Genomic Analysis of C. striatum Outbreak

A clinical sample was obtained from hospitalized patients growing exclusively C. striatum colonies, according to the definition of an outbreak case described by Verroken et al. (14 (link)). A total of 30 C. striatum isolates were isolated from 26 patients from a hospital in Shanxi, China, between 24 March and 23 April 2021. One epidemiologically unrelated outgroup strain was collected from a hospital in Wenzhou, China, in January 2019. Genomic DNA was isolated and purified using the Wizard genomic DNA purification kit (Promega, WI, USA). Whole-genome sequencing was carried out with the Illumina HiSeq X 10 sequencing platform (150-bp paired-end reading). Trimmomatic version 0.39 (53 (link)) was used to remove adapter sequences and low-quality sequences. Assembly was performed using SPAdes v3.11.1 (54 (link)). The CheckM tool was used to assess genome completeness and contamination (55 (link)).

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Kang Y., Chen S., Zheng B., Du X., Li Z., Tan Z., Zhou H., Huang J., Tian L., Zhong J., Ma X., Li F., Yao J., Wang Y., Zheng M, & Li Z. (2022). Epidemiological Investigation of Hospital Transmission of Corynebacterium striatum Infection by Core Genome Multilocus Sequence Typing Approach. Microbiology Spectrum, 11(1), e01490-22.

Publication 2022

Wizard genomic DNA purification kit HiSeq X 10 sequencing platform

Genome Patients Promega Strain Striatum

Corresponding Organization : National Clinical Research Center for Digestive Diseases

Other organizations : Shanxi Medical University, Taizhou Central Hospital, Taizhou University, Xinjiang Uygur Autonomous Region Disease Prevention and Control Center, Tibet University, Shanxi Academy of Medical Sciences

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Genome sequencing and assembly of Corynebacterium striatum isolates

control variables

One epidemiologically unrelated outgroup strain from a hospital in Wenzhou, China, in January 2019

controls

Positive control: None mentioned
Negative control: One epidemiologically unrelated outgroup strain

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