Analysis of the epidemic distribution characteristics of mcr genes in global Klebsiella pneumoniae
Objective To analyze the epidemiological characteristics of mobile colistin resistance(mcr)genes in global Klebsiella pneumoniae(K.pneumoniae).Methods The genomes of K.pneumoniae were downloaded from the NCBI genome database by the As-pera software.After quality filtering using the CheckM v1.1.3 and Quest 5.0.2 software,the genomes were annotated using the Prokka v1.13.All the mcr gene sequences were downloaded from the NCBI website and a database was built using the makeblastdb command.Then,a self-made Perl script program was used to extract the nucleotide sequences of all genes from the annotation file as Query,and the local BLASTN analysis was performed to obtain mcr-positive strains.The gene sequence files and Profiles files of 7 housekeeping genes of K.pneumoniae were downloaded from the PubMLST website as the database,and the nucleotide sequences of the genes were extracted as Query using a self-made Perl script program.The local BLASTN analysis was implemented to determine the sequence type(ST)of each genome.Meta information of each strain,including isolation source,sample type,country,and date,were extracted in batch from the GenBank file of the downloaded K.pneumoniae genomes using a self-written Perl program to analyze the distribution characteristics of mcr-positive strains.The distribution differences of the mcr between different ST types were compared by the Chi-square test.Results Among the 11 429 global K.pneumoniae genomes included in this study,229 mcr genes were detected from 207 strains.Six variants of mcr were identified,mainly mcr-1(87/229,38.0％),mcr-8(59/229,25.8％),and mcr-9(59/229,25.8％).76 STs were identified from 207 strains,with ST15(21/207,10.1％),ST43(17/207,8.2％),ST11(16/207,7.7％),and ST 147(16/207,7.7％)being the predominant.Among 87 mcr-1 positive strains,31 STs were found,with ST43(17/87,19.5％)and ST15(10/87,11.5％)being the main ones.Among 59 mcr-8 positive strains,17 STs were identified,with ST43(17/59,28.8％)and ST11(9/59,15.3％)being the predominant.Among 59 mcr-9 positive strains,27 STs were detected,with ST147(11/59,18.6％)and ST274(11/59,18.6％)being the main ones.There were statistical differences in the variants of mcr genes carried by different ST types.The mcr-positive K.pneumoniae came from 28 countries across five continents worldwide,led by China(68/207,32.9％)and Thailand(45/207,21.7％),which were mainly from the human body(100/207,48.3％)and had a concentrated outbreak time from 2015 to 2018.Conclusion Among the global K.pneumoniae,the prevalence of mcr is mainly domina-ted by mcr-1,mcr-8,and mcr-9.The dominant clones of mcr-1 are mainly ST15 and ST43,while those of mcr-8 are mainly ST11 and ST43.The popularity of mcr-9 is mainly based on ST147 and ST274.Strengthening the monitoring of such bacteria may play an impor-tant role in preventing and controlling nosocomial infections.
万方数据
维普
