Comparison of the Multiple Platforms to Identify Various Aeromonas Species.

Xiaoli Du,Xin Lu,Biao Kan,Yanping Ma,Haijian Zhou,Yujuan Jin,Zhenpeng Li,Jiuyin Liu,Zhe Li,Mengyu Wang,Yan Ren,Zhigang Cui,Daoli Chen,Jialiang Xu,Yang Luan,Xiaoli Wang

doi:10.3389/fmicb.2020.625961

Abstract

We compared several identification methods for Aeromonas genus members, including traditional biochemical testing, multiplex-PCR amplification, mass spectrometry identification, whole-genome sequencing, multilocus phylogenetic analysis (MLPA), and rpoD, gyrA, and rpoD-gyrA gene sequencing. Isolates (n = 62) belonging to the Aeromonas genus, which were came from the bacterial bank in the laboratory, were used to assess the identification accuracy of the different methods. Whole-genome sequencing showed that the Aeromonas spp. isolates comprised A. caviae (n = 21), A. veronii (n = 18), A. dhakensis (n = 8), A. hydrophila (n = 7), A. jandaei (n = 5), A. enteropelogenes (n = 2), and A. media (n = 1). Using the whole-genome sequencing results as the standard, the consistency of the other methods was compared with them. The results were 46.77% (29/62) for biochemical identification, 83.87% (52/62) for mass spectrometric identification, 67.74% (42/62) for multiplex-PCR, 100% (62/62) for MLPA typing, 72.58% for gyrA, and 59.68% for rpoD and gyrA-rpoD. MLPA was the most consistent, followed by mass spectrometry. Therefore, in the public health laboratory, both MLPA and whole-genome sequencing methods can be used to identify various Aeromonas species. However, rapid and relatively accurate mass spectrometry is recommended for clinical lab.

Highlights

Aeromonas, a Gram-negative, opportunistic pathogen bacterium, is prevalent in animals and the environment (Nolla-Salas et al, 2017)
32 Aeromonas species have been identified to date (MartinezMurcia et al, 2011), among which A. caviae, A. hydrophila, and A. veronii are closely associated with the clinical symptoms of diarrhea (Janda and Duffey, 1988; Parker and Shaw, 2011; Li et al, 2015)
A core genomic single-nucleotide polymorphism (SNP) tree was constructed on the 364 whole genomes we downloaded from GenBank, along with the genome sequences obtained in this study

Summary

INTRODUCTION

A Gram-negative, opportunistic pathogen bacterium, is prevalent in animals and the environment (Nolla-Salas et al, 2017). With increasing numbers of clinical cases of Aeromonas-related cases, this species is considered to be a new gastrointestinal disease-causing pathogen in humans and other animals, and infections with it can become serious (Janda and Abbott, 2010). MLPA typing is used to identify the characteristics of microbial isolates This method assesses the degree of bacterial variation in a sample according to the differences existing among house-keeping gene sequences (Maiden et al, 1998; Martínez-Murcia et al, 2016). We compared the consistency of various techniques (i.e., biochemical detection, mass spectrometry identification, multiplex-PCR, MLPA, and rpoD, gyrA, rpoDgyrA house-keeping gene amplification) with that of wholegenome sequencing at identifying Aeromonas species. The aim is to provide suggestion to choose the different method for the identification of Aeromonas according to different laboratory conditions

MATERIALS AND METHODS

RESULTS

DISCUSSION

DATA AVAILABILITY STATEMENT