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. 2008 May;279(5):523-34.
doi: 10.1007/s00438-008-0330-9.

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972

Viktoria Hancock  1 , Aswin S Seshasayee, David W Ussery, Nicholas M Luscombe, Per Klemm
Affiliations

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972

Viktoria Hancock et al. Mol Genet Genomics. 2008 May.

Abstract

Escherichia coli strains are the major cause of urinary tract infections in humans. Such strains can be divided into virulent, UPEC strains causing symptomatic infections, and asymptomatic, commensal-like strains causing asymptomatic bacteriuria, ABU. The best-characterized ABU strain is strain 83972. Global gene expression profiling of strain 83972 has been carried out under seven different sets of environmental conditions ranging from laboratory minimal medium to human bladders. The data reveal highly specific gene expression responses to different conditions. A number of potential fitness factors for the human urinary tract could be identified. Also, presence/ absence data of the gene expression was used as an adaptive genomics tool to model the gene pool of 83972 using primarily UPEC strain CFT073 as a scaffold. In our analysis, 96% of the transcripts filtered present in strain 83972 can be found in CFT073, and genes on six of the seven pathogenicity islands were expressed in 83972. Despite the very different patient symptom profiles, the two strains seem to be very similar. Genes expressed in CFT073 but not in 83972 were identified and can be considered as virulence factor candidates. Strain 83972 is a deconstructed pathogen rather than a commensal strain that has acquired fitness properties.

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Figures

Fig. 1
Fig. 1
The expression levels of CFT073 genes in strain 83972 during seven different growth conditions. The outer blue circle shows the calculated absence (0.0) and presence (1.0) of CFT073 genes in ABU strain 83972. The seven PAIs of CFT073 are indicated in red
Fig. 2
Fig. 2
Number of significantly up- and down-regulated genes in strain 83972 during the different growth conditions (i.e. exponential growth in urine, on urine-agar plates, in urine biofilm, in vivo in three patients) compared with exponential growth in MOPS minimal lab medium. The diagonal boxes (dark blue colour) show the number of significantly changed genes during cultivation in that specific condition compared with MOPS (e.g. 664 genes were up- or down-regulated in urine compared with MOPS and 938 genes were changed in plates compared with MOPS) and the other boxes show the number of significantly changed genes shared between two conditions (e.g. 311 of the 664 and 938 significantly changed genes in urine and plates compared with MOPS were shared between these two conditions, i.e. up- or down-regulated in both urine and plates compared with MOPS). Stronger blue colour indicates larger number of significantly changed genes shared between two conditions
Fig. 3
Fig. 3
Venn diagrams showing the distribution of the 4,109 genes filtered present in strain 83972. The percentages indicated below each strain show how large part of the genome of the corresponding strain was filtered present in strain 83972
Fig. 4
Fig. 4
BLAST atlas comparing the absent (0.0) and present (1.0) CFT073 genes in strain 83972 with other sequenced E. coli and Shigella strains, including the three sequenced UPEC isolates 536, UTI89 and F11. The UPEC CFT073 genome is used as reference. The outer blue circle represents the calculated absence/presence in 83972 followed by the three UPEC isolates; the six inner circles represent Shigella strains. The seven PAIs of CFT073 are indicated in red. The blow-up shows the presence/absence of the fim cluster (c5391–5400) in strain 83972
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References

    1. {'text': '', 'ref_index': 1, 'ids': [{'type': 'PMC', 'value': 'PMC258113', 'is_inner': False, 'url': 'https://pmc.ncbi.nlm.nih.gov/articles/PMC258113/'}, {'type': 'PubMed', 'value': '1879917', 'is_inner': True, 'url': 'https://pubmed.ncbi.nlm.nih.gov/1879917/'}]}
    2. Andersson P, Engberg I, Lidin-Janson G, Lincoln K, Hull R, Hull S, Svanborg C (1991) Persistence of Escherichia coli bacteriuria is not determined by bacterial adherence. Infect Immun 59:2915–2921 - PMC - PubMed
    1. {'text': '', 'ref_index': 1, 'ids': [{'type': 'DOI', 'value': '10.1128/IAI.71.8.4674-4683.2003', 'is_inner': False, 'url': 'https://doi.org/10.1128/iai.71.8.4674-4683.2003'}, {'type': 'PMC', 'value': 'PMC165989', 'is_inner': False, 'url': 'https://pmc.ncbi.nlm.nih.gov/articles/PMC165989/'}, {'type': 'PubMed', 'value': '12874348', 'is_inner': True, 'url': 'https://pubmed.ncbi.nlm.nih.gov/12874348/'}]}
    2. Anjum MF, Lucchini S, Thompson A, Hinton JC, Woodward MJ (2003) Comparative genomic indexing reveals the phylogenomics of Escherichia coli pathogens. Infect Immun 71:4674–4683 - PMC - PubMed
    1. {'text': '', 'ref_index': 1, 'ids': [{'type': 'DOI', 'value': '10.1007/BF00145506', 'is_inner': False, 'url': 'https://doi.org/10.1007/bf00145506'}, {'type': 'PubMed', 'value': '8817199', 'is_inner': True, 'url': 'https://pubmed.ncbi.nlm.nih.gov/8817199/'}]}
    2. Blanco M, Blanco JE, Alonso MP, Blanco J (1996) Virulence factors and O groups of Escherichia coli isolates from patients with acute pyelonephritis, cystitis and asymptomatic bacteriuria. Eur J Epidemiol 12:191–198 - PubMed
    1. {'text': '', 'ref_index': 1, 'ids': [{'type': 'DOI', 'value': '10.1073/pnas.0603038103', 'is_inner': False, 'url': 'https://doi.org/10.1073/pnas.0603038103'}, {'type': 'PMC', 'value': 'PMC1568941', 'is_inner': False, 'url': 'https://pmc.ncbi.nlm.nih.gov/articles/PMC1568941/'}, {'type': 'PubMed', 'value': '16912116', 'is_inner': True, 'url': 'https://pubmed.ncbi.nlm.nih.gov/16912116/'}]}
    2. Brzuszkiewicz E, Brüggemann H, Liesegang H, Emmerth M, Ölschläger T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L, Gottschalk G, Hacker J, Dobrindt U (2006) How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci USA 103:12879–12884 - PMC - PubMed
    1. {'text': '', 'ref_index': 1, 'ids': [{'type': 'DOI', 'value': '10.1073/pnas.0600938103', 'is_inner': False, 'url': 'https://doi.org/10.1073/pnas.0600938103'}, {'type': 'PMC', 'value': 'PMC1424661', 'is_inner': False, 'url': 'https://pmc.ncbi.nlm.nih.gov/articles/PMC1424661/'}, {'type': 'PubMed', 'value': '16585510', 'is_inner': True, 'url': 'https://pubmed.ncbi.nlm.nih.gov/16585510/'}]}
    2. Chen SL, Hung CS, Xu J, Reigstad CS, Magrini V, Sabo A, Blasiar D, Bieri T, Meyer RR, Ozersky P, Armstrong JR, Fulton RS, Latreille JP, Spieth J, Hooton TM, Mardis ER, Hultgren SJ, Gordon JI (2006) Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc Natl Acad Sci USA 103:5977–5982 - PMC - PubMed

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