| Streptococcus pneumoniae is one of the main pathogenic bacteria of respiratory tract infection,which can cause meningitis,pleurisy,septicemia,etc.As the representative of the penicillin beta lactam drugs and using erythromycin as representative of macrolides,was the first-line drug resistance of Streptococcus pneumoniae infection and drug resistance,two drugs rate rising,brought great difficulties to the clinical treatment.In this study,through comparing the drug resistance characteristics of Streptococcus pneumoniae,the whole genome and integrated junction elements of highly virulent strains were analyzed,and the mechanism of resistance was studied.Ojective: The characteristics of drug resistance survey in October 2015 to June 2016 in a hospital of clinical isolated 62 strains of Streptococcus pneumoniae,which provides a basis for the correct understanding of the clinical use of antibiotics;Streptococcus pneumoniae SWU02 genome basic characteristics,analysis of the drug resistance gene;analysis of Streptococcus pneumoniae SWU02 Integrative and Conjugative Element joint element genetic characteristics,study the the spread of drug resistance mechanism.Methods :(1)62 strains of Streptococcus pneumoniae were collected from October 2015 to June 2016 in a hospital in clinical isolates,with French bio Merieux VITEK-2Compact automicroscan strains were identified,the 14 kinds of antimicrobial drug resistance detection by E-test method.(2)through the third generation high-throughput sequencing whole genome sequencing of SWU02 of Streptococcus pneumoniae,mosaic,assembly,gene prediction,gene annotation,resistance genes and virulence gene sequencing analysis of the original.Typing technique with multilocus sequence typing of Streptococcus pneumoniae SWU02 ST type in NCBI Gen Bank database search and download the common serotypes of Streptococcus pneumoniae,19 F,23F,19 A series 6A/B,14B/C,15B/C,Streptococcus pneumoniae serotype SWU02 determined by BLAST comparison.(3)with integrated joint element hidden Markov model identification SWU02 of Streptococcus pneumoniae,Streptococcus pneumoniae integrated joint element search of NCBI database and ICEmerg database(ICE)of the reference sequence,the Streptococcus pneumoniae SWU02 integrated sequence compared with the joint element.Results:(1)62strains of Streptococcus pneumoniae to penicillin(PEN)and erythromycin(ERY)drug resistance rate was 100%,the tetracycline(TE),azithromycin(AZM),amoxicillin(AMC),sulfamethoxazole(SXT)resistance rates were95.2%,75.8%,72.6%,71%.The resistance rates of levofloxacin(LEV),moxifloxacin(MXF),linezolid(LNZ)and vancomycin(VAN)were lower,respectively,12.9%,11.3%,6.4%,0% and 0% respectively.(2)sequencing results showed that the SWU02 genome contained 2092148 BP bases,and G+C bases accounted for 39.77%.A total of 2120 coding genes,2012 CDS(protein coding regions),93 pseudogenes,13 r RNAs(including 5S,16 S,23S),58 t RNAs and 6 nc RNA were identified.The major resistance genes include quinolone resistance genes gyr A and gyr B,macrolide antibiotics resistance genes erm B,mef A,mre C,mre D,and tetracycline antibiotic resistance genes tet A,tet C,and tet M.In addition,there are 12 classical Streptococcus pneumoniae virulence genes psp C,lyt A,lyt B,rrg A,Nana,Ig A,ply,hys A,stk P,clp P,cps2 A,pcs B.The sequence is submitted to the NCBI database and the accession number is CP018347.Genetic evolution analysis is carried out.The genetic distance between the strain and the accession number CP003344 is the closest.SWU02 was identified by multipoint sequence typing and serological typing of type ST271,19 F,which is characterized by multiple drug resistance and simultaneous carrying of erm B and MEF bases.(3)we found that the genome of ORF91 to ORF115 contain ICE structure,the ICE belongs to the Tn916 family,full-length 25881 bp,GC content of 38.7%,contained 24 ORF,encoding a protein as follows: DUF961,DUF961,Fts K,rst A1,erm B,Transposase,conjugal,transfer,protein Ard A,membrane protein,ATP/GTP,conjugative,transposon Nlp C/P60,conjugative transposon,tet M,umu C,Ims C,Yol D,Mel,hypothetical,protein,Mef(A),DNA recombinase hypothetical protein,helix-turn-helix protein,DNA-binding protein,Xis,int.Conclusions:(1)the resistant rate of isolated Streptococcus pneumoniae to beta lactam antibiotics was 32.6-72.3%,and the antibiotic resistance rate of macrolide antibiotics was 75.8-100%,the antibiotic resistance rate of tetracycline antibiotics was 95.2%,and the drug resistance was severe.(2)gene sequencing showed that Streptococcus pneumoniae SWU02 genome is 2092148 BP,the base G+C accounted for 39.77%,containing Erm B,Tet(M),Mef(E)and other resistance genes and 12 virulence genes may lead to the strain on many kinds of antibacterial drugs and multidrug resistance showed high virulence.(3)SWU02(ST271,19F)ICE belongs to the TN916 family,carrying both MEF(A),erm B,tet M,penicillin resistance related protein ATP/GTP,drug resistance genes,and in addition,transposons may be related to the spread of drug-resistant genes. |
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