多位点序列分型（multilocus sequence typing,MLST）是一种基于核酸序列测定的细菌分型方法。这种方法通过PCR扩增多个管家基因内部片段并测定其序列，分析菌株的变异。
MLST操作简单，结果能快速得到并且便于不同实验室的比较，已经用于多种细菌的流行病学监测和进化研究。随着测序速度的加快和成本的降低，以及分析软件的发展，MLST逐渐成为细菌的常规分型方法。
多位点序列分型的原理：MLST方法一般测定6-10个看家基因内部400-600bp的核苷酸序列，每个位点的序列根据其发现的时间顺序赋予一个等位基因编号，每一株菌的等位基因编号按照指定的顺序排列就是它的等位基因谱，也就是这株菌的序列型（sequence type，ST）。这样得到的每个ST均代表一组单独的核苷酸序列信息。通过比较ST可以发现菌株的相关性，即密切相关菌株具有相同的ST或仅有极个别基因位点不同的ST。
PubMLST数据库（https://pubmlst.org/）
提交到PubMLST的菌株
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数据库包含的细菌菌种
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MLST分型软件
(https://github.com/tseemann/mlst)
不同的安装方法
Brew
MacOS系统
% brew install brewsci/bio/mlst
Conda
% conda install -c bioconda -c conda-forge mlst
Source
% cd $HOME
% git clone https://github.com/tseemann/mlst.git% $HOME/mlst/bin/mlst --help
直接输入mlst -h 即可输出帮助文档（服务器26）
mlst -h
使用方法
直接输入组装后的fasta文件即可快速得到分型结果
% mlst contigs.facontigs.fa
neisseria 11149 abcZ(672) adk(3) aroE(4) fumC(3) gdh(8) pdhC(4) pgm(6)% mlst genome.gbk.gzgenome.gbk.gz sepidermidis 184 arcC(16) aroE(1) gtr(2) mutS(1) pyrR(2) tpiA(1) yqiL(1)% mlst --label Anthrax GCF_001941925.1_ASM194192v1_genomic.fna.gzAnthrax bcereus - glp(24) gmk(1) ilv(~83) pta(1) pur(~71) pyc(37) tpi(41)% mlst --nopath *.fnaNC_018936.fna spyogenes 28 gki(4) gtr(3) murI(4) mutS(4) recP(4) xpt(2) yqiL(4)NC_017596.fna spyogenes 11 gki(2) gtr(6) murI(1) mutS(2) recP(2) xpt(2) yqiL(2)NC_008022.fna spyogenes 55 gki(11) gtr(9) murI(1) mutS(9) recP(2) xpt(3) yqiL(4)NC_006086.fna spyogenes 382 gki(5) gtr(52) murI(5) mutS(5) recP(5) xpt(4) yqiL(3)NC_008024.fna spyogenes - gki(5) gtr(11) murI(8) mutS(5) recP(15?) xpt(2) yqiL(1)NC_017040.fna spyogenes 172 gki(56) gtr(24) murI(39) mutS(7) recP(30) xpt(2) yqiL(33)
查看可用的物种和对应的基因名称
mlst --longlist
abaumannii Oxf_gltA Oxf_gyrB Oxf_gdhB Oxf_recA Oxf_cpn60 Oxf_gpi Oxf_rpoDabaumannii_2 Pas_cpn60 Pas_fusA Pas_gltA Pas_pyrG Pas_recAPas_rplB Pas_rpoBachromobacter nusA rpoB eno gltB lepA nuoL nrdAaeromonas gyrB groL gltA metG ppsA recAafumigatus ANX4 BGT1 CAT1 LIP MAT1_2 SODB ZRF2aphagocytophilum pheS glyA fumC mdh sucA dnaN atpAarcobacter aspA atpA glnA gltA glyA pgm tktbbacilliformis ftsZ flaA ribC rnpB rpoB bvrR groELbcc atpD gltB gyrB recA lepA phaC trpBbcereus glp gmk ilv pta pur pyc tpibhampsonii Bha_adh Bha_est Bha_gdh Bha_glpK Bha_pgm Bha_thibhenselae 16S batR ftsZ gltA groEL nlpD ribC rpoBbhyodysenteriae Bhy_adh Bhy_alp Bhy_est Bhy_gdh Bhy_glpK Bhy_pgm Bhy_thibintermedia Bin_adh Bin_alp Bin_est Bin_gdh Bin_glpK Bin_pgm Bin_thiblicheniformis adk ccpA recF rpoB spo0A sucCbordetella adk fumC glyA tyrB icd pepA pgmborrelia clpA clpX nifS pepX pyrG recG rplB uvrAbpilosicoli Bpi_adh Bpi_alp Bpi_est Bpi_gdh Bpi_glpK Bpi_pgm Bpi_thibpseudomallei ace gltB gmhD lepA lipA narK ndhbrachyspira Bra_adh Bra_alp Bra_est Bra_gdh Bra_glp Bra_pgm Bra_thibrucella gap aroA glk dnaK gyrB trpE cobQ int_hyp omp25bsubtilis glpF ilvD pta purH pycA rpoD tpiAcampylobacter aspA glnA gltA glyA pgm tkt uncAcbotulinum aroE mdh aceK oppB rpoB recA hspcconcisus Cco_aspA Cco_atpA Cco_glnA Cco_gltA Cco_glyACco_ilvD Cco_pgmcdifficile adk atpA dxr glyA recA sodA tpicdiphtheriae atpA dnaE dnaK fusA leuA odhA rpoBcfetus Cfe_aspA Cfe_glnA Cfe_gltA Cfe_glyA Cfe_pgm Cfe_tktCfe_uncAcfreundii aspC clpX fadD mdh arcA dnaG lysPcglabrata FKS LEU2 NMT1 TRP1 UGP1 URA3chelveticus Che_aspA Che_atpA Che_glnA Che_gltA Che_glyAChe_pgm Che_tktchlamydiales gatA oppA hflX gidA enoA hemN fumCchyointestinalis Chy_aspA Chy_atpA Chy_glnA Chy_gltA Chy_glyA Chy_pgm Chy_tktcinsulaenigrae Cin_aspA Cin_atpA Cin_glnA Cin_glyA Cin_pgiCin_pgm Cin_tktclanienae Cln_aspA Cln_atpA Cln_glnA Cln_gltA Cln_glyACln_pgm Cln_tktclari Cla_adk Cla_atpA Cla_glnA Cla_glyA Cla_pgi Cla_pgm Cla_tktcmaltaromaticum dapE ddlA glpQ ilvE leuS pyc pyrEcronobacter atpD fusA glnS gltB gyrB infB ppscsepticum ddl dnaK glpK groEL gyrA recA tpicsinensis Actin Cox1 Cox3 Ef_1a Its1 Nad4 Nad5 Tubulincsputorum Csp_aspA Csp_atpA Csp_glnA Csp_gltA Csp_glyACsp_pgm Csp_tktcupsaliensis Cup_adk Cup_aspA Cup_atpA Cup_glnA Cup_glyA Cup_pgi Cup_tktdnodosus dcd dtdA folK recR rlmH rplI tsaEecloacae dnaA fusA gyrB leuS pyrG rplB rpoBecoli adk fumC gyrB icd mdh purA recAecoli_2 dinB icdA pabB polB putP trpA trpB uidAedwardsiella adk atpD dnaJ gapA glnA hsp60 phoR pyrG rpoA tufefaecalis gdh gyd pstS gki aroE xpt yqiLefaecium atpA ddl gdh purK gyd pstS adkfpsychrophilum atpA dnaK fumC gyrB murG trpB tufganatis adk atpD fumC gyrB infB mdh recN thdFhcinaedi 23S_rRNA ppa aspA aroE atpA tkt cdtBhinfluenzae adk atpG frdB fucK mdh pgi recAhparasuis atpD infB mdh rpoB 6pgd g3pd frdBhpylori atpA efp mutY ppa trpC ureI yphChsuis atpA efp mutY ppa trpC ureAB yphCkaerogenes dnaA fusA gyrB leuS pryG rplB rpoBkkingae abcZ adk aroE cpn60 gdh recAkoxytoca gapA infB mdh pgi phoE rpoB tonBkpneumoniae gapA infB mdh pgi phoE rpoB tonBkseptempunctata cox1 rnlleptospira glmU pntA sucA tpiA pfkB mreA caiBleptospira_2 adk_2 glmU_2 icdA_2 lipL32_2 lipL41_2 mreA_2 pntA_2leptospira_3 adk_3 icdA_3 lipL32_3 lipL41_3 rrs2_3 secY_3lmonocytogenes abcZ bglA cat dapE dat ldh lhkAlsalivarius pstB rpsB nrdB rpoA parBmabscessus Mab_argH Mab_cya Mab_gnd Mab_murC Mab_pta Mab_purH Mab_rpoBmagalactiae dnaA gltX gyrB metS tufAmbovis adh1 gltX gpsA gyrB pta2 tdk tktmcanis ack cpn60 fdh pta purA sar tufmcaseolyticus ack cpn60 fdh pta purA sar tufmcatarrhalis abcZ adk efp fumC glyBETA mutY ppa trpEmhaemolytica adk aroE deoD gapDH gnd mdh zwfmhyopneumoniae adk rpoB tpiAmhyorhinis dnaA rpoB gyrB gltX adk gmkmiowae dppC ulaA valS rpoC leuS kdpAmmassiliense Mma_argH Mma_cya Mma_gnd Mma_murC Mma_pta Mma_purH Mma_rpoBmplutonius argE galK gbpB purRmpneumoniae ppa pgm gyrB gmk glyA atpA arcC adkmsynoviae adk atpG efp gmk nagC ppa recAneisseria abcZ adk aroE fumC gdh pdhC pgmorhinotracheale adk aroE fumC gdhA mdh pgi pmiotsutsugamushi gpsA mdh nrdF nuoF ppdK sucB sucDpacnes aroE atpD gmk guaA lepA sodA tly CAMP2paeruginosa acs aro gua mut nuo pps trppdamselae glpF gyrB metG pntA pyrC toxRpfluorescens glnS gyrB ileS nuoD recA rpoB rpoDpgingivalis ftsQ gpdxJ hagB mcmA pepO pga recAplarvae glpF sigF glpT Natrans rpoB ftsA clpCpmultocida_multihost mh_adk mh_aroA mh_deoD mh_gdhA mh_g6pd mh_mdh mh_pgipmultocida_rirdc RIRDC_adk RIRDC_est RIRDC_pmi RIRDC_zwf RIRDC_mdh RIRDC_gdh RIRDC_pgippentosaceus gyrB pyc pgm leuS glnA dalR pgIranatipestifer dnaB groEL gyrA mdh gluD gpi rpoBrhodococcus gapdh tpi mdh icl rpoB recA adksagalactiae adhP pheS atr glnA sdhA glcK tktsaureus arcC aroE glpF gmk pta tpi yqiLsbsec ddl gki glnA mutS mutS2 pheS proS pyrE thrS tpiscanis gki gtr murI mutS recP xpt yqiZsdysgalactiae gki gtr murI mutS recP xpt atoBsenterica aroC dnaN hemD hisD purE sucA thrAsepidermidis arcC aroE gtr mutS pyrR tpiA yqiLsgallolyticus aroE glgB nifS p20 tkt trpD uvrAshaemolyticus arcC SH_1200 hemH leuB SH1431 cfxE Ribose_ABCshominis arcC glpK gtr pta tpiA tufsinorhizobium asd edd gap glnD gnd nuoE1 ordL2 recA sucA zwfslugdunensis aroE dat ddl gmk ldh recA yqiLsmaltophilia atpD gapA guaA mutM nuoD ppsA recAsoralis aroE ddl gdh gki hexB recP xptspneumoniae aroE gdh gki recP spi xpt ddlspseudintermedius ack cpn60 fdh pta purA sar tufspyogenes gki gtr murI mutS recP xpt yqiLssuis aroA cpn60 dpr gki mutS recA thrAsthermophilus ddlA glcK proA ptsI serB tktsthermophilus_2 carB clpX dnaA murC murE pepN pepX pyrG recA rpoBstreptomyces 16S atpD gyrB recA rpoB trpBsuberis arcC ddl gki recP tdk tpi yqiLszooepidemicus arcC nrdE proS spi tdk tpi yqiLtaylorella gltA gyrB fh shmt tyrB adk txntenacibaculum atpA dnaK glyA gyrB infB rlmN tgtvcholerae adk gyrB mdh metE pntA purM pyrCvibrio gyrB pyrH recA atpAvparahaemolyticus dnaE gyrB recA dtdS pntA pyrC tnaAvtapetis atpA fstZ gapA hsp60 pyrH rctB recA rpoA rpoD topAvvulnificus glp gyrB mdh metG purM dtdS lysA pntA pyrC tnaAwolbachia gatB coxA hcpA ftsZ fbpAxfastidiosa leuA petC malF cysG holC nuoL gltTyersinia aarF dfp galR glnS hemA rfaE speAypseudotuberculosis adk argA aroA glnA thrA tmk trpEyruckeri glnA gyrB dnaJ thrA hsp60 recA
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