Detection of mixed-strain infections by FACS and ultra-low input genome sequencing

The epidemiological tracking of a bacterial outbreak may be jeopardized by the presence of multiple pathogenic strains in one patient. Nevertheless, this fact is not considered in most of the epidemiological studies and only one colony per patient is sequenced. On the other hand, the routine whole g...

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Bibliographic Details
Published in:Gut microbes 2020-05, Vol.11 (3), p.305-309
Main Authors: Džunková, Mária, Moya, Andrés, Chen, Xinhua, Kelly, Ciaran, D'Auria, Giuseppe
Format: Article
Language:English
Subjects:
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C. difficile
Clostridioides difficile - classification
Clostridioides difficile - cytology
Clostridioides difficile - genetics
Clostridioides difficile - isolation & purification
Clostridium Infections - diagnosis
Clostridium Infections - microbiology
Coinfection - diagnosis
Coinfection - microbiology
DNA, Bacterial - genetics
epidemiology
FACS-seq
Feces - microbiology
Flow Cytometry
Genome, Bacterial - genetics
Humans
low-input DNA sequencing
Microbiological Techniques - methods
Microbiota - genetics
mixed-strain infection
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
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Summary:The epidemiological tracking of a bacterial outbreak may be jeopardized by the presence of multiple pathogenic strains in one patient. Nevertheless, this fact is not considered in most of the epidemiological studies and only one colony per patient is sequenced. On the other hand, the routine whole genome sequencing of many isolates from each patient would be costly and unnecessary, because the number of strains in a patient is never known a priori. In addition, the result would be biased by microbial culture conditions. Herein we propose an approach for detecting mixed-strain infection, providing C. difficile infection as an example. The cells of the target pathogenic species are collected from the bacterial suspension by the fluorescence activated cell sorting (FACS) and a shallow genome sequencing is performed. A modified sequencing library preparation protocol for low-input DNA samples can be used for low prevalence gut pathogens (
ISSN:1949-0976
1949-0984
1949-0984
DOI:10.1080/19490976.2018.1526578