The Study On Evolutionary Genomics Of Shigella Flexneri In China

Shigella,a gram-negative bacterium of the Enterobacteriaceae family,can cause bacterial dysentery(Shigellosis)through contaminated water or food.There are about 164.7 million Shigella episodes per year,resulting in approximately 1.1 million deaths,which posed a significant threat to public health.The situation of Shigellosis in China is also severe.The incidence of Shigellosis has been among the top four infectious diseases for four consecutive years since 2005,which is a major challenge for the prevention and control of infectious diseases in China.Shigella are classified into four serogroups(S.flexneri,S.sonnei,S.dysenteriae and S.boydii)based on biochemical properties and O-antigen structures.S.flexneri is the major serogroup causing bacterial dysentery worldwide,especially in Asia.The prevalence of Shigella in China is also dominated by S.flexneri.Transnational spread plays an important role in the dissemination of S.flexneri.However,the evolutionary relationship between domestic and foreign strains are still unclear,making it hard to trace the process of S.flexneri enteing China.A total of 17 S.flexneri serotypes has been prevalent in China.The emergence of novel serotypes,coexistence of multiple serotypes and frequent serotype conversion are common in all parts of China,whereas the rules and mechanisms of the formation of serotype diversity are still unclear.The situation of drug resistance of S.flexneri in China is also becoming increasingly serious.The proportion of multidrug resistant strains has exceeded 95%,and the resistance to particular antibiotics has reached a very high level.However,the molecular mechanism mediating the drug resistance of S.flexneri has not been systematically investigated.The answers to these questions will enhance our understanding of the evolution and epidemics of Chinese S.flexneri and lay a solid foundation for the prevention and control of bacterial dysentery in China.In this study,we collected 606 S.flexneri strains from 13 provinces and cities in China over a more than forty-year period.The strains are diverse in serotypes and resistance phenotypes.Based on the whole genome sequencing and phenotypic characteristics of these strains and published foreign data,we carried out the following two aspects of research:1.The genomic evolutionary features of S.flexneri in ChinaThrough genome-wide evolutionary analysis,we found that S.flexneri in China originated from five different lineages in the global S.flexneri evolution system,namely PG1,PG2,PG3,PG4 and PG7.Bangladesh,Pakistan and other surrounding countries are important sources of S.flexneri in China.The introduction of S.flexneri in different phylogenetic groups into China occurred frequently after the 1980 s,and the economic development and the expansion of personnel exchange after reform and opening up may be one of the key driving factors.The introduction from abroad continues to occur in recent years,which should arouse our vigilance.S.flexneri type 6 in China has remarkably different genomic evolutionary features compared with other types of S.flexneri,and have a close relationship with S.boydii.The prevalence of S.flexneri in China is predominantly caused by the large-scale expansion of the PG3 lineage with the combination of local colonization and cross-regional spread.Unlike the rapid replacement of lineages observed in other Shigella species,S.flexneri shows long-term colonization in China,which may be related to its strong viability in the environment.The above results suggest that the prevention and control of S.flexneri in China will be arduous in a long period.Prevention of introduction from abroad and domestic expansion is important.The measures should also focus on the environmental source of infection.Improvement of sanitation is effective for the control of S.flexneri epidemics.2.Molecular mechanisms of the evolution of S.flexneri in ChinaThe formation of S.flexneri serotype diversity in China is mainly caused by two factors.One is that foreign strains introduced into China are of different serotypes,and the other is that at least 145 serotype conversion events have occurred in domestic strains.S.flexneri serotype 6 and S.boydii serotypes 2,4 and 11 shared some identical O antigen genes.The presence of two unique glycosyltransferase genes wfb Y and wfb Z may be the key factor causing the antigenic specificity of S.flexneri serotype 6.S.flexneri in China carries more resistance determinants than foreign strains.The antibiotic resistance of domestic strains is mediated by a variety of genotypes,and the acquisition of genes is also driven by multiple plasmids,indicating that the drug resistance comes from the cumulative effect of multiple molecular mechanisms.Drug resistance determinants have been independently acquired by domestic strains,but no dominant lineages with significant drug resistance have been formed at present.Drug resistant strains coexist with non-resistant strains,indicating that resistance has not yet become a key driving factor for the evolution of S.flexneri.The distribution of virulence factors of S.flexneri in China have also changed.The SHI-1 pathogenicity island and the genes clusters related to type III secretion system show a tendency to spread among diverse types of strains.Conducting relevant studies on virulence phenotypes and assessing the threats to residents in advance will considerably reduce the risk of a new epidemic ourbreak of S.flexneri in China.In summary,this study has adopted high-throughput sequencing technology to conduct an in-depth analysis of S.flexneri in China,and revealed the genomic evolutionary features and molecular mechanisms.This study gained an unstanding of the role of Chinese strains in the global S.flexneri evolution,and revealed the process of S.flexneri entering China and its domestic spread,providing an important theoretical basis for the prevention and control of S.flexneri in China.The molecular mechanisms of changes in serotype,drug resistance and virulence have been deeply investigated,which provided the guidance for the development of measures to control the S.flexneri epidemics.The results suggest that S.flexneri of various serotypes and high drug resistance has been widespread in China,which show great genetic diversity and are driven by complex causes.Strengthening the monitoring of S.flexneri,maintaining sharp vigilance for the continuous introduction from abroad to China,paying close attention to the conversion of serotypes,and controlling the increase in drug resistance are of great importance for the prevention and control of bacterial dysentery in China.