https://orcid.org/0000-0002-1765-0697
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ABSTRACT
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 (< 0.1% of the total microbiome). This FACS-seq approach reduces diagnostics time (no culture is needed) and may promote discoveries of novel strains. Methodological details, possible issues and future directions for the sequencing of these natural pan-genomes are herein discussed.
Disclosure of Potential Conflicts of Interest
No potential conflicts of interest were disclosed.
Acknowledgments
We thank John Tigges and Vasilis Toxavidis from Flow Cytometry Core Facility of Beth Israel Deaconess Medical Center (BIDMC) of Harvard Medical School (MA, USA) for helping us with setting-up of the flow cytometry sorting. We also thank Kelsey Shields and Joshua Hansen from the Department of Gastroenterology of BIDMC for the help with sample collection and Dr. Nuria Jiménez from sequencing laboratory of FISABIO – Public Health, Valencia, Spain for the sequencing of the samples. We also want to thank Lauren Barker for English language corrections.
