Studies On The Evolution Of Emerging Pathogens And Their Interactions With Hosts Based On Omics Data

Since the 1970s,emerging pathogens have been discovered almost every year.Among them,infections and transmission caused by viruses and bacteria have greatly threatened the safety of human life and property,as well as caused huge losses to the human economy.Over the past decade,omics approaches have emerged as powerful tools for basic research on the emerging pathogens.Genomic analysis allows us to quickly understand the basic genomic features of emerging pathogens,thus facilitating targeted prevention and control of emerging pathogens,as well as closely monitoring the evolution and mutation process.Integrated multi-omics analysis can provide a more comprehensive understanding,thus facilitating in-depth studies of complex interactions between emerging pathogens and their hosts.This thesis describes the basic research and application of omics study in the emerging pathogens evolution and their interactions with hosts by three examples:Klebsiella pneumoniae ST967,K.pneumoniae ST307,and SARS-CoV-2.We studied them at the genomic level as well as at the transcriptome and interactome integration level,respectively.K.pneumoniae is a common cause of hospital and community-acquired infections globally,yet its genetic information remains unknown for many regions,particularly in low-and middle-income countries.Here,we report for the first-time whole genome sequencing(WGS)data of a multidrug resistant K.pneumoniae ARM01 recovered from a patient in Armenia.Antibiotic susceptibility testing revealed that ARM01 was resistant to 7 out of 11 antibiotics tested.Genome sequencing analysis revealed that ARM01 belonged to sequence type(ST)967,capsule type K18 and antigen type O1.ARM01 carried 13 antimicrobial resistance(AMR)genes,but only one known virulence factor,yagZ/ecpA,and one plasmid replicon,IncFIB(K)(pCAV1099-114)were detected.Bayesian evolutionary analysis revealed that the most recent common ancestor of K.pneumoniae ST967 lineage was estimated to be 2004(95%CI:1998-2009),implying that the K.pneumoniae ST967 subgroup was a newly emerged clone that had spread across countries in the last two decades.Multilevel comparative analysis revealed high genomic similarity between ARM01 and Qatar isolates(SRR11267909 and SRR1126796).ARM01,SRR11267909 and SRR1126796 shared and had descended from a common ancestor in 2017(95%CI:2017-2018).Besides,we also report for the first-time whole genome sequencing data of four MDR-hypervirulent,sequence type 307 K.pneumoniae isolates recovered from patients in two hospitals in Armenia in 2019 and performed a comparative genomic analysis with global ST307 isolates.Comparative genomic analysis revealed that the core and accessory genomes of all four Armenian isolates were closely related to each other,with the farthest SNP distance being 39.A phylogenetic clade consisting of four isolates(SRR9854284,SRR10615702,SRR11460696 and SRR11460688)showed a very close evolutionary relationship with Armenian strains in the phylogenetic tree and all isolates carried the integrative and conjugative element ICEkp4 that bearing yersiniabactin(ybt)locus.They also shared a same evolutionary origin,with the most recent divergence date of 2005(95%CI:1999-2011).Antibiotic susceptibility testing revealed that Armenian isolates were resistant to 8(n=1)and 9(n=3)of the antibiotics tested.Further studies revealed that the Armenian isolates carried 11(n=2)and 18(n=2)AMR genes.The unique AMR gene mcr-8.1 identified in ARM47 and ARM83,was absent in all other ST127 isolates.In addition to ybt(irp1-2,ybtAEPQSTUX and fyuA),ARM47 and ARM83 also acquired multiple virulence loci,including aerobactin(iucABCD and iutA)and the hypermucoidy locus rmpADC(ARM47 has incomplete rmpA).Our findings suggest that transmission of K.pneumoniae ST307 may have occurred between multiple hospitals across Armenia.At the same time,we speculate that some isolates may have obtained plasmids carrying high virulence genes and AMR genes during the transmission in one of the hospitals and have formed stable transmission within the hospital.Since the outbreak of the COVID-19 pandemic,the SARS-CoV-2 has seriously threatened global public health and caused huge economic losses.The omics study of SARS-CoV-2 can help understand the interaction between virus and host,thereby providing a new perspective for the intervention and treatment of the virus.Since large amount of SARS-CoV-2 omics data have been accumulated in public databases,this study intends to identify key host factors involved in SARS-CoV-2 infection through systematically integration of transcriptome and interactome data.Through manually curated from published studies,we obtained a comprehensive SARS-CoV-2-human protein-protein interactions network,comprising 3591 human proteins interacted with 31 SARS-CoV-2 virus proteins.Using the RobustRankAggreg method we identified 123 multi-cell lines common genes(CLCGs),where 115 up-regulated CLCGs showed host enhanced innate immunity and chemotactic response signature.Combined with the network analysis,co-expression and functional enrichment analysis,we discovered 4 key host factors:IFITM1,SERPINE1,DDX60 and TNFAIP2.Furthermore,SERPINE1 was found to alleviate the endoplasmic reticulum(ER)stress induced by ORF8 protein through interaction with ORF8,and can facilitate SARS-CoV-2 replication.In summary,omics-scale data analysis has played an important role in the study of emerging pathogenic pathogens.The first two parts of this thesis revealed the genomic features and phylogeny of two sub-types of emerging K.pneumoniae(ST967 and ST307)isolates in Armenia by genomic level analysis,respectively.K.pneumoniae ARM01(ST967)was multidrug resistant,carried multiple AMR genes,and might be associated with strains prevalent in Qatar.Four ST307 isolates carried multiple AMR genes and high virulence related factors,two of which also acquired the colistin-resistance gene mcr-8.1 and our findings suggested that both intra-hospital and inter-hospital transmission of K.pneumoniae ST307 might have occurred in Armenia.These two parts of the study highlights the importance of genomic and epidemiological surveillance of these emerging MDR pathogens in order to provide an early warning and suggestions for the prevention and control measures.The third part of this thesis identified four key host factors involved in SARS-CoV-2 infection through an integrated analysis of SARS-CoV-2 interactome and transcriptome data in public databases.In-depth functional studies of SERPINE1 revealed that SERPINE1 could interact with the ORF8 viral protein and attenuated ORF8-induced ER stress,and can promote SARS-CoV-2 replication.This part of the study highlights the value of systematically integration analysis in understanding host infection by emerging pathogens and provides new insights for future research on effective therapeutic targets against SARS-CoV-2.