No isolate, no problem: Using a novel insertion sequence PCR to link rats to human shigellosis cases in an underserved urban community
Abstract Introduction During an investigation into a cluster ofShigella flexneriserotype 2a cases in an underserved community, we assessed the relatedness of human and ratS. flexneriisolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in theShigellagenome characteristic of the cluster strain.Methods Whole genome sequences ofS. flexneri(n=50) associated with the cluster were analyzed.de novogenome assemblies were analyzed by a Geneious V10.2.6 motif search, and 2 unique IS were identified in all humanShigellasequences 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 threeShigellaPCR-positive culture-negative rat intestine specimens from this community.Results Both insertion sites were detected in thede novogenome assemblies of all clinicalS. flexneriisolates (n=50). Two of the three PCR-positive culture-negative rat samples were positive for both unique IS identified in the humanS. flexneriisolates, suggesting that the ratShigellaspp. 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.Conclusions Two unique IS were identified in clinical isolates from a communityS. flexnericluster. Both IS targets were identified in PCR-positive (Shigellaspp.), culture-negative rat tissue and clinical isolates from humans, indicating relatedness..
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Preprint| Erscheinungsjahr: |
2024 |
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| Erschienen: |
2024 |
| Enthalten in: |
bioRxiv.org - (2024) vom: 23. Apr. Zur Gesamtaufnahme - year:2024 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Ritchie, Gordon [VerfasserIn] |
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| doi: |
10.1101/2023.03.02.530678 |
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| PPN (Katalog-ID): |
XBI038868687 |
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| 520 | |a Abstract Introduction During an investigation into a cluster ofShigella flexneriserotype 2a cases in an underserved community, we assessed the relatedness of human and ratS. flexneriisolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in theShigellagenome characteristic of the cluster strain.Methods Whole genome sequences ofS. flexneri(n=50) associated with the cluster were analyzed.de novogenome assemblies were analyzed by a Geneious V10.2.6 motif search, and 2 unique IS were identified in all humanShigellasequences 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 threeShigellaPCR-positive culture-negative rat intestine specimens from this community.Results Both insertion sites were detected in thede novogenome assemblies of all clinicalS. flexneriisolates (n=50). Two of the three PCR-positive culture-negative rat samples were positive for both unique IS identified in the humanS. flexneriisolates, suggesting that the ratShigellaspp. 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.Conclusions Two unique IS were identified in clinical isolates from a communityS. flexnericluster. Both IS targets were identified in PCR-positive (Shigellaspp.), culture-negative rat tissue and clinical isolates from humans, indicating relatedness. | ||
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| 700 | 1 | |a Leung, Victor |e verfasserin |4 aut | |
| 700 | 1 | |a Himsworth, Chelsea G. |e verfasserin |4 aut | |
| 700 | 1 | |a Byers, Kaylee A. |e verfasserin |4 aut | |
| 700 | 1 | |a Lee, Lisa K.F. |e verfasserin |4 aut | |
| 700 | 1 | |a Chorlton, Samuel D. |e verfasserin |0 (orcid)0000-0001-9891-8546 |4 aut | |
| 700 | 1 | |a Stefanovic, Aleksandra |e verfasserin |4 aut | |
| 700 | 1 | |a Romney, Marc G. |e verfasserin |4 aut | |
| 700 | 1 | |a Matic, Nancy |e verfasserin |4 aut | |
| 700 | 1 | |a Lowe, Christopher F. |e verfasserin |4 aut | |
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