Situation
Food borne diseases have become a common issue in Sri Lanka, with outbreaks, hospital admissions and deaths due to food poisoning being reported frequently. The newspapers reported the death of a child upon consumption of sausage contaminated with Shigella spp [1]. In May 2013, a group of students of Ruhuna University were hospitalized due to food poisoning [2]. Another incident was reported in March 2013, nearly 25 were admitted to the hospital as they developed adverse reactions to the food they had consumed [3]. Food poisoning is becoming a public health concern with alarming amounts of people being victimized for repeated outbreaks.
Many bacteria; mainly E.coli, Bacillus cereus, Salmonella spp., Shigella spp., Campylobacter jejuni, Clostridium botulinum, Clostridium perfringens, Listeria monocytogenes, Vibrio cholera, Staphylococcus spp, Yersinia spp. and fungi; Cladosporium, Pecinillium, Aspergillus[4] ect as well as their toxins act as potential food poisoning agents. Considering the ubiquity of the above said pathogens, establishing microbiological standards in food processing industry is extremely essential in order to manufacture pathogen free food products for consumer consumption.
Microbiological assessment for quality and safety of food and beverages traditionally relies upon the enumeration and specific detection of pathogenic organisms. Culturing of microorganisms, isolation of colonies based on morphological features and subjecting them to biochemical, physiological and serological tests are carried out routinely as verified methods of identification tests. Although these methods can provide both quantitative and qualitative information on the information on microorganisms present in food [5], they are generally slow and require a minimum of 7 day period to provide results; and uses a large amount of material and labour. The accuracy of the result may depend on operator expertise. Some organisms can be unculturable, fastidious or spore forming thus hindering the identification process. Certain microbiology laboratories also use modified conventional methods, membrane filtration techniques and immunological assays that can be very expensive in testing of large amounts of samples.
Solution
Therefore, food and beverage manufacturers seek for sensitive, accurate and rapid assays that can screen large number of samples in order to increase the process efficiency. Implementing an innovative technique that can aid such measurements will help to increase the manufacture throughput while an increased number of processed food and beverage batches get screened on routine basis; resulting in higher profits, safer consumer products and good customer feedbacks.
Fig– The most abundant species in soy bean yogurt and the yogurt drink as discovered by 16s rRNA gene sequencing. Numbers indicate the frequencies in percent. [6]
16s rRNA gene sequencing of bacteria and ITS region sequencing of fungi is such an innovative approach that generates results in 48 hours of runtime. The rapidity helps in the increase of process efficiency, increasing the number of samples being subjected to testing each turn and the technique can be used for immediate identification of pathogens during an outbreak. Based on Next Generation Technology it has a dramatically increased throughput and permits parallel testing upto 200 samples per run. Test organisms can be identified up to species level with their relative abundances. High sensitivity of the technique allows identification of intragenic variations among closely related organisms. Therefore, presence of wanted microorganisms confirmed and the presence of pathogens can be ruled out or identification of newer pathogenic strains can be performed with elevated confidence levels. Being a culture independent technique, sequencing of 16s rRNA gene (bacteria) and ITS region (fungi) eliminates the need of culturing of organisms and problems that are often encountered with unculturable and fastidious organisms. Therefore, the technique is used in many laboratories worldwide to ensure the microbial quality of their products [6].
With 16s rRNA gene sequencing of bacteria and ITS region sequencing of fungi coming to the limelight, food and beverage manufacturers can look forward to an era of absolute microbial quality, higher productivity, lesser customer complaints and better customer satisfaction.
To summarize, 16s rRNA Sequencing has following advantages compared to other techniques-
| Conventional techniques | 16s rRNA Sequencing |
|---|---|
| Longer turnaround times. A single test requires a minimum of 7 days | Lesser turnaround times. Extremely rapid with a run time of only 12 hours. |
| Test accuracy is dependent on operator expertise. The accuracy of testing Is,̴80%[9] | Accuracy is operator-independent. Highly accurate with an accuracy of 99.9% |
| Fastidious, unculturable organisms and unusual biochemical reactions impede the identification process. | Test method is culture independent; Growth requirements, biochemical reactions and culture failures do not affect the identification process. |
| Only a limited number of organisms can be identified. Important organisms in a test sample can be missed out. | Identifies the complete range of organisms present in a test sample. |
| The percentage of strains correctly identified to the species level is sometimes less than satisfactory. | Permits identification of complete spectrum of organisms down to species level, their intragenic variations and relative abundances |
| Limited throughput, Sensitivity may vary. | Dramatic increase in throughput; High sensitivity |
Reference-
- D.C.Hettiarachchi. Food contaminated with Shigella bacteria. [ONLINE] Available at:http://www.sundaytimes.lk/050814/ft/9.html. [Accessed 16 September 13].
- Sirasa Newsfirst. 2013. Students hospitalised due to food poisoning. [ONLINE] Available at:http://www.newsfirst.lk/english/node/23721. [Accessed 10 September 13].
- Daily Mirror News paper. 2013. Food Poisoning. [ONLINE] Available at:http://epaper.dailymirror.lk/epaper/viewer.aspx. [Accessed 25 July 13].
- Takatori, K. O. S. U. K. E., M. A. K. I. Aihara, and Y. Sugita-Konishi. “Hazardous food-borne fungi and present and future approaches to the mycotoxin regulations in Japan].” Kokuritsu Iyakuhin Shokuhin Eisei Kenkyūjo hōkoku= Bulletin of National Institute of Health Sciences 124 (2006): 21.
- Deak, Tibor. “TESTING METHODS IN FOOD MICROBIOLOGY.”
- Wahl, Benjamin, et al. “Characterisation of Bacteria in Food Samples by Next Generation Sequencing.”
- Janda, J. Michael, and Sharon L. Abbott. “Bacterial identification for publication: when is enough enough?.” Journal of clinical microbiology 40.6 (2002): 1887-1891.
