Insight Into Whole Genome of Aeromonas veronii Isolated From Freshwater Fish by Resistome Analysis Reveal Extensively Antibiotic Resistant Traits

Aeromonas veronii outbreaks in tilapia farming caused relatively high mortalities, and the bacteria was resistant to many kinds of antimicrobials used in Thailand aquaculture. According to the CLSI standard, the determination of antimicrobials efficacy has been limited to phenotypic analyses, and a genomics study is required. This research aimed to analyze the resistome of A. veronii isolated from diseased tilapia in Chainat, Nong Khai, and Uttaradit provinces in Thailand. A total of 12 isolates of A. veronii were identified based on the gyrB sequencing and then, the MIC values to eight antimicrobials (AMP, AML, GEN, ENR, OXO, OTC, SXT, and FFC) were determined. According to the MIC patterns, whole genome sequencing (WGS) of five representatives and resistome analysis were performed, including 15 genomes of A. veronii isolated from freshwater fish available in the NCBI. All tilapia isolates were susceptible to FFC but resistant to AML and AMP while OTC resistance was the most dominant. In addition to the WGS analysis, 4.5 Mbp of A. veronii was characterized. A total of 20 ARGs were detected by resistome analysis and 16 genes were shared among the A. veronii population. In conclusion, A. veronii strains isolated from tilapia exhibited a resistance to several antimicrobials and multidrug resistance (MDR) which was related to the presence of multiple ARGs. Aeromonas veronii shared the ARGs in their population worldwide with a possibility of a plasmid-mediated acquisition due to the presence of resistance islands.

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Faculty Opinions recommendation of Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1086926.543459 ◽

2007 ◽

Author(s):

John Heritage

Keyword(s):

Staphylococcus Aureus ◽

Multidrug Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Faculty Opinions recommendation of Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1086926.540868 ◽

2007 ◽

Author(s):

Thomas Dougherty

Keyword(s):

Staphylococcus Aureus ◽

Multidrug Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome

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Whole Genome Sequencing of Fusarium fujikuroi Provides Insight into the Role of Secretory Proteins and Cell Wall Degrading Enzymes in Causing Bakanae Disease of Rice

Frontiers in Plant Science ◽

10.3389/fpls.2017.02013 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 9

Author(s):

Bishnu M. Bashyal ◽

Kirti Rawat ◽

Sapna Sharma ◽

Deepika Kulshreshtha ◽

S. Gopala Krishnan ◽

...

Keyword(s):

Cell Wall ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fusarium Fujikuroi ◽

Secretory Proteins ◽

Whole Genome ◽

Cell Wall Degrading Enzymes ◽

Bakanae Disease ◽

Insight Into

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Genetic Characterization of Brucella spp.: Whole Genome Sequencing-Based Approach for the Determination of Multiple Locus Variable Number Tandem Repeat Profiles

Frontiers in Microbiology ◽

10.3389/fmicb.2021.740068 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ana Pelerito ◽

Alexandra Nunes ◽

Teresa Grilo ◽

Joana Isidro ◽

Catarina Silva ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

In Silico ◽

Variable Number Tandem Repeat ◽

Epidemiological Studies ◽

Variable Number ◽

Epidemiological Surveillance ◽

Future Application ◽

Whole Genome

Brucellosis is an important zoonosis that is emerging in some regions of the world, gaining increased relevance with the inclusion of the causing agent Brucella spp. in the class B bioterrorism group. Until now, multi-locus VNTR Analysis (MLVA) based on 16 loci has been considered as the gold standard for Brucella typing. However, this methodology is laborious, and, with the rampant release of Brucella genomes, the transition from the traditional MLVA to whole genome sequencing (WGS)-based typing is on course. Nevertheless, in order to avoid a disruptive transition with the loss of massive genetic data obtained throughout the last decade and considering that the transition timings will vary considerably among different countries, it is important to determine WGS-based MLVA alleles of the nowadays sequenced genomes. On this regard, we aimed to evaluate the performance of a Python script that had been previously developed for the rapid in silico extraction of the MLVA alleles, by comparing it to the PCR-based MLVA procedure over 83 strains from different Brucella species. The WGS-based MLVA approach detected 95.3% of all possible 1,328 hits (83 strains×16 loci) and showed an agreement rate with the PCR-based MLVA procedure of 96.4% for MLVA-16. According to our dataset, we suggest the use of a minimal depth of coverage of ~50x and a maximum number of ~200 contigs as guiding “boundaries” for the future application of the script. In conclusion, the evaluated script seems to be a very useful and robust tool for the in silico determination of MLVA profiles of Brucella strains, allowing retrospective and prospective molecular epidemiological studies, which are important for maintaining an active epidemiological surveillance of brucellosis.

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