{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T06:44:40Z","timestamp":1777445080650,"version":"3.51.4"},"reference-count":89,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T00:00:00Z","timestamp":1584403200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Escherichia coli is a predominant bacterium in the intestinal tracts of animals. Phylogenetically, strains have been classified into seven phylogroups, A, B1, B2, C, D, E, and F. Pathogenic strains have been categorized into several pathotypes such as Enteropathogenic (EPEC), Enterotoxigenic (ETEC), Enteroinvasive (EIEC), Enteroaggregative (EAEC), Diffusely adherent (DAEC), Uropathogenic (UPEC), Shiga-toxin producing (STEC) or Enterohemorrhagic (EHEC) and Extra-intestinal pathogenic E. coli (ExPEC). E. coli also survives as a commensal on the ocular surface. However, under conditions of trauma and immune-compromised states, E. coli causes conjunctivitis, keratitis, endopthalmitis, dacyrocystitis, etc. The phylogenetic affiliation and the pathotype status of these ocular E. coli strains is not known. For this purpose, the whole-genome sequencing of the 10 ocular E. coli strains was accomplished. Based on whole-genome SNP variation, the ocular E. coli strains were assigned to phylogenetic groups A (two isolates), B2 (seven isolates), and C (one isolate). Furthermore, results indicated that ocular E. coli originated either from feces (enteropathogenic and enterotoxigenic), urine (uropathogenic), or from extra-intestinal sources (extra-intestinal pathogenic). A high concordance was observed between the presence of AMR (Antimicrobial Resistance) genes and antibiotic resistance in the ocular E. coli strains. Furthermore, several virulent genes (fimB to fimI, papB to papX, etc.) and prophages (Enterobacteria phage HK97, Enterobacteria phage P1, Escherichia phage D108 etc.) were unique to ocular E. coli. This is the first report on a whole-genome analysis of ocular E. coli strains.<\/jats:p>","DOI":"10.3390\/microorganisms8030422","type":"journal-article","created":{"date-parts":[[2020,3,17]],"date-time":"2020-03-17T09:27:41Z","timestamp":1584437261000},"page":"422","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Phylogenetic Grouping of Human Ocular Escherichia coli Based on Whole-Genome Sequence Analysis"],"prefix":"10.3390","volume":"8","author":[{"given":"Konduri","family":"Ranjith","sequence":"first","affiliation":[{"name":"Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chinthala Reddy","family":"SaiAbhilash","sequence":"additional","affiliation":[{"name":"Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gumpili","family":"Sai Prashanthi","sequence":"additional","affiliation":[{"name":"Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shalem Raj","family":"Padakandla","sequence":"additional","affiliation":[{"name":"Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9979-264X","authenticated-orcid":false,"given":"Savitri","family":"Sharma","sequence":"additional","affiliation":[{"name":"Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sisinthy","family":"Shivaji","sequence":"additional","affiliation":[{"name":"Jhaveri Microbiology Centre, Prof. Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Kallam Anji Reddy campus, Hyderabad, Telangana 500034, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,3,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5408","DOI":"10.1167\/iovs.10-6939","article-title":"Diversity of bacteria at healthy human conjunctiva","volume":"52","author":"Dong","year":"2011","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"5616","DOI":"10.1167\/iovs.07-0588","article-title":"Ocular pathogen or commensal: A PCR-based study of surface bacterial flora in normal and dry eyes","volume":"48","author":"Graham","year":"2007","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.exer.2013.06.003","article-title":"Characterization of the normal microbiota of the ocular surface","volume":"117","author":"Willcox","year":"2013","journal-title":"Exp. Eye Res."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Teweldemedhin, M., Gebreyesus, H., Atsbaha, A.H., Asgedom, S.W., and Saravanan, M. (2017). Bacterial profile of ocular infections: A systematic review. BMC Ophthalmol., 17.","DOI":"10.1186\/s12886-017-0612-2"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1007\/s00580-009-0940-6","article-title":"Successful treatment of severe conjunctivitis and blepharitis caused by Escherichia coli in an ostrich (Struthio camelus)","volume":"19","author":"Ghaffari","year":"2010","journal-title":"Comp. Clin. Path."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1001\/archinte.1980.00330190100029","article-title":"Bilateral Endogenous Escherichia coli Endophthalmitis","volume":"140","author":"Cohen","year":"1980","journal-title":"JAMA Intern. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1128\/CMR.00022-13","article-title":"Recent advances in understanding enteric pathogenic Escherichia coli","volume":"26","author":"Croxen","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Welch, R.A. (2016). Uropathogenic Escherichia coli-Associated Exotoxins. Microbiol. Spectr., 4.","DOI":"10.1128\/microbiolspec.UTI-0011-2012"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Kaas, R.S., Friis, C., Ussery, D.W., and Aarestrup, F.M. (2012). Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes. BMC Genom., 13.","DOI":"10.1186\/1471-2164-13-577"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1128\/MMBR.00015-09","article-title":"Pathogenomics of the virulence plasmids of Escherichia coli","volume":"73","author":"Johnson","year":"2009","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_11","first-page":"141","article-title":"Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?","volume":"6","author":"Holt","year":"2016","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Raimondi, S., Amaretti, A., Gozzoli, C., Simone, M., Righini, L., Candeliere, F., Brun, P., Ardizzoni, A., Colombari, B., and Paulone, S. (2019). Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01575"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"6175","DOI":"10.1128\/jb.172.11.6175-6181.1990","article-title":"Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli","volume":"172","author":"Herzer","year":"1990","journal-title":"J. Bacteriol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e02703-16","DOI":"10.1128\/AEM.02703-16","article-title":"Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water","volume":"83","author":"Gomi","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1086\/315217","article-title":"Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise","volume":"181","author":"Johnson","year":"2000","journal-title":"J. Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1671","DOI":"10.1099\/00221287-147-6-1671","article-title":"Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations","volume":"147","author":"Duriez","year":"2001","journal-title":"Microbiology"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1128\/IAI.67.2.546-553.1999","article-title":"The link between phylogeny and virulence in Escherichia coli extraintestinal infection","volume":"67","author":"Picard","year":"1999","journal-title":"Infect. Immun."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13099-017-0164-2","article-title":"Global gene expression in Escherichia coli, isolated from the diseased ocular surface of the human eye with a potential to form biofilm","volume":"9","author":"Ranjith","year":"2017","journal-title":"Gut Pathog."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Zerbino, D.R. (2010). Using the Velvet de novo assembler for short-read sequencing technologies. Curr. Protoc. Bioinform.","DOI":"10.1002\/0471250953.bi1105s31"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3380","DOI":"10.1093\/bioinformatics\/btw493","article-title":"plasmidSPAdes: Assembling plasmids from whole genome sequencing data","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.plasmid.2015.12.001","article-title":"Whole genome sequencing of diverse Shiga toxin-producing and non-producing Escherichia coli strains reveals a variety of virulence and novel antibiotic resistance plasmids","volume":"83","author":"Losada","year":"2016","journal-title":"Plasmid"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1126\/science.277.5331.1453","article-title":"The complete genome sequence of Escherichia coli K-12","volume":"277","author":"Blattner","year":"1997","journal-title":"Science"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"W54","DOI":"10.1093\/nar\/gkw413","article-title":"tRNAscan-SE On-line: Integrating search and context for analysis of transfer RNA genes","volume":"44","author":"Lowe","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/nar\/gkh152","article-title":"ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences","volume":"32","author":"Laslett","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: Hierarchical and refined dataset for big data analysis\u201410 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"W347","DOI":"10.1093\/nar\/gkr485","article-title":"PHAST: A fast phage search tool","volume":"39","author":"Zhou","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2877","DOI":"10.1093\/bioinformatics\/btv271","article-title":"kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome","volume":"31","author":"Gardner","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Clermont, O., Dixit, O.V.A., Vangchhia, B., Condamine, B., Dion, S., Bridier-Nahmias, A., Denamur, E., and Gordon, D. (2019). Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential. Environ. Microbiol.","DOI":"10.1111\/1462-2920.14713"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Beghain, J., Bridier-Nahmias, A., Le Nagard, H., Denamur, E., and Clermont, O. (2018). Clermontyping: An easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb. Genom.","DOI":"10.1099\/mgen.0.000192"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1128\/JCM.06094-11","article-title":"Multilocus Sequence Typing of Total Genome Sequenced Bacteria","volume":"50","author":"Larsen","year":"2012","journal-title":"J. Clin. Micobiol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Alikhan, N.F., Petty, N.K., Ben Zakour, N.L., and Beatson, S.A. (2011). BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. BMC Genom., 12.","DOI":"10.1186\/1471-2164-12-402"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.1093\/jac\/dkv186","article-title":"WGS accurately predicts antimicrobial resistance in Escherichia coli","volume":"70","author":"Tyson","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_38","first-page":"700","article-title":"Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS","volume":"72","author":"Moran","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1128\/jb.179.7.2274-2280.1997","article-title":"MdfA, an Escherichia coli multidrug resistance protein with an extraordinarily broad spectrum of drug recognition","volume":"179","author":"Edgar","year":"1997","journal-title":"J. Bacteriol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1038\/s41564-019-0496-4","article-title":"Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli","volume":"4","author":"Sun","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1111\/j.1365-2958.1995.tb02299.x","article-title":"Lipopolysaccharides of polymyxin B-resistant mutants of Escherichia coli are extensively substituted by 2-aminoethyl pyrophosphate and contain aminoarabinose in lipid A","volume":"16","author":"Nummila","year":"1995","journal-title":"Mol. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"36077","DOI":"10.1074\/jbc.M706172200","article-title":"An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli","volume":"282","author":"Yan","year":"2007","journal-title":"J. Biol. Chem."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1093\/jac\/dkf240","article-title":"Biochemical analysis of the ceftazidime-hydrolysing extended-spectrum beta-lactamase CTX-M-15 and of its structurally related beta-lactamase CTX-M-3","volume":"50","author":"Poirel","year":"2002","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_44","first-page":"237","article-title":"Plasmid-mediated extended-spectrum beta-lactamase (CTX-M-3 like) from India and gene association with insertion sequence ISEcp1","volume":"201","author":"Karim","year":"2001","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"3758","DOI":"10.1128\/AAC.48.10.3758-3764.2004","article-title":"Complete Nucleotide Sequence of a 92-Kilobase Plasmid Harboring the CTX-M-15 Extended-Spectrum Beta-Lactamase Involved in an Outbreak in Long-Term-Care Facilities in Toronto, Canada","volume":"48","author":"Boyd","year":"2004","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1093\/jac\/dki166","article-title":"Emergence of Enterobacteriaceae producing extended-spectrum beta-lactamases (ESBLs) in the community","volume":"56","author":"Pitout","year":"2005","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1128\/AAC.00150-06","article-title":"Clonal dissemination of a CTX-M-15 beta-lactamase-producing Escherichia coli strain in the Paris area, Tunis, and Bangui","volume":"50","author":"Lavollay","year":"2006","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1093\/jac\/dkn179","article-title":"Antibiotic resistance integrons and extended-spectrum 1-lactamases among Enterobacteriaceae isolates recovered from chickens and swine in Portugal","volume":"62","author":"Machado","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13756-018-0349-6","article-title":"Dissemination of blaNDM-5 gene via an IncX3-type plasmid among non-clonal Escherichia coli in China","volume":"7","author":"Li","year":"2018","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"5999","DOI":"10.1128\/AEM.02844-08","article-title":"Distribution of sulfonamide resistance genes in Escherichia coli and Salmonella isolates from swine and chickens at abattoirs in Ontario and Quebec, Canada","volume":"75","author":"Kozak","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1751-0147-52-47","article-title":"Prevalence and characterization of plasmids carrying sulfonamide resistance genes among Escherichia coli from pigs, pig carcasses and human","volume":"52","author":"Wu","year":"2010","journal-title":"Act. Vet. Scand."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1099\/jmm.0.015008-0","article-title":"Prevalence of trimethoprim resistance genes in Escherichia coli isolates of human and animal origin in Lithuania","volume":"59","author":"Seputiene","year":"2010","journal-title":"J. Med. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e25204","DOI":"10.4161\/mge.25204","article-title":"First report on class 1 integrons and Trimethoprim-resistance genes from dfrA group in uropathogenic E. coli (UPEC) from the Aleppo area in Syria","volume":"3","author":"Mahfoud","year":"2013","journal-title":"Mob. Genet. Elements"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2227","DOI":"10.1128\/AAC.01707-08","article-title":"Resistance Plasmid Families in Enterobacteriaceae","volume":"53","author":"Carattoli","year":"2009","journal-title":"Antimicrob. Agents. Chemother."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1111\/j.1574-6976.2011.00277.x","article-title":"Analysis of antibiotic resistance regions in Gram-negative bacteria","volume":"35","author":"Partridge","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"S20","DOI":"10.1016\/j.amjmed.2006.03.013","article-title":"Resistance in gram-negative bacteria: Enterobacteriaceae","volume":"119","author":"Paterson","year":"2006","journal-title":"Am. J. Med."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1093\/jac\/dkn428","article-title":"Replicon typing of plasmids in Escherichia coli producing extended-spectrum beta-lactamases","volume":"63","author":"Marcade","year":"2009","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1128\/CMR.14.4.933-951.2001","article-title":"Extended-spectrum beta-lactamases in the 21st century: Characterization, epidemiology, and detection of this important resistance threat","volume":"14","author":"Bradford","year":"2001","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1038\/35054089","article-title":"Genome sequence of enterohaemorrhagic Escherichia coli O157:H7","volume":"409","author":"Perna","year":"2001","journal-title":"Nature"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/dnares\/8.1.11","article-title":"Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12","volume":"8","author":"Hayashi","year":"2001","journal-title":"DNA Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1128\/AAC.49.3.931-944.2005","article-title":"Global expression of prophage genes in Escherichia coli O157:H7 strain EDL933 in response to norfloxacin","volume":"49","author":"Herold","year":"2005","journal-title":"Antimicrob. Agents. Chemother."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"188","DOI":"10.3389\/fmicb.2013.00188","article-title":"Molecular characterization of bla ESBL-harboring conjugative plasmids identified in multi-drug resistant Escherichia coli isolated from food-producing animals and healthy humans","volume":"4","author":"Wang","year":"2013","journal-title":"Front. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3521","DOI":"10.1007\/s00253-019-09618-0","article-title":"Natural quorum sensing inhibitors effectively downregulate gene expression of Pseudomonas aeruginosa virulence factors","volume":"103","author":"Ahmed","year":"2019","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"20321","DOI":"10.1038\/srep20321","article-title":"The Quorum Sensing Inhibitor Hamamelitannin Increases Antibiotic Susceptibility of Staphylococcus aureus Biofilms by Affecting Peptidoglycan Biosynthesis and eDNA Release","volume":"6","author":"Brackman","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nature24624","article-title":"Progress in and promise of bacterial quorum sensing research","volume":"551","author":"Whiteley","year":"2017","journal-title":"Nature"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1046\/j.1365-2958.1998.01007.x","article-title":"Crl stimulates RpoS activity during stationary phase","volume":"29","author":"Pratt","year":"1998","journal-title":"Mol. Microbiol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"5540","DOI":"10.1128\/JB.00946-13","article-title":"Cellulose as an architectural element in spatially structured Escherichia coli biofilms","volume":"195","author":"Serra","year":"2013","journal-title":"J. Bacteriol."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1046\/j.1365-2958.2003.03468.x","article-title":"Regulatory and functional co-operation of flagella and type 1 pili in adhesive and invasive abilities of AIEC strain LF82 isolated from a patient with Crohn\u2019s disease","volume":"48","author":"Barnich","year":"2003","journal-title":"Mol. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1172\/JCI16172","article-title":"A novel dispersin protein in enteroaggregative Escherichia coli","volume":"110","author":"Sheikh","year":"2002","journal-title":"J. Clin. Investig."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Rossi, E., Paroni, M., and Landini, P. (2018). Biofilm and motility in response to environmental and host-related signals in Gram negative opportunistic pathogens. J. Appl. Microbiol.","DOI":"10.1111\/jam.14089"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.cell.2010.01.018","article-title":"Second messenger-mediated adjustment of bacterial swimming velocity","volume":"141","author":"Boehm","year":"2010","journal-title":"Cell"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"1308","DOI":"10.3389\/fmicb.2019.01308","article-title":"Gene Targets in Ocular Pathogenic Escherichia coli for Mitigation of Biofilm Formation to Overcome Antibiotic Resistance","volume":"10","author":"Ranjith","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/j.1574-6968.2004.tb09643.x","article-title":"What drives bacteria to produce a biofilm?","volume":"236","author":"Jefferson","year":"2004","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"2624","DOI":"10.1128\/JB.183.8.2624-2633.2001","article-title":"Biofilm formation by Staphylococcus epidermidis depends on functional RsbU, an activator of the sigB operon: Differential activation mechanisms due to ethanol and salt stress","volume":"183","author":"Knobloch","year":"2001","journal-title":"J. Bacteriol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"6824","DOI":"10.1128\/JB.182.23.6824-6826.2000","article-title":"Alternative transcription factor sigma(B) is involved in regulation of biofilm expression in a Staphylococcus aureus mucosal isolate","volume":"182","author":"Rachid","year":"2000","journal-title":"J. Bacteriol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"6283","DOI":"10.1128\/AEM.68.12.6283-6291.2002","article-title":"Multiple Streptococcus mutans Genes Are Involved in Biofilm Formation","volume":"68","author":"Yoshida","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1007\/BF00382277","article-title":"Mutants of Escherichia coli defective in the degradation of guanosine 5\u2032-triphosphate, 3\u2032-diphosphate (pppGpp)","volume":"169","author":"Somerville","year":"1979","journal-title":"Mol. Gen. Genet."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/S1097-2765(02)00656-1","article-title":"Dissection of the mechanism for the stringent factor RelA","volume":"10","author":"Wendrich","year":"2002","journal-title":"Mol. Cell"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1099\/13500872-145-5-1005","article-title":"The large plasmids of Shiga-toxin-producing Escherichia coli (STEC) are highly variable genetic elements","volume":"145","author":"Brunder","year":"1999","journal-title":"Microbiology"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1089\/fpd.2007.0087","article-title":"Extraintestinal pathogenic Escherichia coli","volume":"4","author":"Smith","year":"2007","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"289","DOI":"10.7883\/yoken.JJID.2009.289","article-title":"Escherichia coli pathotypes associated with diarrhea in Romanian children younger than 5 years of age","volume":"62","author":"Usein","year":"2009","journal-title":"Jpn. J. Infect. Dis."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1111\/j.1462-2920.2007.01341.x","article-title":"Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches","volume":"9","author":"Walk","year":"2007","journal-title":"Environ. Microbiol."},{"key":"ref_83","first-page":"17","article-title":"Antibiotic resistance profile and virulence genes of uropathogenic Escherichia coli isolates in relation to phylogeny","volume":"31","author":"Adib","year":"2014","journal-title":"Trop. Biomed."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"241","DOI":"10.4103\/2141-9248.160192","article-title":"Characterization of Escherichia coli Phylogenetic Groups Associated with Extraintestinal Infections in South Indian Population","volume":"5","author":"Chakraborty","year":"2015","journal-title":"Ann. Med. Health Sci. Res."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"2962","DOI":"10.1128\/JCM.43.6.2962-2964.2005","article-title":"Quinolone-resistant uropathogenic Escherichia coli strains from phylogenetic group B2 have fewer virulence factors than their susceptible counterparts","volume":"43","author":"Horcajada","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1089\/fpd.2008.0176","article-title":"Molecular analysis of antimicrobial-susceptible and -resistant Escherichia coli from retail meats and human stool and clinical specimens in a rural community setting","volume":"6","author":"Hannah","year":"2009","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ijfoodmicro.2010.06.025","article-title":"Broiler chickens, broiler chicken meat, pigs and pork as sources of ExPEC related virulence genes and resistance in Escherichia coli isolates from community-dwelling humans and UTI patients","volume":"142","author":"Jakobsen","year":"2010","journal-title":"Int. J. Food Microbiol."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1016\/j.micinf.2005.10.011","article-title":"Enhanced persistence in the colonic microbiota of Escherichia coli strains belonging to phylogenetic group B2: Role of virulence factors and adherence to colonic cells","volume":"8","author":"Nowrouzian","year":"2006","journal-title":"Microbes Infect."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/j.juro.2006.08.081","article-title":"Biofilm formation in uropathogenic Escherichia coli strains: Relationship with prostatitis, urovirulence factors and antimicrobial resistance","volume":"177","author":"Soto","year":"2007","journal-title":"J. Urol."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/3\/422\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:07:29Z","timestamp":1760173649000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/8\/3\/422"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3,17]]},"references-count":89,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2020,3]]}},"alternative-id":["microorganisms8030422"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms8030422","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,17]]}}}