Complete Genome Sequence Of Extensively Drug-resistant Acinetobacter Baumannii Strain XDR-BJ83 And Comparative Genome Sequence Studies

Background and objectives:Acinetobacter baumannii is an opportunistic nosocomial pathogen responsible for a variety of serious infections,especially in intensive care units.The genome of A.baumannii has the characteristics of rapid evolution.The mechanism of antibiotic resistance is complex and diverse.In addition to the inherent resistance genes,gene mutations could also lead to antibiotic resistance.A.baumance.A.acquired resistance genes may be encoded in plasmids,resistance islands,transponsons or integrons.These mobile genetic elements increase the dissemination of resistance among species.It has emerged as a challenging pathogen,with a high mortality especially in patients infected with multidrug-resistant strain.There was a nosocomial outbreak due to A.baumannii at our hospital in 2007.The preliminary work of our research group collected 60 A.baumannii strains during this outbreak;these strains were mainly multidrug-resistant bacteria.PFGE analysis revealed that the main clones were type A1,B1 and C1.In this study,MLST analysis was performed.An extensively drug-resistant strain was selected for whole genome sequencing by SMRT sequencing.The sequence was analyzed and annotated by using bioinformatics technology.And to explore the antibiotic resistance mechanism of A.baumannii,we carried out comparative genomics studies.Methods and results:1.Tweenty nine strains of clone A1,11 strains of clone B1 and 4 strains of clone C1 were amplified blaOxA-51-like gene by PCR.Except for strain 34,all of the other strains were identified as A.baumannii.Oxford MLST analysis was performed.The results showed that ST368 was the most prevalent ST(28,65.2%),followed by ST369(13,30.2%).eBURST analysis showed that all the prevalent strains belonged to CC208(also named as CC92).2.A clone A1 strain(XDR-BJ83)with ST368 was selected for whole genome sequencing by SMRT.The assembled XDR-BJ83 genome consisted of a chromosome(4,011,552bp)with 39.0%G+C content,containing 3899 genes;and a plasmid(69,069bp)with 33.8%G+C content,containing 88 genes.The XDR-BJ83 genome carried multiple antibiotic resistance genes and antibiotic efflux pump genes.The results showed that there were 31 ISs and 6 RIs.PRI3,PRI5 and AbaRXDR-BJ83 carried a variety of resistance genes,transponsons,class I integrin,etc.3.Two IC-II strains(BJAB07104 and MDR-ZJ06)and one IC-I strain(AYE)werecompared in the whole genome with strain XDR-BJ83.SNP and InDel between these strains were basically homogeneous distribution in the genome,with no obvious position and gene function classification specificity.Plasmid pBJ83 was a conjugative plasmid carrying T4SS.Phylogenetic and collinearity analysis showed that pBJ83 was closely related to pABTJl,p2BJAB0868,and p1BJAB07104.The T4SS genes were highly homologous.Plasmid and chromosome of A.baumannii showed inconsistent in evolution.4.Five CSAB strains and twenty non-CSAB strains were selected in the GenBank database.The amino acid sequence of PBPs and proteins in the upstream of PBPs in peptidoglycan synthesis pathway were compared between these two groups.The results showed that the genomes of A.baumannii carrying 7 PBP genes and one monofunctional MGT gene.Hot spot mutations were observed in PBPlb,PBP3,PBP5/6,PBP6b,PBP7/8,EC 6.3.2.8,and EC 3.6.1.27 in the peptidoglycan synthesis pathway.Conclusions:1.The main sequence type of A.baumannii strains during this outbreak was ST368,and all the prevalent strains belonged to CC208(also named as CC92).2.The assembled XDR-BJ83 genome consists of a circular chromosome with 4,01 1,552bp and a plasmid(pBJ83)with 69,069bp.The genome carries a variety of antibiotic resistance genes,efflux pumps and mobile genetic elements.3.The genome of A.baumannii is highly variable,and there are no significant differences in position specificity and genetic function in SNP and InDel distribution.4.Plasmid pBJ83 carrying type A T4SS.The plasmid and chromosome of A.baumannii shows inconsistent in evolution.5.The genomes of A.baumannii carrying 7 PBP genes and one MGT gene.PBP genes and their upstream genes mutation may be related to carbapenem resistance.