Systematic Review and Meta-Analysis of Antimicrobial Susceptibility among Aeromonas spp. from a One Health perspective

Daniel Christopher Jones, Jenna Lewis, Emily Lou LaMartina, Andrew James Dahl, Nischala Nagesh Holavanahalli, Ryan Newton, Troy A Skwor

Microbial community 16S rRNA gene sequence datasets

Estimate proportions of Aeromonas in each dataset

1. Obtain raw FASTQs

• NCBI Short Read Archive. Find published studies with 16S rRNA gene amplicon sequencing done on seafood-associated samples (see ./SRA_code).
• UWM archives. Compile aquatic-environmental datasets from previously published works.
• see Aeromonas_16S_metadata.csv

2. Process raw 16S rRNA gene reads

• DADA2. Quality filter, merge paired-end reads, remove chimeric sequences, assign taxonomy with DADA2 (see ./DADA2_code).

3. Parse sequences classified as genus Aeromonas

• see Aeromonas_metanalyis.R