Comparison of automatic methods MALDI-TOF, VITEK2 and manual methods for the identification of intestinal microbial communities on the example of samples from alpacas (Vicugna pacos)
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Aujoulat F., Romano-Bertrand.S., Masnou A., Marchandin H., Jumas-Bilak.E.: Niches, population structure and genome reduction in Ochrobactrum intermedium: Clues to technology-driven emergence of pathogens. PLoS One 2014, 9, e83376, doi: 10.1371/journal.pone.0083376.AujoulatF.Romano-BertrandS.MasnouA.MarchandinH.Jumas-BilakE.: Niches, population structure and genome reduction in Ochrobactrum intermedium: Clues to technology-driven emergence of pathogens. PLoS One2014, 9, e83376, DOI: 10.1371/journal.pone.0083376.Open DOISearch in Google Scholar
Burton A.J., Nydam D.V., Mitchell K.J., Bowman D.D.: Fecal shedding of cryptosporidium oocysts in healthy alpaca crias and their dams. J Am Vet Med Assoc 2012, 241, 496–498, doi: 10.2460/javma.241.4.496.BurtonA.J.NydamD.V.MitchellK.J.BowmanD.D.: Fecal shedding of cryptosporidium oocysts in healthy alpaca crias and their dams. J Am Vet Med Assoc2012, 241, 496–498, DOI: 10.2460/javma.241.4.496.Open DOISearch in Google Scholar
Carroll C.: The Relationship Between Microbiota, Diet, and Energy Production in the Alpaca. Theses and Dissertations, 6943, Brigham Young University, Provo, UT 2017. https://scholarsarchive. byu.edu/etd/6943.CarrollC.: The Relationship Between Microbiota, Diet, and Energy Production in the Alpaca. Theses and Dissertations, 6943, Brigham Young University, Provo, UT2017. https://scholarsarchive.byu.edu/etd/6943.Search in Google Scholar
Carroll C., Olsen K.D., Ricks N.J., Dill-McFarland.K.A., Suen G., Robinson T.F., Chaston J.M.: Bacterial communities in the alpaca gastrointestinal tract vary with diet and body site. Front Microbiol 2019, 9, 3334, doi: 10.3389/fmicb.2018.03334.CarrollC.OlsenK.D.RicksN.J.Dill-McFarlandK.A.SuenG.RobinsonT.F.ChastonJ.M.: Bacterial communities in the alpaca gastrointestinal tract vary with diet and body site. Front Microbiol2019, 9, 3334, DOI: 10.3389/fmicb.2018.03334.Open DOISearch in Google Scholar
Chao R., Xia C., Pei C., Huo W., Liu Q., Zhang C., Ren Y.: Comparison of the microbial communities of alpacas and sheep fed diets with three different ratios of corn stalk to concentrate. J Anim Physiol Anim Nutr (Berl) 2021, 105, 26–34, doi: 10.1111/jpn. 13442.ChaoR.XiaC.PeiC.HuoW.LiuQ.ZhangC.RenY.: Comparison of the microbial communities of alpacas and sheep fed diets with three different ratios of corn stalk to concentrate. J Anim Physiol Anim Nutr (Berl)2021, 105, 26–34, DOI: 10.1111/jpn. 13442.Open DOISearch in Google Scholar
Clark A.E., Kaleta E.J., Arora A., Wolk D.M.: Matrix-assisted laser desorption ionization-time of flight mass spectrometry: A fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2013, 26, 547–603, doi: 10.1128/CMR.00072-12.ClarkA.E.KaletaE.J.AroraA.WolkD.M.: Matrix-assisted laser desorption ionization-time of flight mass spectrometry: A fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev2013, 26, 547–603, DOI: 10.1128/CMR.00072-12.Open DOISearch in Google Scholar
Devanga Ragupathi N.K., Muthuirulandi Sethuvel D.P., Inbanathan F.Y., Veeraraghavan B.: Accurate differentiation of Escherichia coli and Shigella serogroups: challenges and strategies. New Microbe New Infect 2018, 21, 58–62, doi: 10.1016/j.nmni.2017.09.003.Devanga RagupathiN.K.Muthuirulandi SethuvelD.P.InbanathanF.Y.VeeraraghavanB.: Accurate differentiation of Escherichia coli and Shigella serogroups: challenges and strategies. New Microbe New Infect2018, 21, 58–62, DOI: 10.1016/j.nmni.2017.09.003.Open DOISearch in Google Scholar
Godmer A., Benzerara Y., Normand C., Veziris N., Gallah S., Eckert C.: Revisiting species identification within the Enterobacter cloacae complex by matrix-assisted laser desorption ionization–time of flight mass spectrometry. Microbiol Spectr 2021, 9, e0066121, doi: 10.1128/Spectrum.00661-21.GodmerA.BenzeraraY.NormandC.VezirisN.GallahS.EckertC.: Revisiting species identification within the Enterobacter cloacae complex by matrix-assisted laser desorption ionization–time of flight mass spectrometry. Microbiol Spectr2021, 9, e0066121, DOI: 10.1128/Spectrum.00661-21.Open DOISearch in Google Scholar
Golyshin P.N., Werner J., Chernikova T.N., Tran H., Ferrer M., Yakimov M.M., Teeling H., Golyshina O.V., Consortium M.S. MAMBA Scientific Consortium: Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T). Genome Announc 2013, 1, e0014113, doi: 10.1128/genomeA.00141-13.GolyshinP.N.WernerJ.ChernikovaT.N.TranH.FerrerM.YakimovM.M.TeelingH.GolyshinaO.V.ConsortiumM.S.MAMBA Scientific Consortium: Genome Sequence of Thalassolituus oleivorans MIL-1 (DSM 14913T). Genome Announc2013, 1, e0014113, DOI: 10.1128/genomeA.00141-13.Open DOISearch in Google Scholar
Gontia I., Kavita K., Schmid M., Hartmann A., Jha B.: Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential. Int J Syst Evol Microbiol 2011, 61, 2799–2804, doi: 10.1099/ijs. 0.023176-0.GontiaI.KavitaK.SchmidM.HartmannA.JhaB.: Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential. Int J Syst Evol Microbiol2011, 61, 2799–2804, DOI: 10.1099/ijs.0.023176-0.Open DOISearch in Google Scholar
Guerrero-Olmos K., Báez J., Valenzuela N., Gahona J., Del Campo R., Silva J.: Molecular characterization and antibiotic resistance of Enterococcus species from gut microbiota of Chilean Altiplano camelids. Infect Ecol Epidemiol 2014, 4, doi: 10.3402/iee.v4.24714.Guerrero-OlmosK.BáezJ.ValenzuelaN.GahonaJ.Del CampoR.SilvaJ.: Molecular characterization and antibiotic resistance of Enterococcus species from gut microbiota of Chilean Altiplano camelids. Infect Ecol Epidemiol2014, 4, DOI: 10.3402/iee.v4.24714.Open DOISearch in Google Scholar
Halsby K., Twomey D.F., Featherstone C., Foster A., Walsh A., Hewitt K., Morgan D.: Zoonotic diseases in South American camelids in England and Wales. Epidemiol Infect 2017, 145, 1037–1043, doi: 10.1017/S0950268816003101.HalsbyK.TwomeyD.F.FeatherstoneC.FosterA.WalshA.HewittK.MorganD.: Zoonotic diseases in South American camelids in England and Wales. Epidemiol Infect2017, 145, 1037–1043, DOI: 10.1017/S0950268816003101.Open DOISearch in Google Scholar
Was 14 Hirai J., Yamagishi Y., Sakanashi D., Koizumi Y., Suematsu H., Mikamo H.: A Case of Bacteremia Caused by Ochrobactrum intermedium (in Japanese). Kansenshogaku Zasshi 2016, 90, 129–133, doi: 10.11150/kansenshogakuzasshi. 90.129.Was 14 HiraiJ.YamagishiY.SakanashiD.KoizumiY.SuematsuH.MikamoH.: A Case of Bacteremia Caused by Ochrobactrum intermedium (in Japanese). Kansenshogaku Zasshi2016, 90, 129–133, DOI: 10.11150/kansenshogakuzasshi. 90.129.Open DOISearch in Google Scholar
Was 13 Hosseini S., Martinez-Chapa.S.O.: SpringerBriefs in Applied Sciences and Technology: Fundamentals of tissue engineering and application of MALDI-ToF-MS in analysis of the scaffold materials, edited by A. Kumar, Allam Appa Rao, Springer, Singapore, 2017, doi: 10.1007/978-981-10-2356-9_3.Was 13 HosseiniS.Martinez-ChapaS.O.: SpringerBriefs in Applied Sciences and Technology: Fundamentals of tissue engineering and application of MALDI-ToF-MS in analysis of the scaffold materials, edited by KumarA.RaoAllam Appa, Springer, Singapore, 2017, DOI: 10.1007/978-981-10-2356-9_3.Open DOISearch in Google Scholar
Kapustka J., Garbiec A.: Alpacas in Poland: Health, welfare, and anti-parasitic prophylaxis. Med Weter 2022, 78, 68–73, doi: 10.21521/mw.6614.KapustkaJ.GarbiecA.: Alpacas in Poland: Health, welfare, and anti-parasitic prophylaxis. Med Weter2022, 78, 68–73, DOI: 10.21521/mw.6614.Open DOISearch in Google Scholar
Kassab I., Sarsam N., Affas S., Ayas M., Baang J.H.: A Case of Ochrobactrum intermedium Bacteremia Secondary to Cholangitis With a Literature Review. Cureus 2021, 13, 2–7, doi: 10.7759/cureus.14648.KassabI.SarsamN.AffasS.AyasM.BaangJ.H.: A Case of Ochrobactrum intermedium Bacteremia Secondary to Cholangitis With a Literature Review. Cureus2021, 13, 2–7, DOI: 10.7759/cureus.14648.Open DOISearch in Google Scholar
Khot P.D., Fisher M.A.: Novel approach for differentiating Shigella species and Escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013, 51, 3711–3716, doi: 10.1128/JCM.01526-13.KhotP.D.FisherM.A.: Novel approach for differentiating Shigella species and Escherichia coli by matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol2013, 51, 3711–3716, DOI: 10.1128/JCM.01526-13.Open DOISearch in Google Scholar
Krajewska-Wędzina M., Didkowska A., Sridhara A.A., Elahi R., Johnathan-Lee.A., Radulski Ł., Lipiec M., Anusz K., Lyashchenko K.P., Miller M.A., Waters W.R.: Transboundary tuberculosis: Importation of alpacas infected with Mycobacterium bovis from the United Kingdom to Poland and potential for serodiagnostic assays in detecting tuberculin skin test false-negative animals. Transbound Emerg Dis 2020, 67, 1306–1314, doi: 10.1111/tbed.13471.Krajewska-WędzinaM.DidkowskaA.SridharaA.A.ElahiR.Johnathan-LeeA.RadulskiŁ.LipiecM.AnuszK.LyashchenkoK.P.MillerM.A.WatersW.R.: Transboundary tuberculosis: Importation of alpacas infected with Mycobacterium bovis from the United Kingdom to Poland and potential for serodiagnostic assays in detecting tuberculin skin test false-negative animals. Transbound Emerg Dis2020, 67, 1306–1314, DOI: 10.1111/tbed.13471.Open DOISearch in Google Scholar
Kuijpers S.C., Klouwens M., de Jong K.H., Langeslag J.C.P., Kuipers S., Reubsaet F.A.G., van Leeuwen E.M.M., de Bree G.J., Hovius J.W., Grobusch M.P.: Primary cutaneous melioidosis acquired in Nepal – Case report and literature review. Travel Med Infect Dis 2021, 42, 102080, doi: 10.1016/j.tmaid.2021.102080.KuijpersS.C.KlouwensM.de JongK.H.LangeslagJ.C.P.KuipersS.ReubsaetF.A.G.van LeeuwenE.M.M.de BreeG.J.HoviusJ.W.GrobuschM.P.: Primary cutaneous melioidosis acquired in Nepal – Case report and literature review. Travel Med Infect Dis2021, 42, 102080, DOI: 10.1016/j.tmaid.2021.102080.Open DOISearch in Google Scholar
Lazar V., Ditu L.M., Gradisteanu G., Pircalabioru I.G., Curutiu C., Holban A.M., Picu A., Pectu L., Chifiriuc M.C.: Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Front Immunol 2018, 9, 1830, doi:10.3389/fimmu.2018.01830.LazarV.DituL.M.GradisteanuG.PircalabioruI.G.CurutiuC.HolbanA.M.PicuA.PectuL.ChifiriucM.C.: Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Front Immunol2018, 9, 1830, DOI:10.3389/fimmu.2018.01830.Open DOISearch in Google Scholar
Liu Q., Li J., Wei B., Zhang X., Zhang L., Zhang Y., Fang J.: Leeuwenhoekiella nanhaiensis sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol 2016, 66, 1352–1357, doi: 10.1099/ijsem.0.000883.LiuQ.LiJ.WeiB.ZhangX.ZhangL.ZhangY.FangJ.: Leeuwenhoekiella nanhaiensis sp. nov., isolated from deep-sea water. Int J Syst Evol Microbiol2016, 66, 1352–1357, DOI: 10.1099/ijsem.0.000883.Open DOISearch in Google Scholar
Lu Y., Zhao H., Sun J., Liu Y., Zhou X., Beier R.C., Wu G., Hou X.: Characterization of Multidrug-Resistant Salmonella enterica Serovars Indiana and Enteritidis from Chickens in Eastern China. PLoS One 2014, 9, e96050, doi: 10.1371/journal.pone. 0096050.LuY.ZhaoH.SunJ.LiuY.ZhouX.BeierR.C.WuG.HouX.: Characterization of Multidrug-Resistant Salmonella enterica Serovars Indiana and Enteritidis from Chickens in Eastern China. PLoS One2014, 9, e96050, DOI: 10.1371/journal.pone.0096050.Open DOISearch in Google Scholar
Manzulli V., Rondinone V., Buchicchio A., Serrecchia L., Cipolletta D., Fasanella A., Parisi A., Difato L., Iatarola M., Aceti A., Poppa E., Tolve F., Pace L., Petruzzi F., Rovere I.D., Raele D.A., Del Sambro L., Giangrossi L., Galante D.: Discrimination of Bacillus cereus Group Members by MALDI-TOF Mass Spectrometry. Microorganisms 2021, 9, 1202, doi: 10.3390/microorganisms9061202.ManzulliV.RondinoneV.BuchicchioA.SerrecchiaL.CipollettaD.FasanellaA.ParisiA.DifatoL.IatarolaM.AcetiA.PoppaE.TolveF.PaceL.PetruzziF.RovereI.D.RaeleD.A.Del SambroL.GiangrossiL.GalanteD.: Discrimination of Bacillus cereus Group Members by MALDI-TOF Mass Spectrometry. Microorganisms2021, 9, 1202, DOI: 10.3390/microorganisms9061202.Open DOISearch in Google Scholar
Murata K., Ozawa K., Kawakami H., Mochizuki K., Ohkusu K.: Brachybacterium paraconglomeratum Endophthalmitis Postcataract Operation. Case Rep Ophthalmol Med 2020, 2020, 1513069, doi: 10.1155/2020/1513069.MurataK.OzawaK.KawakamiH.MochizukiK.OhkusuK.: Brachybacterium paraconglomeratum Endophthalmitis Postcataract Operation. Case Rep Ophthalmol Med2020, 2020, 1513069, DOI: 10.1155/2020/1513069.Open DOISearch in Google Scholar
Park S.K., Kim M.S., Jung M.J., Nam Y., Do Park E.J., Roh S.W., Bae J.W.: Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood. Int J Syst Evol Microbiol 2011, 61, 1118–1122, doi: 10.1099/ijs.0.022517-0.ParkS.K.KimM.S.JungM.J.NamY.Do ParkE.J.RohS.W.BaeJ.W.: Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood. Int J Syst Evol Microbiol2011, 61, 1118–1122, DOI: 10.1099/ijs.0.022517-0.Open DOISearch in Google Scholar
Rivero M., Alonso J., Ramón M.F., Gonzales N., Pozo A., Marín I., Navascués A., Juanbeltz R.: Infections due to Cellulosimicrobium species: Case report and literature review. BMC Infect Dis 2019, 19, 816, doi: 10.1186/s12879-019-4440-2.RiveroM.AlonsoJ.RamónM.F.GonzalesN.PozoA.MarínI.NavascuésA.JuanbeltzR.: Infections due to Cellulosimicrobium species: Case report and literature review. BMC Infect Dis2019, 19, 816, DOI: 10.1186/s12879-019-4440-2.Open DOISearch in Google Scholar
Ryan M.P., Tony Pembroke J.: The genus Ochrobactrum as major opportunistic pathogens. Microorganisms 2020, 8, 1797, doi: 10.3390/microorganisms8111797.RyanM.P.Tony PembrokeJ.: The genus Ochrobactrum as major opportunistic pathogens. Microorganisms2020, 8, 1797, DOI: 10.3390/microorganisms8111797.Open DOISearch in Google Scholar
Salvá B.K., Zumalacárregui J.M., Figueira A.C., Osorio M.T., Mateo J.: Nutrient composition and technological quality of meat from alpacas reared in Peru. Meat Sci 2009, 82, 450–455, doi: 10.1016/j.meatsci.2009.02.015.SalváB.K.ZumalacárreguiJ.M.FigueiraA.C.OsorioM.T.MateoJ.: Nutrient composition and technological quality of meat from alpacas reared in Peru. Meat Sci2009, 82, 450–455, DOI: 10.1016/j.meatsci.2009.02.015.Open DOISearch in Google Scholar
Sting R., Schwabe I., Kieferl M., Münch M., Rau J.: Fatal Infection in an Alpaca (Vicugna pacos) Caused by Pathogenic Rhodococcus equi. Animals 2022, 12, 1303, doi: 10.3390/ani12101303.StingR.SchwabeI.KieferlM.MünchM.RauJ.: Fatal Infection in an Alpaca (Vicugna pacos) Caused by Pathogenic Rhodococcus equi. Animals2022, 12, 1303, DOI: 10.3390/ani12101303.Open DOISearch in Google Scholar
Twomey D.F., Barlow A.M., Bell S., Chalmers R.M., Elwin K., Giles M., Higgins R.J., Robinson G., Stringer R.M.: Cryptosporidiosis in two alpaca (Lama pacos) holdings in the South-West of England. Vet J 2008, 175, 419–422, doi: 10.1016/j.tvjl.2007.01.017.TwomeyD.F.BarlowA.M.BellS.ChalmersR.M.ElwinK.GilesM.HigginsR.J.RobinsonG.StringerR.M.: Cryptosporidiosis in two alpaca (Lama pacos) holdings in the South-West of England. Vet J2008, 175, 419–422, DOI: 10.1016/j.tvjl.2007.01.017.Open DOISearch in Google Scholar