲍曼不动杆菌分离株。通过 gyrB PCR 确定分离株的身份。269 株分离株的序列通过 Illumina 测序确定，并通过 Kraken 2 程序和 ANI 推断其分类。
结果
所有 269 株分离株均通过 Kraken 2 和 ANI 确认为鲍曼不动杆菌。
结论
与金标准基于 WGS 的检测法相比，gyrB PCR 检测法现已得到验证，可用于方便地鉴定鲍曼不动杆菌。
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