How to become a uropathogen Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains Elzbieta Brzuszkiewicz Holger Bru ggemann Heiko Liesegang Melanie Emmerth Tobias O lschla ger Ga bor Nagy Kaj Albermann Christian Wagner Carmen Buchrieser Levente Emo dy Gerhard Gottschalk Jo rg Hacker and Ulrich Dobrindt Go ttingen Genomics Laboratory Institute of Microbiology and Genetics Georg August Universita t Go ttingen Grisebachstrasse 8 37077 Go ttingen Germany Institute for Molecular Biology of Infectious Diseases Bayerische Julius Maximilians Universita t Wu rzburg Ro ntgenring 11 97070 Wu rzburg Germany Institute of Medical Microbiology and Immunology University of Pe cs Szigeti ut 12 7624 Pe cs Hungary Biomax Informatics AG Lochhamerstrasse 9 82152 Martinsried Germany and Laboratoire de Ge nomique des Microorganismes Pathoge nes Institut Pasteur 75724 Paris Cedex 15 France Edited by Roy Curtiss Arizona State University Tempe AZ and approved July 2 2006 received for review April 18 2006 fitness genome comparison uropathogenic Escherichia coli U ropathogenic Escherichia coli UPEC are the most common cause of community acquired urinary tract infection UTI and are responsible for 70 90 of the estimated 150 million UTIs diagnosed annually 1 UPEC also cause 40 of all nosocomial UTI thus representing one of the most frequently isolated nosocomial pathogens 2 These frequencies illustrate the magnitude of the problem but do not reflect disease diversity in the urinary tract UTI may be acute symptomatic with a varying severity and localization but may also be sporadic recurrent or chronic It is essential to understand the molecular basis of disease diversity on the bacterial side that determines the different disease types UPEC are a geno and phenotypically heterogeneous group of isolates restricted to a small number of O serogroups that seem to represent different subclasses of facultative pathogens 3 5 UPEC virulence factors are frequently encoded on pathogenicity islands PAIs 6 9 The two O6 strains 536 pyelonephritis isolate and CFT073 urosepsis isolate became generally accepted UPEC model organisms and several PAIs of them have been described in detail 10 16 The complete CFT073 genome sequence shows a mosaic structure in terms of the distribution of backbone genes conserved in E coli and foreign genes which www pnas org cgi doi 10 1073 pnas 0603038103 presumably have been acquired horizontally 17 Genome comparison of CFT073 O157 H7 strain EDL933 and K 12 strain MG1655 revealed that only 39 2 of their combined set of proteins are common to all three strains 17 20 underlining the astonishing diversity among E coli Furthermore the genome sequence of CFT073 revealed 1 623 strain specific genes 21 2 Comparison of both UPEC phenotypes and their genomes with other complete E coli genome sequences should therefore help to identify sets of UPEC specific and strain specific proteins respectively that may form the basis of their different individual phenotypes and uropathogenic potential Results and Discussion E coli 536 Genome Sequence Determination and Comparative Analysis The genome consists of a single circular chromosome of 4 938 875 bp No plasmids were found The 536 genome is 292 kb smaller than that of strain CFT073 Essentially the additional DNA in CFT073 harbors genes of five cryptic prophages which are absent from strain 536 as well as genes that are located in islands absent from other E coli The E coli 536 genome contains one cryptic prophage region For the 536 genome 4 747 putative coding sequences were predicted 3 650 of which 77 have highly similar orthologs in MG1655 Fig 1 From the remaining ORFs 524 are also present in CFT073 which means that 89 of all ORFs of E coli 536 have highly similar orthologs in the UPEC CFT073 genome Table1 and Table 4 which is published as supporting information on the PNAS web site Further comparison with the genome sequences of enterohemorrhagic E coli EHEC O157 H7 strains Sakai and EDL933 18 19 revealed 3 560 ORFs 75 with highly similar orthologs in all published complete E coli genomes Of the remaining ORFs present in the genomes of strain 536 and at least one of these other four E coli strains 427 are mainly located within a region of the cryptic prophage or within the major PAIs of strain 536 Table 5 which is published as supporting information on the PNAS web site Key features of the completely sequenced E coli genomes are Conflict of interest statement No conflicts declared This paper was submitted directly Track II to the PNAS office Abbreviations EHEC enterohemorrhagic E coli ExPEC extraintestinal pathogenic E coli IPEC intestinal pathogenic E coli PAI pathogenicity islands PTS phosphotransferase system UPEC uropathogenic E coli UTI urinary tract infection Data deposition The complete genome sequence of E coli strain 536 has been deposited in the GenBank database accession no CP000247 To whom correspondence should be addressed at Institut fu r Molekulare Infektionsbiologie Ro ntgenring 11 D 97070 Wu rzburg Germany E mail ulrich dobrindt mail uni wuerzburg de 2006 by The National Academy of Sciences of the USA PNAS August 22 2006 vol 103 no 34 12879 12884 MICROBIOLOGY Uropathogenic Escherichia coli UPEC strain 536 O6 K15 H31 is one of the model organisms of extraintestinal pathogenic E coli ExPEC To analyze this strain s genetic basis of urovirulence we sequenced the entire genome and compared the data with the genome sequence of UPEC strain CFT073 O6 K2 H1 and to the available genomes of nonpathogenic E coli strain MG1655 K 12 and enterohemorrhagic E coli The genome of strain 536 is 292 kb smaller than that of strain CFT073 Genomic differences between both UPEC are mainly restricted to large pathogenicity islands parts of which are unique to strain 536 or CFT073 Genome comparison underlines that repeated insertions and deletions in certain parts of the genome contribute to genome evolution Furthermore 427 and 432 genes are only present in strain 536 or in both UPEC respectively The majority of the latter genes is encoded within smaller horizontally acquired DNA regions scattered all over the genome Several of these genes are involved in increasing the pathogens fitness and adaptability Analysis of virulence associated traits expressed in the two UPEC O6 strains together with genome comparison demonstrate the marked genetic and phenotypic variability among UPEC The ability to accumulate and express a variety of