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. 2019 Jul 1:12:1783-1794.
doi: 10.2147/IDR.S203238. eCollection 2019.

Whole genome analysis reveals new insights into the molecular characteristics of Clostridioides difficile NAP1/BI/027/ST1 clinical isolates in the People's Republic of China

Tao Lv #  1 , Yunbo Chen #  1 , Lihua Guo  1 , Qiaomai Xu  1 , Silan Gu  1 , Ping Shen  1 , Jiazheng Quan  1 , Yunhui Fang  1 , Lifeng Chen  2 , Qiaodi Gui  3 , Guangyong Ye  4 , Lanjuan Li  1
Affiliations

Whole genome analysis reveals new insights into the molecular characteristics of Clostridioides difficile NAP1/BI/027/ST1 clinical isolates in the People's Republic of China

Tao Lv et al. Infect Drug Resist. .

Abstract

Background: The epidemic new strain NAP1/BI/027/ST-1 of Clostridioides difficile (C. difficile) causes more severe coliti and a higher mortality rate than historical strains. However, C. difficile NAP1/BI/027/ST-1 (C. difficile RT027) infections have been rarely reported in Asia, particularly in China. Purpose: The objective of this study was to strengthen the understanding of the molecular characterizations of C. difficile RT027 in China. Patients and methods: Two C. difficile NAP1/BI/027/ST-1 were detected from two patients, and no additional isolates were found. Whole genome sequencing (WGS) was used to characterize two C. difficile RT027 isolates and control strain CD6 (from Hong Kong), and comparative genomic analysis was performed to compare genomic differences between seven isolates from Mainland China, CD6, and 10 isolates from North America and Europe. Results: The comparative genomic analysis revealed that isolates obtained from Mainlan China were outside of the two epidemic lineages, FQR1 and FQR2, and might have decreased virulence and transmissibility for outbreak. Furthermore, unique SNP mutations were detected in isolates obtained from Mainland China, which may affect the biological function of C. difficile. Conclusion: We speculate that C. difficile RT027 isolates in Mainland China may have different features, compared to those in North America and Europe.

Keywords: Clostridioides difficile infection; People's Republic of China; multilocus sequence typing; whole genome sequencing.

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Conflict of interest statement

The authors report no conflicts of interest in this work.

Figures

Figure 1
Figure 1
(A) PCR ribotyping of Clostridioides difficile (C. difficile) PCR ribotype 027 reference strains (A-01) and two clinical isolates (A-02 and B-03) identified in the present study. (B) Pulsed-field gel electrophoresis of C. difficile PCR ribotype 027 reference strains (A-01) and two clinical isolates (A-02 and B-03). Marker: Xba 1 was used for the reference marker, Salmonella H9812. Line A-01=CD06; Line A-02=14,042,403; Line B-03=14,061,807.
Figure 2
Figure 2
Patterns of molecular variation in 18 strains of C. difficile RT027, including the three isolates in this study, the other five strains from the People's Republic of China and the ten from North America and Europe. (A) Annotation by RAST revealed several SNPs, which were significantly different between the strains obtained from Mainland China and North America and Europe. The symbol arrow indicates the four different SNPs between two isolates in this study. (B) Maximum-likelihood phylogenetic analysis of based on core genome SNPs which were grouped into three different clades. The previously described strains of fluoroquinolone-resistant C. difficile RT027 were clustered into two clades (FQR1 and FQR 2), whereas the isolates from Mainland China were classified into a third clade.
Figure 3
Figure 3
Heatmap reconstruction of 18 strains resulting from SNPs. A total of 3,944 genes were identified, including 3,397 common core genes without soft core genes, 295 different shell genes, and 252 different cloud genes. Two isolates in this study are labeled with point brackets.
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