Performance of molecular methods for the detection of <i>Salmonella</i> in human stool specimens.

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Chirambo, Angeziwa Chunga ORCID: 0000-0001-6500-2902, Nyirenda, Tonney S, Jambo, Ndaru, Msefula, Chisomo ORCID: 0000-0003-2304-886X, Kamng'ona, Arox ORCID: 0000-0002-0841-7586, Molina, Sandra ORCID: 0000-0001-9574-1845, Mandala, Wilson L, Heyderman, Robert S ORCID: 0000-0003-4573-449X, Iturizza-Gomara, Miren, Henrion, Marc YR ORCID: 0000-0003-1242-839X et al (show 1 more authors) and Gordon, Melita A ORCID: 0000-0002-0629-0884 (2020) Performance of molecular methods for the detection of <i>Salmonella</i> in human stool specimens. Wellcome open research, 5. 237-.

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Abstract

<b>Background:</b> The relationship between asymptomatic <i>Salmonella</i> exposure within the gastrointestinal tract and <i>Salmonella</i> 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 <i>Salmonella</i> in the stool. The study aimed to determine a reliable molecular diagnostic test for <i>Salmonella</i> in stool specimens. <b>Methods:</b> We optimised an in-house monoplex real-time polymerase chain reaction (PCR) for the detection of <i>Salmonella</i> <i>ttr</i> and <i>InvA</i> genes in stool by including a selenite broth pre-culture step for <i>Salmonella</i> 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 <i>ttr</i> and <i>InvA</i> 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 12 months. We employed a latent Markov model to estimate the specificities and sensitivities of PCR methods. <b>Results</b>: <i>Ttr</i> and <i>InvA</i> primers were both able to detect all the different <i>Salmonella</i> serovars tested and had superior limits of detection when DNA was extracted after selenite pre-culture. T <i>tr</i> sensitivity and specificity for monoplex-PCR were (99.53%, 95.46%) and for multiplex-PCR (90.30%, 99.30%) respectively. <i>InvA</i> 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 monoplex- <i>ttr</i> had the highest NPV (99.67%). <b>Conclusion:</b> Test methods demonstrated high concordance, although stool culture and monoplexed <i>ttr</i> primers had superior specificity and sensitivity, respectively. The use of selenite pre-enrichment step increased <i>Salmonella</i> detection rate. Taken together, molecular detection methods used here could be used to reveal the true extent of both asymptomatic and symptomatic <i>Salmonella</i> 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 Feb 2024 09:52
DOI:	10.12688/wellcomeopenres.16305.2
Open Access URL:	http://doi.org/10.12688/wellcomeopenres.16305.1
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3125561