{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T17:25:02Z","timestamp":1768843502326,"version":"3.49.0"},"publisher-location":"New York, NY","reference-count":41,"publisher":"Springer US","isbn-type":[{"value":"9781071602423","type":"print"},{"value":"9781071602430","type":"electronic"}],"license":[{"start":{"date-parts":[[2020,1,1]],"date-time":"2020-01-01T00:00:00Z","timestamp":1577836800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020]]},"DOI":"10.1007\/978-1-0716-0243-0_13","type":"book-chapter","created":{"date-parts":[[2020,2,22]],"date-time":"2020-02-22T16:02:37Z","timestamp":1582387357000},"page":"217-230","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Detection of Microorganisms by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid"],"prefix":"10.1007","author":[{"given":"Ricardo","family":"Oliveira","sequence":"first","affiliation":[]},{"given":"Carina","family":"Almeida","sequence":"additional","affiliation":[]},{"given":"Nuno F.","family":"Azevedo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,2,23]]},"reference":[{"key":"13_CR1","doi-asserted-by":"publisher","first-page":"3089","DOI":"10.1128\/JCM.00858-07","volume":"45","author":"N Guimar\u00e3es","year":"2007","unstructured":"Guimar\u00e3es N, Azevedo NF, Figueiredo C et al (2007) Development and application of a novel peptide nucleic acid probe for the specific detection of Helicobacter pylori in gastric biopsy specimens. J Clin Microbiol 45:3089\u20133094. https:\/\/doi.org\/10.1128\/JCM.00858-07","journal-title":"J Clin Microbiol"},{"key":"13_CR2","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.canlet.2006.12.030","volume":"249","author":"J Bayani","year":"2007","unstructured":"Bayani J, Squire JA (2007) Application and interpretation of FISH in biomarker studies. Cancer Lett 249:97\u2013109. https:\/\/doi.org\/10.1016\/j.canlet.2006.12.030","journal-title":"Cancer Lett"},{"key":"13_CR3","doi-asserted-by":"publisher","first-page":"620","DOI":"10.2136\/sssaj2006.0105","volume":"71","author":"SW Rogers","year":"2007","unstructured":"Rogers SW, Moorman TB, Ong SK (2007) Fluorescent in situ hybridization and micro-autoradiography applied to ecophysiology in soil. Soil Sci Soc Am J 71:620. https:\/\/doi.org\/10.2136\/sssaj2006.0105","journal-title":"Soil Sci Soc Am J"},{"key":"13_CR4","doi-asserted-by":"publisher","first-page":"161","DOI":"10.2144\/000112519","volume":"43","author":"IJ Dmochowski","year":"2007","unstructured":"Dmochowski IJ, Tang X (2007) Taking control of gene expression with light-activated oligonucleotides. Biotechniques 43:161, 163, 165 passim","journal-title":"Biotechniques"},{"key":"13_CR5","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1016\/j.cellbi.2007.03.012","volume":"31","author":"P Catalina","year":"2007","unstructured":"Catalina P, Cobo F, Cort\u00e9s JL et al (2007) Conventional and molecular cytogenetic diagnostic methods in stem cell research: a concise review. Cell Biol Int 31:861\u2013869. https:\/\/doi.org\/10.1016\/j.cellbi.2007.03.012","journal-title":"Cell Biol Int"},{"key":"13_CR6","doi-asserted-by":"publisher","first-page":"1360","DOI":"10.1126\/science.2466341","volume":"243","author":"EF DeLong","year":"1989","unstructured":"DeLong EF, Wickham GS, Pace NR (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360\u20131363","journal-title":"Science"},{"key":"13_CR7","doi-asserted-by":"publisher","first-page":"2833","DOI":"10.1242\/jcs.00633","volume":"116","author":"JM Levsky","year":"2003","unstructured":"Levsky JM, Singer RH (2003) Fluorescence in situ hybridization: past, present and future. J Cell Sci 116:2833\u20132838. https:\/\/doi.org\/10.1242\/jcs.00633","journal-title":"J Cell Sci"},{"key":"13_CR8","doi-asserted-by":"publisher","first-page":"2925","DOI":"10.1128\/AEM.02470-08","volume":"75","author":"C Almeida","year":"2009","unstructured":"Almeida C, Azevedo NF, Iversen C et al (2009) Development and application of a novel peptide nucleic acid probe for the specific detection of Cronobacter genomospecies (enterobacter sakazakii) in powdered infant formula. Appl Environ Microbiol 75:2925\u20132930. https:\/\/doi.org\/10.1128\/AEM.02470-08","journal-title":"Appl Environ Microbiol"},{"key":"13_CR9","doi-asserted-by":"publisher","first-page":"1944","DOI":"10.3390\/ijms9101944","volume":"9","author":"L Cerqueira","year":"2008","unstructured":"Cerqueira L, Azevedo NF, Almeida C et al (2008) DNA mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (FISH). Int J Mol Sci 9:1944\u20131960. https:\/\/doi.org\/10.3390\/ijms9101944","journal-title":"Int J Mol Sci"},{"key":"13_CR10","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1016\/j.fm.2014.09.002","volume":"46","author":"A Rohde","year":"2015","unstructured":"Rohde A, Hammerl JA, Appel B et al (2015) FISHing for bacteria in food \u2013 a promising tool for the reliable detection of pathogenic bacteria? Food Microbiol 46:395\u2013407. https:\/\/doi.org\/10.1016\/j.fm.2014.09.002","journal-title":"Food Microbiol"},{"issue":"5","key":"13_CR11","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/nrmicro1888","volume":"6","author":"R Amann","year":"2008","unstructured":"Amann R, Fuchs BM (2008) Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 6(5):339\u2013348","journal-title":"Nat Rev Microbiol"},{"key":"13_CR12","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1016\/0003-2697(82)90340-2","volume":"120","author":"H Felix","year":"1982","unstructured":"Felix H (1982) Permeabilized cells. Anal Biochem 120:211\u2013234","journal-title":"Anal Biochem"},{"key":"13_CR13","doi-asserted-by":"publisher","first-page":"400","DOI":"10.4103\/0973-029X.102496","volume":"16","author":"R Thavarajah","year":"2012","unstructured":"Thavarajah R, Mudimbaimannar VK, Elizabeth J et al (2012) Chemical and physical basics of routine formaldehyde fixation. J Oral Maxillofac Pathol 16:400\u2013405. https:\/\/doi.org\/10.4103\/0973-029X.102496","journal-title":"J Oral Maxillofac Pathol"},{"key":"13_CR14","unstructured":"Azevedo N (2005) Survival of Helicobacter pylori in drinking water and associated biofilms. Dissertation for PhD degree in Chemical and Biological Engineering. University of Minho"},{"key":"13_CR15","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1016\/S1369-5274(98)80041-6","volume":"1","author":"R Amann","year":"1998","unstructured":"Amann R, K\u00fchl M (1998) In situ methods for assessment of microorganisms and their activities. Curr Opin Microbiol 1:352\u2013358. https:\/\/doi.org\/10.1016\/S1369-5274(98)80041-6","journal-title":"Curr Opin Microbiol"},{"key":"13_CR16","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1016\/j.fm.2010.04.008","volume":"27","author":"V Jasson","year":"2010","unstructured":"Jasson V, Jacxsens L, Luning P et al (2010) Alternative microbial methods: an overview and selection criteria. Food Microbiol 27:710\u2013730. https:\/\/doi.org\/10.1016\/j.fm.2010.04.008","journal-title":"Food Microbiol"},{"key":"13_CR17","doi-asserted-by":"publisher","first-page":"1497","DOI":"10.1126\/science.1962210","volume":"254","author":"PE Nielsen","year":"1991","unstructured":"Nielsen PE, Egholm M, Berg RH, Buchardt O (1991) Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 254:1497\u20131500","journal-title":"Science"},{"key":"13_CR18","first-page":"830","volume":"3","author":"H Stender","year":"1999","unstructured":"Stender H, Mollerup TA, Lund K et al (1999) Direct detection and identification of Mycobacterium tuberculosis in smear-positive sputum samples by fluorescence in situ hybridization (FISH) using peptide nucleic acid (PNA) probes. Int J Tuberc Lung Dis 3:830\u2013837","journal-title":"Int J Tuberc Lung Dis"},{"key":"13_CR19","doi-asserted-by":"publisher","first-page":"155","DOI":"10.2166\/wst.2003.0307","volume":"47","author":"NF Azevedo","year":"2003","unstructured":"Azevedo NF, Vieira MJ, Keevil CW (2003) Establishment of a continuous model system to study Helicobacter pylori survival in potable water biofilms. Water Sci Technol 47:155\u2013160","journal-title":"Water Sci Technol"},{"key":"13_CR20","doi-asserted-by":"publisher","first-page":"7456","DOI":"10.1128\/AEM.00845-07","volume":"73","author":"T Juhna","year":"2007","unstructured":"Juhna T, Birzniece D, Larsson S et al (2007) Detection of Escherichia coli in biofilms from pipe samples and coupons in drinking water distribution networks. Appl Environ Microbiol 73:7456\u20137464. https:\/\/doi.org\/10.1128\/AEM.00845-07","journal-title":"Appl Environ Microbiol"},{"key":"13_CR21","doi-asserted-by":"publisher","first-page":"387","DOI":"10.2166\/wst.2007.282","volume":"55","author":"SM Bragan\u00e7a","year":"2007","unstructured":"Bragan\u00e7a SM, Azevedo NF, Sim\u00f6es LC et al (2007) Use of fluorescent in situ hybridisation for the visualisation of Helicobacter pylori in real drinking water biofilms. Water Sci Technol 55:387\u2013393","journal-title":"Water Sci Technol"},{"key":"13_CR22","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1080\/08927010902802232","volume":"25","author":"MS Gi\u00e3o","year":"2009","unstructured":"Gi\u00e3o MS, Wilks SA, Azevedo NF et al (2009) Comparison between standard culture and peptide nucleic acid 16S rRNA hybridization quantification to study the influence of physico-chemical parameters on Legionella pneumophila survival in drinking water biofilms. Biofouling 25:335\u2013343. https:\/\/doi.org\/10.1080\/08927010902802232","journal-title":"Biofouling"},{"key":"13_CR23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0014786","volume":"6","author":"C Almeida","year":"2011","unstructured":"Almeida C, Azevedo NF, Santos S et al (2011) Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH). PLoS One 6:e14786. https:\/\/doi.org\/10.1371\/journal.pone.0014786","journal-title":"PLoS One"},{"key":"13_CR24","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1007\/s10482-011-9595-9","volume":"100","author":"NF Azevedo","year":"2011","unstructured":"Azevedo NF, Jardim T, Almeida C et al (2011) Application of flow cytometry for the identification of Staphylococcus epidermidis by peptide nucleic acid fluorescence in situ hybridization (PNA FISH) in blood samples. Antonie van Leeuwenhoek 100:463\u2013470. https:\/\/doi.org\/10.1007\/s10482-011-9595-9","journal-title":"Antonie van Leeuwenhoek"},{"key":"13_CR25","doi-asserted-by":"publisher","first-page":"781","DOI":"10.1007\/s10096-012-1808-2","volume":"32","author":"C Almeida","year":"2013","unstructured":"Almeida C, Azevedo NF, Bento JC et al (2013) Rapid detection of urinary tract infections caused by Proteus spp. using PNA-FISH. Eur J Clin Microbiol Infect Dis 32:781\u2013786. https:\/\/doi.org\/10.1007\/s10096-012-1808-2","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"13_CR26","doi-asserted-by":"publisher","first-page":"4476","DOI":"10.1128\/AEM.01678-09","volume":"76","author":"C Almeida","year":"2010","unstructured":"Almeida C, Azevedo NF, Fernandes RM et al (2010) Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of salmonella spp. in a broad spectrum of samples. Appl Environ Microbiol 76:4476\u20134485. https:\/\/doi.org\/10.1128\/AEM.01678-09","journal-title":"Appl Environ Microbiol"},{"key":"13_CR27","doi-asserted-by":"publisher","first-page":"6293","DOI":"10.1128\/AEM.01009-13","volume":"79","author":"C Almeida","year":"2013","unstructured":"Almeida C, Sousa JM, Rocha R et al (2013) Detection of Escherichia coli O157 by peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) and comparison to a standard culture method. Appl Environ Microbiol 79:6293\u20136300. https:\/\/doi.org\/10.1128\/AEM.01009-13","journal-title":"Appl Environ Microbiol"},{"key":"13_CR28","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.ijfoodmicro.2012.09.024","volume":"162","author":"A Machado","year":"2013","unstructured":"Machado A, Almeida C, Carvalho A et al (2013) Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Lactobacillus spp. in milk samples. Int J Food Microbiol 162:64\u201370. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2012.09.024","journal-title":"Int J Food Microbiol"},{"key":"13_CR29","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/j.ijfoodmicro.2012.11.014","volume":"161","author":"C Almeida","year":"2013","unstructured":"Almeida C, Cerqueira L, Azevedo NF, Vieira MJ (2013) Detection of Salmonella enterica serovar Enteritidis using real time PCR, immunocapture assay, PNA FISH and standard culture methods in different types of food samples. Int J Food Microbiol 161:16\u201322. https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2012.11.014","journal-title":"Int J Food Microbiol"},{"key":"13_CR30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0196522","volume":"13","author":"R Rocha","year":"2018","unstructured":"Rocha R, Almeida C, Azevedo NF (2018) Influence of the fixation\/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria. PLoS One 13:e0196522. https:\/\/doi.org\/10.1371\/journal.pone.0196522","journal-title":"PLoS One"},{"key":"13_CR31","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1186\/1471-2180-11-101","volume":"11","author":"L Cerqueira","year":"2011","unstructured":"Cerqueira L, Fernandes RM, Ferreira RM et al (2011) PNA-FISH as a new diagnostic method for the determination of clarithromycin resistance of Helicobacter pylori. BMC Microbiol 11:101. https:\/\/doi.org\/10.1186\/1471-2180-11-101","journal-title":"BMC Microbiol"},{"key":"13_CR32","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/S0958-1669(00)00170-1","volume":"12","author":"PE Nielsen","year":"2001","unstructured":"Nielsen PE (2001) Peptide nucleic acid: a versatile tool in genetic diagnostics and molecular biology. Curr Opin Biotechnol 12:16\u201320","journal-title":"Curr Opin Biotechnol"},{"key":"13_CR33","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0167-7012(01)00303-7","volume":"47","author":"H Perry-O\u2019Keefe","year":"2001","unstructured":"Perry-O\u2019Keefe H, Rigby S, Oliveira K et al (2001) Identification of indicator microorganisms using a standardized PNA FISH method. J Microbiol Methods 47:281\u2013292","journal-title":"J Microbiol Methods"},{"key":"13_CR34","first-page":"472","volume":"19","author":"H Orum","year":"1995","unstructured":"Orum H, Nielsen PE, J\u00f8rgensen M et al (1995) Sequence-specific purification of nucleic acids by PNA-controlled hybrid selection. Biotechniques 19:472\u2013480","journal-title":"Biotechniques"},{"key":"13_CR35","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.micres.2016.07.002","volume":"192","author":"L Mendes","year":"2016","unstructured":"Mendes L, Rocha R, Azevedo AS et al (2016) Novel strategy to detect and locate periodontal pathogens: the PNA-FISH technique. Microbiol Res 192:185\u2013191. https:\/\/doi.org\/10.1016\/j.micres.2016.07.002","journal-title":"Microbiol Res"},{"key":"13_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S0167-7012(01)00340-2","volume":"48","author":"H Stender","year":"2002","unstructured":"Stender H, Fiandaca M, Hyldig-Nielsen JJ, Coull J (2002) PNA for rapid microbiology. J Microbiol Methods 48:1\u201317. https:\/\/doi.org\/10.1016\/S0167-7012(01)00340-2","journal-title":"J Microbiol Methods"},{"key":"13_CR37","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/S1369-5274(03)00054-7","volume":"6","author":"M Wagner","year":"2003","unstructured":"Wagner M, Horn M, Daims H (2003) Fluorescence in situ hybridisation for the identification and characterisation of prokaryotes. Curr Opin Microbiol 6:302\u2013309. https:\/\/doi.org\/10.1016\/S1369-5274(03)00054-7","journal-title":"Curr Opin Microbiol"},{"key":"13_CR38","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1128\/JCM.38.1.444-447.2000","volume":"38","author":"FA Drobniewski","year":"2000","unstructured":"Drobniewski FA, More PG, Harris GS (2000) Differentiation of Mycobacterium tuberculosis complex and nontuberculous mycobacterial liquid cultures by using peptide nucleic acid-fluorescence in situ hybridization probes. J Clin Microbiol 38:444\u2013447","journal-title":"J Clin Microbiol"},{"key":"13_CR39","doi-asserted-by":"publisher","first-page":"762","DOI":"10.1128\/JB.172.2.762-770.1990","volume":"172","author":"RI Amann","year":"1990","unstructured":"Amann RI, Krumholz L, Stahl DA (1990) Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacteriol 172:762\u2013770","journal-title":"J Bacteriol"},{"key":"13_CR40","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1080\/10408410490266410","volume":"30","author":"KA Stevens","year":"2004","unstructured":"Stevens KA, Jaykus LA (2004) Bacterial separation and concentration from complex sample matrices: a review. Crit Rev Microbiol 30:7\u201324. https:\/\/doi.org\/10.1080\/10408410490266410","journal-title":"Crit Rev Microbiol"},{"key":"13_CR41","doi-asserted-by":"publisher","first-page":"7126","DOI":"10.1128\/AEM.70.12.7126-7139.2004","volume":"70","author":"LS Yilmaz","year":"2004","unstructured":"Yilmaz LS, Noguera DR (2004) Mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization. Appl Environ Microbiol 70:7126\u20137139. https:\/\/doi.org\/10.1128\/AEM.70.12.7126-7139.2004","journal-title":"Appl Environ Microbiol"}],"container-title":["Methods in Molecular Biology","Peptide Nucleic Acids"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-0243-0_13","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,16]],"date-time":"2022-10-16T08:37:22Z","timestamp":1665909442000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-0716-0243-0_13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"ISBN":["9781071602423","9781071602430"],"references-count":41,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-0243-0_13","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020]]},"assertion":[{"value":"23 February 2020","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}