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Rigby, Jonathan (2022) To develop and optimise methods for the detection and isolation of Salmonella Typhi from the environment., Thesis (Doctoral), Liverpool School of Tropical Medicine.
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J Rigby_00217885_Thesis_2022_V4.pdf - Accepted Version Download (15MB) | Preview |
Abstract
Introduction: Salmonella Typhi is a globally important pathogen that causes Typhoid fever, responsible for an estimated 11.9-26.9 million cases and 129,000-216,510 typhoid-related deaths per year worldwide. Surveillance of clinical disease based on quality assured diagnostic clinical microbiology services is often not performed, making it difficult to understand the true burden of typhoid. Environmental surveillance (ES) has the potential to be a cheaper alternative to clinical surveillance of Typhoid and S. Typhi in endemic settings that does not rely on patients attending hospitals or consenting to research. Between April 2015 and January 2017, 546 culture-confirmed cases were reported at Queen Elizabeth Central Hospital in Malawi, however it is likely that case numbers are under-reported, and ES data can provide supplementary insight for spatially targeted interventions.
Methods: A novel culture method for S. Typhi was developed at the UK Health Security Agency in London and optimized in Blantyre, Malawi with environmental samples collected in 2019, including water (via trap and gran methods), sediments, food, and biofilms. The method used two enrichment broths (2% bile, then selenite F broths) before plating onto modified chromogenic agar for Salmonella esterase agar. Isolates were identified by real-time PCR and confirmed by biochemistry and serology. The method was validated and used for city-wide surveillance in Blantyre, Malawi between May 2021 and April 2022, alongside a method proposed by the Bill and Melinda Gates Foundation S. Typhi ES working group. After findings between these two methods, further refinements to the culture pathway were started.
Results: The six-month pilot study, from 2019 to 2020, isolated six S. Typhi cultures from three Moore swabs, two water samples, and one biofilm. PCR positivity was confirmed by biochemistry and serology. Non-typhoidal salmonellae (NTS) accounted for 377 isolates, 16 of which amplified staG. Between 2021 and 2022, 33 samples were S. Typhi positive and 80 positives for NTS by direct PCR detection only, with two S. Typhi and 255 NTS positive isolates cultured. An alternative extraction method for PCR was shown to have good performance under laboratory conditions, but the inclusion of antimicrobial-containing broths required further development.
Conclusion: This work demonstrates that ES of Typhoid by culture is achievable in low- and middle-income countries. Moore swabs yielded a higher detection rate than water samples. Direct detection by PCR appeared to be more sensitive than culture, but still had a low positivity rate. This low positivity rate coincided with the lowest rates of blood culture positivity in a decade and the SARS-CoV-2 pandemic. Work to integrate a PCR screening tool before culture is ongoing but shows potential viability.
| Item Type: | Thesis (Doctoral) | ||||||||
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| Subjects: | WC Communicable Diseases > WC 20 Research (General) WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 269 Salmonella infections WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 270 Typhoid fever |
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| Faculty: Department: | Clinical Sciences & International Health > Clinical Sciences Department | ||||||||
| Depositing User: | Lynn Roberts-Maloney | ||||||||
| Date Deposited: | 09 Mar 2023 09:52 | ||||||||
| Last Modified: | 09 Jun 2023 01:09 | ||||||||
| URI: | https://archive.lstmed.ac.uk/id/eprint/22109 |
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