Case study on recent Leptospirosis outbreaks in Sri Lanka- A life saving approach with 16s rRNA sequencing
Situation
Leptospirosis, commonly known as Rat fever is an infectious disease caused by a particular type of Bacteria called a Spirochete of the genus Leptospira that affects humans and a wide range of animals,including mammals, birds, amphibians and reptiles.
Over the years, it has been emerging as a major public health threat in Sri Lanka and the country reported the worst ever Leptospirosis outbreak in 2008 in its history with more than 7000 reported cases1. The outbreak caused a total of 204 deaths with a case fatality rate of 2.9%2. In 2009, 4,980 cases and 145 deaths were reported and the outbreak persisted in 2010 with 4,553cases and 121 deaths7.
To implement efficient diagnosis and prevention of the disease, a combination of laboratory confirmed conventional tests were employed such as, Microscopic Agglutination Test, culture based identification of pathogenic Leptospira species from a normally sterile site, detection of Leptospira species in clinical samples by histological, histochemical or immuno-staining technique, and pathogenic Leptospira species DNA detected by PCR3,but their longer turnaround times hampered rapid identification of the disease which was essential for saving the lives of people who were affected.
Solution
Drawbacks of conventional methods were a huge challenge to overcome in establishing effective disease diagnosis and control, and implementing a rapid diagnosis technique was critical since the disease was life threatening to those who were affected. Thus, understanding the timely need a group of researchers7 performed 16s ribosomal RNA gene sequencing for disease identification.
Benefits
16s ribosomal RNA gene sequencing is a very rapid, culture independent method, to identify any bacteria and differentiate between intragenic variations with a high level of accuracy. In this case, the researchers could successfully identify the different serotypes7 of the causal organism simultaneously eliminating the need of serological tests.
This technique can be an extremely powerful tool during an outbreak, accounting to its ability to generate massively parallel data only in 48 hours of run time, maintaining the same accuracy throughout.
As the only service provider with access to this life-saving technology, we are determined enhance and upgrade health care facilities in Sri Lanka by providing our stakeholders with the most innovative methods of microbial sequencing.
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 |
References-
- Agampodi, Suneth B., et al. “Do people know adequately about leptospirosis? A knowledge assessment survey in post-outbreak situation in Sri Lanka.”International journal of preventive medicine 1.3 (2010): 158. (Pubuduni Weerakoon, Research Assistant, Real-Time Biosurveillance Program-Study of Leptospirosis outbreak in Sri Lanka In Kurunagala District -2008)
- Agampodi, Suneth. “Case definitions in Leptospirosis: a note to Sri Lankan researchers.” Sri Lankan Journal of Infectious Diseases 2.2 (2012): 55-57.
- OIE Terrestrial Manual 2008- Chapter 2.1.9. – Leptospirosis
- org.uk. 2013. HPA – Leptospira Reference Unit (LRU). [online] Available at: http://www.hpa.org.uk/ProductsServices/MicrobiologyPathology/LaboratoriesAndReferenceFacilities/LeptospiraReferenceUnit/ [Accessed: 22 Nov 2013].
- Diagnositic update-IDEXX Reference laboratories.August 2009
- Suneth B. Agampodi ,Sharon J. Peacock , Vasanthi Thevanesam , Danaseela B. Nugegoda , Lee Smythe, Janjira Thaipadungpanit, Scott B. Craig, Mary Ann Burns, Michael Dohnt, Siriphan Boonsilp, Thamarasi Senaratne, Athula Kumara , Paba Palihawadana , Sahan Perera , and Joseph M. Vinetz- Leptospirosis Outbreak in Sri Lanka in 2008: Lessons for Assessing the Global Burden of Disease
- Janda, J. Michael, and Sharon L. Abbott. “Bacterial identification for publication: when is enough enough?.”
Journal of clinical microbiology 40.6 (2002): 1887-1891.
