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No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community

During an investigation into a cluster of Shigella flexneri serotype 2a cases in an underserved community, we assessed the relatedness of human and rat S. flexneri isolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in the Shigella genome characteristic of the cluste...

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Autores principales: Ritchie, Gordon, Leung, Victor, Himsworth, Chelsea G., Byers, Kaylee A., Lee, Lisa K. F., Chorlton, Samuel D., Stefanovic, Aleksandra, Romney, Marc G., Matic, Nancy, Lowe, Christopher F.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10434041/
https://www.ncbi.nlm.nih.gov/pubmed/37255425
http://dx.doi.org/10.1128/spectrum.04777-22
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author Ritchie, Gordon
Leung, Victor
Himsworth, Chelsea G.
Byers, Kaylee A.
Lee, Lisa K. F.
Chorlton, Samuel D.
Stefanovic, Aleksandra
Romney, Marc G.
Matic, Nancy
Lowe, Christopher F.
author_facet Ritchie, Gordon
Leung, Victor
Himsworth, Chelsea G.
Byers, Kaylee A.
Lee, Lisa K. F.
Chorlton, Samuel D.
Stefanovic, Aleksandra
Romney, Marc G.
Matic, Nancy
Lowe, Christopher F.
author_sort Ritchie, Gordon
collection PubMed
description During an investigation into a cluster of Shigella flexneri serotype 2a cases in an underserved community, we assessed the relatedness of human and rat S. flexneri isolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in the Shigella genome characteristic of the cluster strain. Whole-genome sequences of S. flexneri (n = 50) associated with the cluster were analyzed. De novo genome assemblies were analyzed by a Geneious V10.2.6 motif search, and two unique IS were identified in all human Shigella sequences of the local cluster. Hydrolysis probe PCR assays were designed to detect these sequences consisting of forward and reverse primers to amplify across each insertion site and a hydrolysis probe spanning the insertion site. IS-PCR was performed for three Shigella PCR-positive culture-negative rat intestine specimens from this community. Both insertion sites were detected in the de novo genome assemblies of all clinical S. flexneri isolates (n = 50). Two of the three PCR-positive culture-negative rat samples were positive for both unique ISs identified in the human S. flexneri isolates, suggesting that the rat Shigella species strains were closely related to the human strains in the cluster. The cycle threshold (Ct) values were >35, indicating that the bacterial load was very low in the rat samples. Two unique IS were identified in clinical isolates from a community S. flexneri cluster. Both IS targets were identified in PCR-positive (Shigella spp.), culture-negative rat tissue and clinical isolates from humans, indicating relatedness. IMPORTANCE This article describes a novel molecular method to show relatedness between bacterial infections, which may not be able to grow in the laboratory due to treatment with antibiotics or for bacteria requiring unique conditions to grow well. Uniquely, we applied this technique to Shigella isolates from human cases associated with a local cluster in an underserved community, as well as rat samples from the same community. We believe that this novel approach can serve as a complementary method to support outbreak/cluster investigation for Shigella spp.
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spelling pubmed-104340412023-08-18 No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community Ritchie, Gordon Leung, Victor Himsworth, Chelsea G. Byers, Kaylee A. Lee, Lisa K. F. Chorlton, Samuel D. Stefanovic, Aleksandra Romney, Marc G. Matic, Nancy Lowe, Christopher F. Microbiol Spectr Observation During an investigation into a cluster of Shigella flexneri serotype 2a cases in an underserved community, we assessed the relatedness of human and rat S. flexneri isolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in the Shigella genome characteristic of the cluster strain. Whole-genome sequences of S. flexneri (n = 50) associated with the cluster were analyzed. De novo genome assemblies were analyzed by a Geneious V10.2.6 motif search, and two unique IS were identified in all human Shigella sequences of the local cluster. Hydrolysis probe PCR assays were designed to detect these sequences consisting of forward and reverse primers to amplify across each insertion site and a hydrolysis probe spanning the insertion site. IS-PCR was performed for three Shigella PCR-positive culture-negative rat intestine specimens from this community. Both insertion sites were detected in the de novo genome assemblies of all clinical S. flexneri isolates (n = 50). Two of the three PCR-positive culture-negative rat samples were positive for both unique ISs identified in the human S. flexneri isolates, suggesting that the rat Shigella species strains were closely related to the human strains in the cluster. The cycle threshold (Ct) values were >35, indicating that the bacterial load was very low in the rat samples. Two unique IS were identified in clinical isolates from a community S. flexneri cluster. Both IS targets were identified in PCR-positive (Shigella spp.), culture-negative rat tissue and clinical isolates from humans, indicating relatedness. IMPORTANCE This article describes a novel molecular method to show relatedness between bacterial infections, which may not be able to grow in the laboratory due to treatment with antibiotics or for bacteria requiring unique conditions to grow well. Uniquely, we applied this technique to Shigella isolates from human cases associated with a local cluster in an underserved community, as well as rat samples from the same community. We believe that this novel approach can serve as a complementary method to support outbreak/cluster investigation for Shigella spp. American Society for Microbiology 2023-05-31 /pmc/articles/PMC10434041/ /pubmed/37255425 http://dx.doi.org/10.1128/spectrum.04777-22 Text en Copyright © 2023 Ritchie et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Observation
Ritchie, Gordon
Leung, Victor
Himsworth, Chelsea G.
Byers, Kaylee A.
Lee, Lisa K. F.
Chorlton, Samuel D.
Stefanovic, Aleksandra
Romney, Marc G.
Matic, Nancy
Lowe, Christopher F.
No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community
title No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community
title_full No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community
title_fullStr No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community
title_full_unstemmed No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community
title_short No Isolate, No Problem: Using a Novel Insertion Sequence PCR to Link Rats to Human Shigellosis Cases in an Underserved Urban Community
title_sort no isolate, no problem: using a novel insertion sequence pcr to link rats to human shigellosis cases in an underserved urban community
topic Observation
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10434041/
https://www.ncbi.nlm.nih.gov/pubmed/37255425
http://dx.doi.org/10.1128/spectrum.04777-22
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