Human infections caused by pathogens transmitted from fish or aquatic environment are very common, depending on the dietary habits as well as the immune system of the individual. Health complications due to contaminated fish consumption have become a health burden globally, while many cases are being reported in Sri Lanka. Besides causing serious health impacts on consumer health fish contaminations can pose alarming economical situations, since marine fisheries sector contributes to approximately 2.8% of the gross domestic production of the island.  Avoiding bacterial contamination and unnecessary nutrient losses of harvested fish by measuring highly sensitive quality parameters is therefore very important to maintain microbial and nutritional quality of fish.
The number and the nature of bacteria on fish depends on many factors such as seawater pollution, temperature, method of capture, preservation method applied, transportation and handling practices.  Vibrio parahaemolyticus, Vibrio cholera, Escherichia coli, Aeromonas spp, Salmonella, Staphylococcus aureus, Listeria monocytogenes, Clostridium botulinum, Clostridium perfringens and Campylobacter jejuni are some of the major foodborne human pathogens associated with fish and fish products.  Organisms such as Vibrio cholera, Salmonella, Escherichia coli and other Coliforms are present in substantial numbers in fish contaminated with human and animal fecal matter. Knowledge of the source of contamination and the type of organisms present contribute significantly to avoid further spoilage, whilst sustaining its quality.
Current microbiological testing of contaminated fish is mainly based on plating of microorganisms and has had been in use as a gold standard method for the past few decades. Plating techniques is used to determine different parameters such as Total Viable Bacterial Counts (TVBC), Total Coliform Counts (TCC), Total Fecal Coliform Counts (TFCC), Total Pseudomonas Counts (TPC), Total Yeast Counts (TYC), Total Molds Counts (TMC) and qualitative analysis of Salmonella and Vibrio counts. Although plating method is commonly used in daily practice, it is a time consuming, laborious process that is often hindered by fastidious growth requirements, culture failures, unusual morphological characteristics or lack of previous recognition of bacteria. Such a technique can have major drawbacks if used for a spontaneous outbreak, for it requires a minimum turnaround time of one week. Alternative test methods with lesser turnaround times and higher sensitivity should be employed for testing of contaminants, in order to meet the ever increasing demand for food quality. At present, many novel technologies with higher analysis capabilities have displaced the conventional methodologies generating results with higher specificity and accuracy.
With high quality food trending in the world food market today, Sri Lanka also requires adopt newer technologies that can facilitate faster and accurate identification of bacteria. One such approach is identifying microorganisms by testing of 16s r RNA gene, which allows identification of bacteria at a wider scale. 16s rRNA gene testing is a universal method which aids identification of the whole spectrum of bacteria in a single test in just 21 hours, and can be used as a perfect substitution for an entire regiment of conventional tests. Based on a next- generation sequencing platform, this test results an enormously increased output of data, combined with highest accuracy and speed. 16s rRNA gene sequencing assist identification of intragenic variances or the differences among bacteria of the same species as well as their relative abundances meeting targets that were always beyond the reach of conventional techniques. With 16s rRNA sequencing, bacterial identification has become rapider and easier than ever.
- Mattakkuliya, Colombo. “BACTERIAL CONTAMINATION OF FISH SOLD IN FISH MARKETS IN THE CENTRAL PROVINCE OF SRI LANKA.” (2005).
- Novotny, L., et al. “Fish: a potential source of bacterial pathogens for human beings.” Veterinarni Medicina9 (2004): 343-358.