Culture-dependent bacteria in commercial fishes: Qualitative assessment and molecular identification using 16S rRNA gene sequencing

Abstract

Fish contamination has been extensively investigated along the Saudi coasts, but studies pertaining to bacterial pathogens are scarce. We conducted qualitative assessment and molecular identification of culture-dependent bacteria in 13 fish species from three coastal sites and a local fish market in Jeddah, Saudi Arabia. Bacterial counts of gills, skin, gut and muscle were examined on agar plates of Macconkey's (Mac), Eosin Methylene Blue (EMB) and Thiosulfate Citrate Bile Salts (TCBS) culture media. Bacterial counts significantly differed between species, sources and feeding habits of examined fishes. exhibited higher counts on TCBS (all body parts), Mac (gills, muscle and gut) and EMB (gills and muscle). Fishes from Area I had higher bacterial loads, coinciding with those in seawater and sediment from the same site, indicating direct association between habitat conditions and the levels of bacterial contamination. By feeding habit, detritivorous fish harbored higher counts than herbivorous and carnivorous species. Bacterial counts of skin were higher in fish from market than field sites, and positively correlated with other body parts indicating the relation of surface bacterial load on the overall quality of fish. (Enterobacteriaceae) and (Vibrionaceae) were among the dominant species from fish muscle based on 16S rRNA sequencing. These species are known human pathogens capable of causing foodborne illness with severe antibiotic resistance. Opportunistic pathogens, e.g. sp. (Enterobacteriaceae) and (Pseudomonadaceae) also occurred in fish muscle. The inclusion of bacterial contamination in future monitoring efforts is thus crucial.

Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish (Tenualosa ilisha) marketed for human consumption in Bangladesh

“…Alongside resident microbes, the fish gut is also considered the principal reservoir for the colonization of pathogenic bacteria (Alikunhi et al . ). Poor handling, preservation and transportation methods make fish potential carriers of pathogenic bacteria.…”

“…The microbiota in the gastrointestinal tracts of fish plays important roles in digestion, nutrition, immunity, reproduction and the overall health of fish (Ghanbari et al 2015). Alongside resident microbes, the fish gut is also considered the principal reservoir for the colonization of pathogenic bacteria (Alikunhi et al 2017). Poor handling, preservation and transportation methods make fish potential carriers of pathogenic bacteria.…”

Selected Viruses Detected on and in our Food

“…In contrast to traditional diagnostic methods, metagenomic approaches by NGS are untargeted and require no specific knowledge of the viral genome. For bacteria, conserved genetic markers such as 16S rRNA allow for amplicon sequencing and subsequent taxonomic analysis resulting in an efficient representation of the bacterial abundance in a sample [10]. Since there are no conserved genetic markers present in different virus families, metagenomic analysis of viral populations is based on untargeted shotgun sequencing.…”

Physiological and bacteriological profile of the fish Clarias gariepinus (Siluriformes: Clariidae) chronically exposed to different concentrations of municipal waste leachate in Nigeria

“…It could be inferred that Micrococcus is a resident flora in the muscle. Although fish muscles have been considered by some researchers to be sterile (Apun, Yusof, & Jugang, 1999), other authors have reported the presence of bacteria in them (Alikunhi, Batang, AlJahdali, Aziz, & Al-Suwailem, 2016). Escherichia coli was the most predominated isolate recovered from this study and occurred mostly in the gill, followed by the skin and least in the muscle (Table 5).…”