Abstract
One of the trademarks of extraintestinal pathogenic Escherichia coli is adaptation of metabolism and basic physiology to diverse host sites. However, little is known how this common human pathogen adapts to permit survival and growth in blood. We used label-free quantitative proteomics to characterize five E. coli strains purified from clinical blood cultures associated with sepsis and urinary tract infections. Further comparison of proteome profiles of the clinical strains and a reference uropathogenic E. coli strain 536 cultivated in blood culture and on two different solid media distinguished cellular features altered in response to the pathogenically relevant condition. The analysis covered nearly 60% of the strains predicted proteomes, and included quantitative description based on label-free intensity scores for 90% of the detected proteins. Statistical comparison of anaerobic and aerobic blood cultures revealed 32 differentially expressed proteins (1.5% of the shared proteins), mostly associated with acquisition and utilization of metal ions critical for anaerobic or aerobic respiration. Analysis of variance identified significantly altered amounts of 47 proteins shared by the strains (2.7%), including proteins involved in vitamin B6 metabolism and virulence. Although the proteomes derived from blood cultures were fairly similar for the investigated strains, quantitative proteomic comparison to the growth on solid media identified 200 proteins with substantially changed levels (11% of the shared proteins). Blood culture was characterized by up-regulation of anaerobic fermentative metabolism and multiple virulence traits, including cell motility and iron acquisition. In a response to the growth on solid media there were increased levels of proteins functional in aerobic respiration, catabolism of medium-specific carbon sources and protection against oxidative and osmotic stresses. These results demonstrate on the expressed proteome level that expression of extraintestinal virulence factors and overall cellular metabolism closely reflects specific growth conditions. Data are available via ProteomeXchange with identifier PXD002912.
Highlights
From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; §Department of Clinical Science; University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
Pathogenic islands acquired by horizontal gene transfer and containing genes directly linked to extraintestinal pathogenic E. coli (ExPEC) virulence [6], together with an exceptionally high level of recombination of ExPEC isolates when compared with commensal strains [7], 1 The abbreviations used are: ExPEC, Extraintestinal Pathogenic E. coli; false discovery rates (FDR), False Discovery Rate; HUH, Haukeland University Hospital; label-free quantification (LFQ), Label-Free Quantification; LTQ, Linear Trap Quadrupole; MEDFASP, Multiple Enzymes for sample Digestion – Filter-Aided Sample Preparation; NCBI, National Center for Biotechnology Information; Principal component analysis (PCA), Principal Component Analysis; UniProtKB, Universal Protein KnowledgeBase; uropathogenic E. coli (UPEC), Uropathogenic E. coli; urinary tract infections (UTI), Urinary Tract Infection
ExPEC solates from Clinical Blood Cultures Associated with Sepsis—Patient blood is one of the most important specimens in clinical microbiology and it is collected in commercial blood culture bottles containing growth-promoting additives, which are subsequently incubated in an automated microbial detection system
Summary
The interpretation of the genome content, i.e. the presence or absence of specific genes, is alone not sufficient for drawing a detailed picture of bacterial pathogenesis In this context, cell-wide descriptions of protein quantitative levels, which point to the level of gene regulation, are essential in order to expand strategies for treatment and prevention of ExPEC infections. Extraintestinal virulence is a multigenic process including genes encoding transcriptional regulators [11], iron and heme receptors [12], fimbrial adhesins [13], toxins [14], and proteins functional in cell motility [15, 16] and biosynthesis of lipopolysaccharides and polysaccharide capsules [17] It appears that many of the factors responsible for virulence are primarily associated with gut colonization rather than being typical virulence factors directly involved in infection [18, 19]. To pathogenic islands carrying virulence genes, metabolic pathways encoded by horizontally acquired genomic elements can provide an advantage and allow adaptation to niches unable to be colonized by commensal E. coli strains [6]
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