Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/SaureusAMPTMT10SET10mc160422.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/SaureusAMPTMT10SET20mc160422.msfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_64.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_77.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_73.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_47.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_42.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_46.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_68.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_76.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_82.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_33.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_38.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_65.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_50.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_39.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_52.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_80.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_35.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_48.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_72.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_78.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_43.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_34.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_69.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_81.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_51.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_79.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_36.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_66.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_84.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_44.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_71.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_49.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_74.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_37.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_67.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_41.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_70.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_45.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_32.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_83.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_40.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/09/PXD004036/Fusion_160226_75.rawprimaryOK200003010dan.andersson@imbim.uu.seEgor VorontsovMass SpectrometryShotgun proteomicsNot availableAntimicobial resistanceTmtHigh-ph reverse-phase fractionationStaphylococcus aureusOrbitrap fusionAntimicrobial peptidehttp://www.ebi.ac.uk/pride/archive/projects/PXD004036The cell cultures were lysed using the FastPrep-24 instrument. Cell lysates were centrifuged, 50 μg of each sample from the supernatants were digested with trypsin using the filter-aided sample preparation (FASP) method overnight. Protein samples were reduced with 100 mM dithiothreitol and alkylated with 10 mM methyl methanethiosulfonate. Digested peptides were labeled using TMT 10-plex isobaric mass tagging reagents according to the manufacturer instructions.PrideTMTNo PTMs are included in the datasetData analysis was performed using Proteome Discoverer version 1.4 (Thermo Fisher Scientific). Reference proteome database for Staphylococcus aureus strain NCTC 8325 (March 2016) was downloaded from Uniprot and supplemented with common proteomic contaminants. Mascot 2.3.2.0 (Matrix Science) was used as a search engine with precursor mass tolerance of 5 ppm and fragment mass tolerance of 0.5 Da. Percolator was used for the validation of identification results; target false discovery rate of 1% was used as a threshold to filter confident peptide identifications. Modified peptides were fractionated into 21 fractions using reversed-phase XBridge C18 3.5 μm, 3.0x150 mm column. Each fraction was analyzed on Orbitrap Fusion Tribrid mass spectrometer interfaced with Easy-nLC nanoflow liquid chromatography system.ProteomicsDan I. AnderssonOrbitrap Fusion ETDPARTIALDepartment of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123, Uppsala, SwedenStaphylococcus Aureus27650186 <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <title>307 Temporary Redirect</title> </head><body> <h1>Temporary Redirect</h1> <p>The document has moved <a href="https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi/efetch.fcgi?db=pubmed&id=27650186&rettype=docsum&retmode=text">here</a>.</p> </body></html>yegor.msu@gmail.comBiologicalBiomedicalProteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, SwedenSweden<h4>Background</h4>The clinical development of antimicrobial peptides (AMPs) is currently under evaluation to combat the rapid increase in MDR bacterial pathogens. However, many AMPs closely resemble components of the human innate immune system and the ramifications of prolonged bacterial exposure to AMPs are not fully understood.<h4>Objectives</h4>We show that in vitro serial passage of a clinical USA300 MRSA strain in a host-mimicking environment containing host-derived AMPs results in the selection of stable AMP resistance.<h4>Methods</h4>Serial passage experiments were conducted using steadily increasing concentrations of LL-37, PR-39 or wheat germ histones. WGS and proteomic analysis by MS were used to identify the molecular mechanism associated with increased tolerance of AMPs. AMP-resistant mutants were characterized by measuring in vitro fitness, AMP and antibiotic susceptibility, and virulence in a mouse model of sepsis.<h4>Results</h4>AMP-resistant Staphylococcus aureus mutants often displayed little to no fitness cost and caused invasive disease in mice. Further, this phenotype coincided with diminished susceptibility to both clinically prescribed antibiotics and human defence peptides.<h4>Conclusions</h4>These findings suggest that therapeutic use of AMPs could select for virulent mutants with cross-resistance to human innate immunity as well as antibiotic therapy. Thus, therapeutic use of AMPs and the implications of cross-resistance need to be carefully monitored and evaluated.Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides.Kubicek-Sutherland Jessica Z JZ, Lofton Hava H, Vestergaard Martin M, Hjort Karin K, Ingmer Hanne H, Andersson Dan I DICleland Reagent, d230, Reagent, instrument configuration, FBN, 4-dimercapto-, dTAFII250, protein, R*)-, protein-containing complex, EfW1, dmTAF[[II]]230, peptide, Polypeptides, method, protein polypeptide chains, peptido, polypeptide chain, reduced, dmTAF1, Taf230, subnumerary, ECTOL1, method used in an experiment, 1, 2, tiny, protein aggregate, present in fewer numbers in organism, MMTS, WMS, TAF250, (R*, Taf200, dTAF[[II]]250, TFIID TAF250, peptides, dermoid cyst with malignant transformation, cel, cell, beta-Trypsin, hypoplasia, Taf1p, proteins, decreased number, OCTD, dTAF250, decreased, Sputolysin, sample, methyl methanesulfonothioate, peptidos, TAF, GPHYSD2, thiol methyltransferase activity, SGS, small, dTAF[[II]]230, TAF[[II]]250, protein complex, TAF200, Clelands Reagent, l(3)84Ab, BG:DS00004.13, TAFII-250, TAF250/230, Cell, Peptide, dTAF230, ACMICD, polypeptide, TAFII250, S-adenosyl-L-methionine:thiol S-methyltransferase activity, native protein, natural protein, Cleland, p230, Protein, TAF[[II]]250/230, TFIID, MFS1, WMS2, teratoma with malignant transformation, Cleland's, Taf[[II]]250, TAF[[II]]230, instrument, underdeveloped, Tripcellim, methyl methanethiolsulfonate, TAF[II]250, 3-Butanediol, MASS, CG17603, TAF[[II]], beta Trypsin, sample population, SSKS., plan specification, Cleland's Reagent, Trypure, DmelCG17603, Taf250, SR3-5, Peptid, Polypeptide, TMT, TAF230, TAF1antibiotic, antimicrobial, Staphylococcus aureus subsp. anaerobius, human being, peptides, antibiotique, antimicrobials, Staphilococcus aureus, Antibiotika, antimicrobial agents, Micrococcus aureus, man, Peptide, human, Streptococcus aureus, polypeptide, peptide, Polypeptides, microbicides, Micrococcus pyogenes, Staphylococcus pyogenes aureus, ClvPrd, peptido, resistance, microbicide, Peptid, peptidos, Polypeptide, Staphylococus aureus, Staphlococcus pyogenes citreus, Peptide., antibiotics, AntibiotikumAW549739, False, immune system tolerance, Liquid Chromatography, total expressed protein, FBN, Search, precursor, backward, results, Peptide, Engine, strain, ACMICD, polypeptide, peptide, Polypeptides, Drug Tolerance, Immune Tolerance, ClvPrd, peptido, ECTOL1, C18, body system., B1, Immunologic Tolerance, MFS1, system, cultivar, Analysis, connected anatomical system, Staphlococcus pyogenes citreus, WMS, Data Base, WMS2, C79691, parent ion, Search Engines, proportion, F, anatomical systems, Staphylococcus aureus subsp. anaerobius, peptides, Analyses, Staphilococcus aureus, proportionality, common, Sciences, rate, Micrococcus aureus, MASCOT, MASS, ecotype, Streptococcus aureus, Lccp, OCTD, organ system, mKIAA0989, Micrococcus pyogenes, Staphylococcus pyogenes aureus, Self Tolerance, precursor ion, Tolerance, 10^[-6], column, Data, ppm, D1, SSKS, quotient, Peptid, peptidos, Staphylococus aureus, Polypeptide, GPHYSD2, Proteomes, Data Analyses, drug tolerance, PTHB1, SGS, reversed, Immunological Tolerance, ratiohost organism, Adenosine 5' Phosphate, insensitive, Immune Systems, dAmph, single-organism developmental process, APRTD, antimicrobials, Laboratory, selection process, Adenylic Acid, Mus domesticus, nonspecific immune response, antimicrobial agents, CASP-14, 5'-Adenosine monophosphate, PAdo, 5'-adenylic acid, House Mouse, peptide, Polypeptides, 6-(D-(2-amino-2-phenylacetamido))-3, microbicides, damph, peptido, diseases, ampicillin acid, AP, Adenosine-5'-monophosphoric acid, symptoms, Impacts, aminobenzylpenicillin, diseases and disorders, Ampicillin, Environmental Impacts, antimicrobial, treatment, ampicillin anhydrous, human disease, 3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID, peptides, 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polypeptide, Environmental, ampicillin, AMP, Amp, Mus, Systems, 5'-Adenylic Acid, CG8604, condition, Adenosine Phosphate, D-(-)-ampicillin, Adenosine 5'-phosphate, 6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3, susceptibility, Phosphate Dipotassium, ABPC, adenosine-5'P, pA, House Mice, 2-dimethylpenam-3alpha-carboxylic acid, Disodium, Adenosine 2'-Phosphate, Laboratory Mice, cost, Adenosine Phosphate Disodium, Dipotassium, Environments, Peptid, 2' Adenylic Acid, Laboratory Mouse, Adenylic acidPyohemia, host organism, Ghrfr, Pyemias, retinol (vitamin A1) dehydrogenase activity, Adenosine 5' Phosphate, Immune Systems, dAmph, insensitive, single-organism developmental process, APRTD, antimicrobials, Laboratory, selection process, Adenylic Acid, Blood, Mus domesticus, nonspecific immune response, MRSA bacteremia, Abcb1, antimicrobial agents, Antimicrobial Peptide, CASP-14, 5'-Adenosine monophosphate, PAdo, Infection in blood stream, 5'-adenylic acid, infectivity, House Mouse, peptide, 6-(D-(2-amino-2-phenylacetamido))-3, Histone H2b, Pyaemias, Polypeptides, Techniques, Histone H2a, damph, microbicides, peptido, methicillin-resistant Staphylococcus aureus (MSSA) bacteremia, diseases, Method, ampicillin acid, AP, Adenosine-5'-monophosphoric acid, symptoms, Impacts, aminobenzylpenicillin, diseases and disorders, Ampicillin, Pyemia, Environmental Impacts, Staphlococcus pyogenes citreus, retinal reductase activity, antimicrobial, increased, viral infection, ampicillin anhydrous, human disease, 3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID, peptides, Staphilococcus aureus, Antibiotika, retinol:NAD+ oxidoreductase activity, Swiss Mice, virus process, Micrococcus aureus, procedures, ASL, adenosine phosphate, wheat, ecotype, 5'-Adenylic acid, phosphate d'adenosine, Tricum aestivum, common wheat, Environmental Impact, Immune, ampicilina, Methodological Studies, scientific observation, Histone H5, Histone H4, Histone H7, Homo sapiens disease, all-trans 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with malignant transformation, Streptococcus aureus, presence or absence in organism301trueAntimicrobial resistance of Staphylococcus aureus by quantitative proteomics with TMT-labellingThe clinical development of antimicrobial peptides (AMPs) is currently under evaluation to combat the rapid increase in multi-drug resistant bacterial pathogens. However, many AMPs closely resemble components of the human innate immune system, and the ramifications of prolonged bacterial exposure to AMPs are not fully understood. Here we show that in vitro serial passage of a clinical USA300 methicillin-resistant Staphylococcus aureus strain in a host-mimicking environment containing host-derived AMPs results in the selection of stable AMP-resistance. AMP-resistant S. aureus mutants often displayed little to no fitness cost and caused invasive disease in mice. Further, this phenotype coincided with diminished susceptibility to both clinically prescribed antibiotics and human defense peptides. These findings suggest that therapeutic use of AMPs could select for virulent mutants with cross-resistance to human innate immunity as well as antibiotic therapy. Thus, therapeutic use of AMPs and the implications of cross-resistance need to be carefully monitored and evaluated.2016-09-262016-04-22PXD0040364466449917558258038804333029535851114512067811080612461962461972842188090320637522995811363350906836351524260275838538791187947398007186801NCBITaxon:1280572307688881114301187263555571468351452627412583649117571508472746707364113546138855821803582329031388869152167786889539978447512951398704351123294126246942229692812397713311809933995232310343043654813583334607925198183659219813143205971293818826826558194762149363295726373719222212502321979116938197912NCBITaxon:1272111957741247818661328388281395584345135867221755437294914081694595418045416193426683413903634530586112041623264460711210411706127443210859561496367469412831666943694559729452811320810039241065837514633087936944784475174206542208964317447127020896344597413797912838411946694006671454587932993529320101981264690410661145755121659940483392512165972165954550131528269731606212133128312821280339523218108323217825252920435315227794476237628112353153454349825741948147871720309498019752555536231439841356742951053948824261914548140479NCBITaxon:21571150621551531292439899037122857782996597532059687623193516309800588845586978181780817363094317910369056606989361604885661409859104782566416242515059071187023482118705320491381693630638632355543204663222618663312994565860688453515126232172192174592161295671713604410016023587002642036945694101676341021076127735113165821504802392547279332160428146100291358430357861746331325291118700215764180969975665457744491566667547604452467675684030191726518130194111929439633664113633672175111764510239870932025NCBITaxon:4055932582359092788396523652649821787074982163472565691569387224982116544872056973474951666905108944835525663661410NCBITaxon:4932871556891758543102459808108944475741755518100058945268087322875351908323311561263730069303911415542193255521872587268723872487298727123598755529NCBITaxon:475154762422314146547730551800664417725564843376771581419198822445299767446982510216998231174673897641041051155744689444474153NCBITaxon:5055796016776744685100036487529600NCBITaxon:58116534911822637082483341475480557841946751299114578458359741276473194439137086326547876569835566369838192011164034624136810893161001428099612NCBITaxon:548681NCBITaxon:582054641498523077479464098609958652283637379196627290587668960596061572951372218759446708756227086266596417110133548330903497412982998603878348106267566430615127936543194747033424947223598596108961588655974649987039202111072878272154078211908503757075298351170828206189257771480418985487350247158779627300251563041190252867463604614796469644375939491146247274612874601134506253256648452659197221963819155263858859652639NCBITaxon:6157505210283071105172375059576131302409720002634196105264110909469407722774694163485689961123869497515NCBITaxon:2NCBITaxon:135231703612506174767927450627249159615384005257313246432136861505962697968666299034694171344346360347515363296440421018194301086731018510976063558633149616128628724620096692729422729435133813216968583551865368595968912801726071018568729411009118696141633316780781186941436183NCBITaxon:6191118698840231719475932118691443906NCBITaxon:102982100071257118348824387279694836419080218787864515970384766425731055347095145122578656870861822607046183260705260707NCBITaxon:7803906NCBITaxon:1502451516658457702921158612184519307920928520131974707856100713370565295076192126385454195NCBITaxon:3055504457391538337991399878168192875NCBITaxon:10239NCBITaxon:7142829126806315327341478281309570547044830064175158592381055524159084128108228233446900815025754122810451930174830085210977970671356225833136185509924NCBITaxon:56938268830640527796179469958334240906151015151034809NCBITaxon:63124067448242813076707087613837047592723708281677285035158199011951953370249240536088817562615835583337602126719285321773572671193501846451772998086167879177437371110490563712153481724073714121532395767690147266470913170475712562745790311333550372885962859634792491308126387121203511082332648373153214693NCBITaxon:9615383235946331858626079914126220029813141313493760833344926701311111497019281239655833325283010184138569591110065812375612750454266625515197887492003750360094129349715300910766204114903524725175014012573983649908515151438992NCBITaxon:1155237453988374744544641521399274356235931179286643235983906288705158059553611945993271602938511497861603293338922853422999810894535936457428412754121536024271831627713512251179948875058NCBITaxon:1040724271550277916797181673871349130627415895521010306502780291595412629158660025515849376532715957021002263388942345128768913558867551293094514647920312421641331051528038280351928434369093581539858089462108034817939211825902878892950274560990690174934681927256322732189038292867572279011247190400727NCBITaxon:5796537457114311233523562114020641198108713554771424507229533796983555222212916347087141045775126216115429315754613962242139299287139077020206032818573231143193382935508332923074112922114816402784896160106772526499975744727580240550717629925122968335366581926832140535762294128160783957632066724005402965432823122737777298184318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