Cryptic Carriers of Resistance: A Metagenomic Sentinel Case of Vibrio and CARB-7 β-Lactamase in a Lagos Marine Crab

Metagenomic characterization of foodborne pathogens in Nigerian seafood remains critically limited. This sentinel case investigated Vibrio species in a single crab (Callinectes spp.) from Eleko Beach, Lagos, Nigeria, using shotgun metagenomic sequencing on the PacBio Onso platform. Taxonomy was assigned via Kraken2/Bracken with Krona visualization. Diversity analyses used the vegan package in R. Phylogenetic analysis employed MAFFT, RAxML, and ape. Functional annotation used Prodigal and InterProScan. Antimicrobial resistance genes were detected using RGI/CARD. Taxonomic classification revealed 2,379 Vibrio fragments (0.04% of classified reads), identifying seventeen species including V. anguillarum (1,097), V. harveyi group (616), V. parahaemolyticus (237), V. cholerae (6), and V. vulnificus (10). Photobacterium included P. ganghwense (97) and P. damselae (15). Eukaryota constituted 45.6% of reads, with Homo sapiens at 6.44%, indicating human DNA contamination. Other pathogens included E. coli, S. aureus, L. monocytogenes, and C. jejuni. Alpha diversity was moderate (Shannon = 2.10; Chao1 = 287). Beta diversity revealed significant group differences (PERMANOVA: R² = 0.2345, p = 0.001). Phylogenetic analysis resolved seven genera, with Vibrio as a well-supported clade (bootstrap ≥ 90%). Functional annotation identified protein kinase domains and reverse transcriptases. The CARB-7 β-lactamase gene was detected. This sentinel case identified seventeen Vibrio species and a β-lactamase resistance gene in a single Lagos crab. The high human DNA contamination emphasizes the urgent need for effective decontamination protocols in seafood metagenomics.