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Using next-generation sequencing to develop a Shigella species threshold and profile faecal samples from suspected diarrhoea cases

Smith, Ann


Ann Smith


Globally, it is estimated that there are 2 billion cases of diarrhoeal disease each year, with 525,000 children under the age of 5years, dying from diarrhoea. This also affects 1 in 5 people in the UK each year. Rapid diagnosis, appropriate treatment and infection control measures are, therefore, particularly important. Currently, Public Health Wales and England Microbiology Division test for five key bacterial gastrointestinal pathogens, i.e. Escherichia coli O157 (VTEC), Shigella dysenteriae, Salmonella spp., Campylobacter spp. and Clostridioides difficile. There is, however, a poor success rate with identification of these pathogens, leaving the patient at risk from untreated infections. This study has developed effective and reliable tools with a high positive outcome for diagnosis of diarrhoeal infection. The study blindly analysed 592 samples, with the most abundant species being Shigella sonnei at 15%, and the top genus Bacteroides at 26%. Campylobacter spp. had an abundance of 4%, Clostridium difficile 3%, and Salmonella spp. 0.2%. There were also significant differences in abundance at genus level, between the Flemish Gut project and diarrhoea samples, with respect to Shigella (0.2%) and Campylobacter (0.1%). The project introduced a novel Shigella spp. (Escherichia) threshold of 5.32% to determine (Escherichia) a healthy or unhealthy community. A DMBiome model was developed to integrate the 5.32% threshold of Shigella spp., the Public Health laboratory tested pathogens, and two emerging enteropathogens. The overall positive outcome was that 89% of all samples were diagnosed with diarrhoea infections, leaving 11% unknown.


Smith, A. (2021). Using next-generation sequencing to develop a Shigella species threshold and profile faecal samples from suspected diarrhoea cases. Folia Microbiologica, 66(3), 399-410.

Journal Article Type Article
Acceptance Date Dec 21, 2020
Online Publication Date Feb 10, 2021
Publication Date Jun 1, 2021
Deposit Date Jun 25, 2021
Journal Folia Microbiologica
Print ISSN 0015-5632
Electronic ISSN 1874-9356
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 66
Issue 3
Pages 399-410
Keywords Microbiology; General Medicine
Public URL
Additional Information Received: 25 June 2020; Accepted: 21 December 2020; First Online: 10 February 2021; : ; : Ethical approval was not necessary as this project used raw samples from a previous study.; : I had consent from Public Health Wales to use the raw samples for my own research interest, and there were no patient and/or microbiological data attached to the samples.