{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T17:46:12Z","timestamp":1775151972609,"version":"3.50.1"},"reference-count":34,"publisher":"American Society for Microbiology","issue":"1","license":[{"start":{"date-parts":[[2007,1,1]],"date-time":"2007-01-01T00:00:00Z","timestamp":1167609600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2007,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The ability to distinguish between\n            <jats:italic>Escherichia coli<\/jats:italic>\n            strains is critical for outbreak investigations. Binary typing, based on the presence or absence of genetic material, provides a high-throughput alternative to gel- and PCR-based typing techniques that generate complex banding patterns and lack uniform interpretation criteria. We developed, validated, and determined the discriminatory power of an\n            <jats:italic>E. coli<\/jats:italic>\n            binary typing method, probe hybridization array typing (PHAT). In PHAT, the absence or presence of genetic material is identified by using DNA hybridization to produce a reproducible and portable fingerprint for each genome. PHAT probes were generated from genome subtractive hybridization experiments. We PHAT typed the ECOR collection of strains from a variety of geographical locations, and 33 rectal\n            <jats:italic>E. coli<\/jats:italic>\n            strains selected from college-aged women with urinary tract infection. In the set of 33 human rectal strains, the discriminatory power of PHAT (98%) equaled that of multilocus sequence typing (MLST) and pulsed-field gel electrophoresis. However, for ECOR strains, which include nonhuman strains, the current set of PHAT probes was less discriminating than MLST, ribotyping, and enterobacterial repetitive intergenic consensus sequence PCR (80% versus 97, 92, and 97%, respectively). When we limited the analysis to ECOR strains of B2 and D lineage, which are associated with human infection, current PHAT probes were highly discriminatory (94%). PHAT can be applied in a high-throughput format (i.e., \u201clibrary on a slide\u201d), the discriminatory ability can be varied based on the probe set, and PHAT is readily adapted to other bacterial species with high variation in genetic content.\n          <\/jats:p>","DOI":"10.1128\/jcm.01543-06","type":"journal-article","created":{"date-parts":[[2006,12,29]],"date-time":"2006-12-29T20:27:57Z","timestamp":1167424077000},"page":"206-214","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":9,"title":["Probe Hybridization Array Typing: a Binary Typing Method for\n            <i>Escherichia coli<\/i>"],"prefix":"10.1128","volume":"45","author":[{"given":"U.","family":"Srinivasan","sequence":"first","affiliation":[{"name":"Department of Epidemiology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"L.","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Epidemiology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"A. M.","family":"France","sequence":"additional","affiliation":[{"name":"Department of Epidemiology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D.","family":"Ghosh","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"W.","family":"Shalaby","sequence":"additional","affiliation":[{"name":"Department of Epidemiology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Epidemiology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"C. F.","family":"Marrs","sequence":"additional","affiliation":[{"name":"Department of Epidemiology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B.","family":"Foxman","sequence":"additional","affiliation":[{"name":"Department of Epidemiology"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","unstructured":"A phylogenetic perspective on molecular epidemiology 2002 vol. 1"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.mi.40.100186.001153"},{"key":"e_1_3_2_4_2","unstructured":"Bauer R. J. 2003. Molecular epidemiologic discovery of uropathogenic Escherichia coli virulence and transmission factors. Ph.D. thesis. University of Michigan Ann Arbor."},{"key":"e_1_3_2_5_2","first-page":"1521","volume":"185","year":"1521","unstructured":"Bauer, R. J., L. Zhang, B. Foxman, A. Siitonen, M. E. Jantunen, H. Saxen, and C. F. Marrs. 1521. Molecular epidemiology of three putative virulence genes for Escherichia coli urinary tract infection\u2014usp, iha, and iroN (E. coli). J. Infect. Dis.185:1521-1524.","journal-title":"J. Infect. 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C. Tang L. Zhang A. Zhang and M. Ramanathan. 2000. First SIAM International conference on data mining. http:\/\/www.cs.buffalo.edu\/pub\/WWW\/DBGROUP\/bioinformatics\/papers\/MaxEnt.pdf\n."},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.41.1.285-289.2003"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.33.9.2233-2239.1995"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0923-2508(98)80004-1"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.37.3.664-674.1999"},{"key":"e_1_3_2_28_2","first-page":"82","volume":"6","year":"2000","unstructured":"Vogel, L., E. van Oorschot, H. M. Maas, M. B., and L. Dijkshoorn. 2000. Epidemiologic typing of Escherichia coli using RAPD analysis, ribotyping and serotyping. Clin. Microbiol. Infect.6:82-87.","journal-title":"Clin. Microbiol. 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