Performance of molecular methods for the detection of Salmonella in human stool specimens



Chirambo, Angeziwa Chunga ORCID: 0000-0001-6500-2902, Nyirenda, Tonney, Jambo, Ndaru, Msefula, Chisomo ORCID: 0000-0003-2304-886X, Kamng'ona, Arox ORCID: 0000-0002-0841-7586, Molina, Sandra, Mandala, Wilson, Heyderman, Robert ORCID: 0000-0003-4573-449X, Iturizza-Gomara, Miren, Henrion, Marc YR ORCID: 0000-0003-1242-839X
et al (show 1 more authors) (2020) Performance of molecular methods for the detection of Salmonella in human stool specimens.

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Abstract

Background: The relationship between asymptomatic Salmonella exposure within the gastrointestinal tract and Salmonella bacteraemia is poorly understood, in part due to the low sensitivity of stool culture, and the lack of validated molecular diagnostic tests for the detection of Salmonella in stool. The study aimed to determine a reliable molecular diagnostic test for Salmonella in stool specimens. Methods: We optimized an in-house monoplex real time polymerase chain reaction (PCR) for the detection of Salmonella TTR and InvA genes in stool by including a selenite broth pre-culture step for Salmonella before DNA extraction, and validated their specificity against other local common pathogens. Then we assessed their performance  against a well-validated multiplex PCR targeting the same TTR and InvA genes, and against stool culture using clinical stool specimens collected from a cohort of 50 asymptomatic healthy Malawian children that were sampled at 1-month intervals over a period of 12 months. We employed a latent Markov model to estimate the specificities and sensitivities of PCR methods. Results : TTR and InvA primers were both able to detect all the different Salmonella serovars tested, and had superior limits of detection if DNA was extracted after selenite pre-culture. TTR sensitivity and specificity for monoplex-PCR were (99.53%, 95.46%) and for multiplex-PCR (90.30%, 99.30%) respectively. InvA specificity and specificity for using monoplex-PCR was (95.06%, 90.31%) and multiplex-PCRs (89.41%, 98.00%) respectively. Sensitivity and specificity for standard stool culture were 62.88% and 99.99% respectively. Culture showed the highest PPV (99.73%) and mono-TTR had the highest NPV (99.67%). Conclusion: Test methods demonstrated high concordance although stool culture and monoplexed TTR primers had superior specificity and sensitivity respectively. The use of selenite pre-enrichment step increased Salmonella detection rate. Taken together, molecular detection methods used here could be used to reveal the true extent of both asymptomatic and symptomatic Salmonella exposure events.

Item Type: Article
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 08 Jun 2021 07:20
Last Modified: 01 Oct 2021 07:29
DOI: 10.12688/wellcomeopenres.16305.1
Open Access URL: http://doi.org/10.12688/wellcomeopenres.16305.1
URI: https://livrepository.liverpool.ac.uk/id/eprint/3125560