Comparison of the Multiple Platforms to Identify Various Aeromonas Species

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.

Aeromonas hydrophila ST251 and Aeromonas dhakensis are major emerging pathogens of striped catfish in Vietnam

“…Rep-PCR with a single repetitive primer such as ( GTG ) 5 has long been exploited in bacterial strain typing due to the relative simplicity, low cost, and discriminative power of the assay to subspecies level (Ishii and Sadowsky, 2009 ), and the continued relevance of this genotyping methodology was demonstrated. Although rep-PCR performed well to describe the population structure of strains associated with the MAS outbreaks, MLST provides a more objective approach to genotyping and a scheme has been established for the Aeromonas genus (Martino et al, 2011 ; Du et al, 2021 ). MLST allows the assignment of definitive genotypes for reliable comparisons to previous studies, but the approach can be relatively costly through reliance on Sanger sequencing technology.…”

Comparative genomic analysis of Aeromonas dhakensis and Aeromonas hydrophila from diseased striped catfish fingerlings cultured in Vietnam

“…With modern molecular-based detection methods it is now possible to distinguish A. dhakensis from A. hydrophila . Whole genome sequencing and multilocus phylogenetic analysis are to date the most accurate methods of identification ( Chen et al, 2016 ; Du et al, 2021 ), but such methods are not routinely used for diagnostic purposes in Vietnam and most other countries. The PCR primers initially used to identify the A. hydrophila is based on an article published in 1990 ( Pollard et al, 1990 ), before A. dhakensis was identified as a distinct species.…”

Non‐antibiotic approaches to combat motile Aeromonas infections in aquaculture: Current state of knowledge and future perspectives

“…In addition, confirmatory diagnosis using sequence analysis of gyrB gene or rpoD gene has been encouraged in research and diagnostic laboratories 80,85–87 . For the classification of aeromonads, multilocus phylogenetic analysis (MLPA) using the sequence of housekeeping genes ( gyrA , gyrB , rpoB , rpoD , recA , dnaJ , dnaK , dnaX , atpD , gltA , radA , zipA , cnp60 , mdh , metG , ppsA , tsf ) is one of the most accurate methods with classification accuracy up to 100% 88–91 . In recent years, core genome multilocus sequence typing (cgMLST) or whole‐genome multilocus sequence typing (wgMLST) offered an excellent platform for bacterial strain‐level identification and characterization 92–96 .…”

“…80,[85][86][87] For the classification of aeromonads, multilocus phylogenetic analysis (MLPA) using the sequence of housekeeping genes ( gyrA, gyrB, rpoB, rpoD, recA, dnaJ, dnaK, dnaX, atpD, gltA, radA, zipA, cnp60, mdh, metG, ppsA, tsf ) is one of the most accurate methods with classification accuracy up to 100%. [88][89][90][91] In recent years, core genome multilocus sequence typing (cgMLST) or whole-genome multilocus sequence typing (wgMLST) offered an excellent platform for bacterial strain-level identification and characterization. [92][93][94][95][96] The novel platform based on whole-genome sequencing should be investigated in Aeromonas-related studies in the future.…”