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BACKGROUND Transfusion-transmitted bacterial infections (TTBIs) are the main residual infectious complications of transfusions. Escherichia coli and platelet (PLT) concentrates may be epidemiologically associated, leading to severe, if not lethal, TTBIs. We investigated the genotypic and phenotypic reasons for this clinically deleterious combination. STUDY DESIGN AND METHODS We investigated a French national E. coli strain collection related to six independent episodes of TTBIs. Their phenotypic characterizations included antibiotic susceptibility testing, growth testing under different culture conditions, serum survival assays, and virulence in a sepsis mouse model. Their genotypic characterizations included polymerase chain reaction phylotyping, whole genome sequencing, and a subsequent in silico analysis. RESULTS We highlighted a selection process of highly extraintestinal virulent strains, mainly belonging to the B2 phylogroup, adapted to the hostile environment (high citrate concentration and a bactericidal serum effect) of apheresis-collected platelet concentrates (PCs). Compared to controls, the E. coli TTBI strains grew faster in the PCs due to a superior ability to capture iron. The in vitro growth performances were highly compatible with blood-derived product real-life conditions, including storage conditions and delays. The consistent serum resistance of TTBI strains promotes their survival in both the donor's and the receiver's blood and in the PCs. CONCLUSION This study pointed out that E. coli strains responsible for TTBI exhibit very specific traits. They belong to the extraintestinal pathogenic phylogroups and have a high intrinsic virulence. They can be resistant to complement, capture iron, and grow in the apheresis-collected PCs. These findings therefore support the reinforcement of the postdonation information.

To gain insights into the adaptation of the Escherichia coli species to different environments, we monitored protein abundances using quantitative proteomics and measurements of enzymatic activities of central metabolism in a set of five representative strains grown in four contrasted culture media including human urine. Two hundred and thirty seven proteins representative of the genome-scale metabolic network were identified and classified into pathway categories. We found that nutrient resources shape the general orientation of metabolism through coordinated changes in the average abundances of proteins and in enzymatic activities that all belong to the same pathway category. For example, each culture medium induces a specific oxidative response whatever the strain. On the contrary, differences between strains concern isolated proteins and enzymes within pathway categories in single environments. Our study confirms the predominance of genotype by environment interactions at the proteomic and enzyme activity levels. The buffering of genetic variation when considering life-history traits suggests a multiplicity of evolutionary strategies. For instance, the uropathogenic isolate CFT073 shows a deregulation of iron demand and increased oxidative stress response.

Isolates of Escherichia coli, except Shigella, are generally prototrophic; they do not require any growth factors to grow in mineral medium. However, a nicotinic acid requirement is common among B2 phylogroup STc95 O18 E. coli clone strains. Nicotinic acid is a precursor of nicotinamide adenine dinucleotide (NAD), an essential molecule that plays central role in cellular metabolism. The defect in NAD synthesis of these strains is due to alterations in de novo biosynthesis pathway nadB gene. Here, by studying growth on minimal medium with glycolytic (glucose) or gluconeogenic (pyruvate or succinate) substrates as the carbon supply in a large panel of E. coli natural isolates representative of the species diversity, we identify an absolute nicotinic acid requirement in non-STc95 strains due in one case to a nadA inactivation. The growth on glucose medium of some extraintestinal pathogenic E. coli strains belonging to various non-O18 B2 phylogroup STc95 clones is restored either by aspartate or nicotinate, demonstrating that the nicotinic acid requirement can also be due to an intracellular aspartate depletion. The auxotrophic requirements depend on the carbon source available in the environment. Moreover, some strains prototrophic in glucose medium become auxotrophic in succinate medium, and conversely, some strainsauxotrophic in glucose medium become prototrophic in succinate medium. Finally, a partial depletion of intracellular aspartate can be observed in some prototrophic strains belonging to various phylogroups. The observed more or less significant depletion according to isolates may be due to differences in tricarboxylic acid cycle enzyme activities. These metabolic defects could be involved in the adaptation of E. coli to its various niches.

International audience; Gene expression is known to be the principle factor explaining how fast genes evolve. Highly transcribed genes evolve slowly because any negative impact caused by a particular mutation is magnified by protein abundance. However, gene expression is a phenotype that depends both on the environment and on the strains or species. We studied this phenotypic plasticity by analyzing the transcriptome profiles of four Escherichia coli strains grown in three different culture media, and explored how expression variability was linked to gene allelic diversity. Genes whose expression changed according to the media and not to the strains were less polymorphic than other genes. Genes for which transcription depended predominantly on the strain were more polymorphic than other genes and were involved in sensing and responding to environmental changes, with an overrepresentation of two-component system genes. Surprisingly, we found that the correlation between transcription and gene diversity was highly variable among growth conditions and could be used to quantify growth efficiency of a strain in a medium. Genetic variability was found to increase with gene expression in poor growth conditions. As such conditions are also characterized by down-regulation of all DNA repair systems, including transcription-coupled repair, we suggest that gene expression under stressful conditions may be mutagenic and thus leads to a variability in mutation rate among genes in the genome which contributes to the pattern of protein evolution.

To assess the extent of intra-species diversity and the links between phylogeny, lifestyle (habitat and pathogenicity) and phenotype, we assayed the growth yield on 95 carbon sources of 168 Escherichia strains. We also correlated the growth capacities of 14 E. coli strains with the presence ⁄ absence of enzyme-coding genes. Globally, we found that the genetic distance, based on multilocus sequence typing data, was a weak indicator of the metabolic phenotypic distance. Besides, lifestyle and phylogroup had almost no impact on the growth yield of non-Shigella E. coli strains. In these strains, the presence ⁄ absence of the metabolic pathways, which was linked to the phylogeny, explained most of the growth capacities. However, few discrepancies blurred the link between metabolic phenotypic distance and metabolic pathway distance. This study shows that a prokaryotic species structured into well-defined genetic and lifestyle groups can yet exhibit continuous phenotypic diversity, possibly caused by gene regulatory effects.

The search for new molecules to fight Pseudomonas aeruginosa is of paramount importance. Carbon monoxide (CO) is known to act as an effective inhibitor of the respiratory chain in P. aeruginosa, but the practical use of this gas as an antibacterial molecule is hampered by its toxicity and difficulty to manipulate. Here, we show that a water-soluble CO releaser (CORM-3) possesses bactericidal properties against laboratory and antibiotic-resistant P. aeruginosa. CORM-3 reduced the bacterial count by 4 logs 180 min after in vitro treatment. CORM-3-treated bacteria had a lower O(2) consumption than vehicle-treated bacteria, and the decrease in O(2) consumption temporally preceded the bactericidal action of CORM-3. These results support the hypothesis that the antimicrobial effect of CORM-3 is mediated by an interaction of CO liberated by the carrier with the bacterial respiratory chain. The antibacterial effect occurred at concentrations of CORM-3 that are 50-fold lower than toxic concentrations for eukaryotic cells. CORM-3 treatment compared to vehicle treatment decreased bacterial counts in the spleen and increased survival in immunocompetent and immunosuppressed mice following P. aeruginosa bacteremia. Our results suggest that CORMs could form the basis for developing a new therapeutic strategy against P. aeruginosa-induced infection.

The iron-regulatory peptide hepcidin exhibits antimicrobial activity. Having previously shown hepcidin expression in the kidney, we addressed its role in urinary tract infection (UTI), which remains largely unknown. Experimental UTI was induced in wild-type (WT) and hepcidin-knockout (Hepc-/-) mice using the uropathogenic Escherichia coli CFT073 strain. Compared with infected WT mice, infected Hepc-/- mice showed a dramatic increase in renal bacterial load. Moreover, bacterial invasion was significantly dampened by the pretreatment of WT mice with hepcidin. Infected Hepc-/- mice exhibited decreased iron accumulation in the renal medulla and significant attenuation of the renal inflammatory response. Notably, we demonstrated in vitro bacteriostatic activity of hepcidin against CFT073. Furthermore, CFT073 repressed renal hepcidin, both in vivo and in cultured renal cells, and reduced phosphorylation of SMAD kinase in vivo, suggesting a bacterial strategy to escape the antimicrobial activities of hepcidin. In conclusion, we provide new mechanisms by which hepcidin contributes to renal host defense and suggest that targeting hepcidin offers a strategy to prevent bacterial invasion.

OBJECTIVE In the context of increasing microbial resistance and limited new antimicrobials, we aimed to study the antimicrobial effects of cranberry proanthocyanidin extracts on Escherichia coli growth, adhesion to epithelial cells, and lung infection. DESIGN Experimental in vitro and in vivo investigation. SETTING University research laboratory. SUBJECTS Seventy-eight 6- to 8-week-old male Balb/C mice. INTERVENTIONS In vitro, the effect of increasing concentrations of cranberry proanthocyanidin on bacterial growth of different clinical E. coli isolates was evaluated. Ex vivo, adhesion of E. coli to fresh human buccal epithelial cells was measured in the presence or absence of cranberry proanthocyanidin using microscopy. In vivo, lung bacterial count, pulmonary immune response (neutrophil murine chemokine keratinocyte-derived cytokine measurement and polymorphonuclear recruitment in bronchoalveolar lavage fluid), and lethality were evaluated in a pneumonia mouse model with E. coli precultured with or without cranberry proanthocyanidin. E. coli isolates originated from ventilated ICU patients with respiratory tract colonization or ventilator- associated pneumonia. They differed in number of virulence genes. MEASUREMENTS AND MAIN RESULTS A significant inhibition of bacterial growth was observed with increasing concentration of cranberry proanthocyanidin, affecting both time to maximal growth and maximal growth rate (p

E. coli bacteria were encapsulated within silica gels and aged at room temperature in the absence of nutrients. Their viability was studied as a function of time using different viability tests. The plate count technique gives the number of culturable bacteria that remain able to form colonies in the presence of a culture medium. Their metabolic activity toward glycolysis was followed by 14C titration and 13C NMR spectroscopy. Several sol–gel matrices were tested in order to improve the viability of the trapped bacteria. The best results were obtained when encapsulation is performed in the presence of glycerol showing that almost 50% of the bacteria were still able to form metabolites after one month of ageing. Moreover, this study demonstrates that a wide range of viability tests can be adapted for use with cells encapsulated in mineral matrices.

Culturable cells and non-culturable cells of fecal coliforms, obtained by irradiation at 312 nm were submitted to the combined stress conditions of salinity and starvation. After 14 days, β-galactosidase activity of UV-irradiated cells was at least twice the value of non-irradiated cells. UV-irradiated cells thus contribute more than non-irradiated cells to the enzyme assay after incubation in saline water. This finding is essential for the interpretation of quantitative investigations into the environment using enzymatic methods.

The addition of exogenous pyrophosphate increases the growth yield and cAMP synthesis in stationary phase when Escherichia coli is grown in minimal medium. Pyrophosphate increases the yield by altering the enterobactin uptake system. We studied the physiological effects and examined how the E. coli transcriptome was modified when two structural analogs of pyrophosphate were added to the growth medium. Methylenediphosphonic acid or a high concentration of iron had the same positive effects as pyrophosphate on growth yield, cAMP synthesis and the repression of Fur-regulated genes. In contrast, imidodiphosphate did not affect these cellular processes significantly. The transcriptome modifications generated by pyrophosphate or methylenediphosphonic acid were more similar than those generated by imidodiphosphate or excess iron. The transcriptome data also indicated that processes other than iron uptake might be involved in the cellular response to exogenous pyrophosphate or methylenediphosphonic acid.

Whole E. coli bacteria have been trapped within silica gels obtained via the acidification of sodium silicate and silica nanoparticles solutions. Their β-galactosidase enzymatic activity increases with time, suggesting that their membrane is partially lysed during the encapsulation process. Such a lysis can be greatly reduced when encapsulation is performed in the presence of gelatin. The biocatalytic activity of trapped bacteria remains almost constant for more than a week. Moreover bacteria trapped in such gels remain able to incorporate glucose, showing that their viability has been preserved.

The viability of bacteria in the presence of sol–gel reagents has been studied in order to define the best experimental conditions for the sol–gel encapsulation of E. coli. The β-galactosidase activity of these bacteria, trapped in sol–gel silica matrices, was then analyzed. Two routes, using alkoxide and aqueous precursors, have been used and compared. It appears that the aqueous route is less damaging than the alkoxide one. Moreover the aqueous silica matrix appears to slow down the lysis of cell membranes when bacteria are aged without nutrient.

Sixteen Pseudomonas strains have been tested with a view to developing medium-chain length polyhydroxyalkanoates. Four strains were selected and it is shown that their ability for producing three different polyesters with variable properties was dependent on the strains and substrates. Otherwise, Pseudomonas oleovorans was grown on a mixture of sodium octanoate and undecenoate salts at a 90/10 mol/mol ratio. The corresponding copolymer, bearing lateral double bonds, was chemically modified in the carboxy group. Finally, the ability to tailor-make functional bacterial polyesters aimed at temporary therapeutic applications is demonstrated.

Thirteen strains of a new acetogenic bacterium were isolated from the rumen contents of lambs, llamas and bisons. This paper is the first report of Gram-positive coccoid spore-forming bacteria occurring in chains and able to use H2 + CO2 as energy source and produce acetate from this gas mixture. One of them, chosen as the reference strain for its efficiency in utilizing H2/CO2 likely via the acetyl-CoA pathway, was characterized in detail. The G + C ratio of the DNA of the organism was 46.5 mol%. The temperature and pH optimum were 37 degrees-40 degrees C and 6.3-6.8, respectively. Numerous organic substrates including some o-methylate aromatic compounds were used heterotrophically. The full 16S rRNA gene sequence was determined. The phylogeny, physiology, morphology and numerous features described here are sufficiently different from those of any bacteria described today to justify the definition of a new species. The name "New acetogenic bacterium" is temporarily proposed, awaiting a future taxonomic revision of the genus Clostridium.

Un test enzymatique simple, rapide et peu couteux a ete utilise pour detecter la presence d'une glycerol-deshydrogenase de type II (induite par le glycerol et l'hydroxyacetone) ou de type IV (induite seulement par l'hydroxyacetone) chez 1.000 souches appartenant a Escherichia coli et Shigella. Une glycerol-deshydrogenase de type II a ete trouvee chez 97 % des souches de E. coli testees. Cette activite n'a ete detectee chez aucune espece de Shigella a l'exception de S. flexneri serotype 6 biotype Manchester. Une glycerol-deshydrogenase de type IV a ete trouvee chez S. dysenteriae serotype 1, S. flexneri serotype 6 biotypes Boyd 88, Manchester «variant» et Herfordshire, et S. boydii serotypes 7, 11, 13, 14 et 15. Les autres serotypes de Shigella ne presentent aucune de ces deux activites enzymatiques.

Background Critically ill patients including trauma patients are at high risk of urinary tract infection (UTI). The composition of urine in trauma patients may be modified due to inflammation, systemic stress, rhabdomyolysis, life support treatment and/or urinary catheter insertion. Methods Prospective, single-centre, observational study conducted in patients with severe trauma and without a history of UTIs or recent antibiotic treatment. The 24-hour urine samples were collected on the first and the fifth days and the growth of Escherichia coli in urine from patients and healthy volunteers was compared. Biochemical and hormonal modifications in urine that could potentially influence bacterial growth were explored. Results Growth of E. coli in urine from trauma patients was significantly higher on days 1 and 5 than in urine of healthy volunteers. Several significant modifications of urine composition could explain these findings. On days 1 and 5, trauma patients had an increase in glycosuria, in urine iron concentration, and in the concentrations of several amino acids compared to healthy volunteers. On day 1, the urinary osmotic pressure was significantly lower than for healthy volunteers. Conclusion We showed that urine of trauma patients facilitated growth of E. coli when compared to urine from healthy volunteers. This effect was present in the first 24 hours and until at least the fifth day after trauma. This phenomenon may be involved in the pathophysiology of UTIs in trauma patients. Further studies are required to define the exact causes of such modifications.

The anaerobic glycerol pathway was studied in seven enterobacterial species selected as representative of different behaviours in terms of anaerobic glycerol dissimilation. The presence of oxidative and reductive pathways of the dha regulon in Klebsiella pneumoniae enabled the cells to grow fermentatively on glycerol. The first two enzymes of the dha regulon (glycerol dehydrogenase type I and dihydroxyacetone kinase) represent the oxidative branch, while the latter two (glycerol dehydratase and 1,3-propanediol dehydrogenase) represent the reductive branch of glycerol fermentation. The slower utilization of glycerol by K. oxytoca was attributed to low production of 1,3-propanediol. K. oxytoca lacked glycerol dehydratase and demonstrated low 1,3-propanediol dehydrogenase activity. K. planticola and K. ozaenae differed from K. pneumoniae and K. oxytoca in lacking the ability to grow on glycerol. K. planticola lacked both enzymes of the reductive branch of glycerol fermentation, and K. ozaenae possessed glycerol dehydrogenase only. K. rhinoscleromatis and Hafnia alvei, like Escherichia coli, did not possess a dha regulon. The glycerol dehydrogenase type II of H. alvei was distinct from that of E. coli. The phenotypic diversity of anaerobic glycerol dissimilation may have taxonomic applications.

The encapsulation of enzymes within silica gels has been extensively studied during the past decade for the design of biosensors and bioreactors. Yeast spores and bacteria have also been recently immobilized within silica gels where they retain their enzymatic activity, but the problem of the long-term viability of whole cells in an inorganic matrix has never been fully addressed. It is a real challenge for the development of sol-gel processes. Generic tests have been performed to check the viability of Escherichia coli bacteria in silica gels. Surprisingly, more bacteria remain culturable in the gel than in an aqueous suspension. The metabolic activity of the bacteria towards glycolysis decreases slowly, but half of the bacteria are still viable after one month. When confined within a mineral environment, bacteria do not form colonies. The exchange of chemical signals between isolated bacteria rather than aggregates can then be studied, a point that could be very important for 'quorum sensing'.

Escherichia coli exhibits a wide range of lifestyles encompassing commensalism and various pathogenic behaviors which its highly dynamic genome contributes to develop. How environmental and host factors shape the genetic structure of E. coli strains remains, however, largely unknown. Following a previous study of E. coli genomic diversity, we investigated its diversity at the metabolic level by building and analyzing the genome-scale metabolic networks of 29 E. coli strains (8 commensal and 21 pathogenic strains, including 6 Shigella strains). Using a tailor-made reconstruction strategy, we significantly improved the completeness and accuracy of the metabolic networks over default automatic reconstruction processes. Among the 1,545 reactions forming E. coli panmetabolism, 885 reactions were common to all strains. This high proportion of core reactions (57%) was found to be in sharp contrast to the low proportion (13%) of core genes in the E. coli pangenome, suggesting less diversity of metabolic functions compared to that of all gene functions. Core reactions were significantly overrepresented among biosynthetic reactions compared to the more variable degradation processes. Differences between metabolic networks were found to follow E. coli phylogeny rather than pathogenic phenotypes, except for Shigella networks, which were significantly more distant from the others. This suggests that most metabolic changes in non- Shigella strains were not driven by their pathogenic phenotypes. Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models.

Although polymicrobial infections, caused by combinations of viruses, bacteria, fungi and parasites, are being recognised with increasing frequency, little is known about the occurrence of within-species diversity in bacterial infections and the molecular and evolutionary bases of this diversity. We used multiple approaches to study the genomic and phenotypic diversity among 226 Escherichia coli isolates from deep and closed visceral infections occurring in 19 patients. We observed genomic variability among isolates from the same site within 11 patients. This diversity was of two types, as patients were infected either by several distinct E. coli clones (4 patients) or by members of a single clone that exhibit micro-heterogeneity (11 patients); both types of diversity were present in 4 patients. A surprisingly wide continuum of antibiotic resistance, outer membrane permeability, growth rate, stress resistance, red dry and rough morphotype characteristics and virulence properties were present within the isolates of single clones in 8 of the 11 patients showing genomic micro-heterogeneity. Many of the observed phenotypic differences within clones affected the trade-off between self-preservation and nutritional competence (SPANC). We showed in 3 patients that this phenotypic variability was associated with distinct levels of RpoS in co-existing isolates. Genome mutational analysis and global proteomic comparisons in isolates from a patient revealed a star-like relationship of changes amongst clonally diverging isolates. A mathematical model demonstrated that multiple genotypes with distinct RpoS levels can co-exist as a result of the SPANC trade-off. In the cases involving infection by a single clone, we present several lines of evidence to suggest diversification during the infectious process rather than an infection by multiple isolates exhibiting a micro-heterogeneity. Our results suggest that bacteria are subject to trade-offs during an infectious process and that the observed diversity resembled results obtained in experimental evolution studies. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies., Author Summary We investigated whether an infection is a site of pathogen within-species diversity. Our results indicate that there is indeed extensive diversity during human extraintestinal infections by Escherichia coli. This diversity was of two types, not mutually exclusive, as we found that patients were infected either by several distinct E. coli clones or by members of a single clone that exhibit micro-heterogeneity. The high degree of phenotypic diversity, including antibiotic resistance, suggests that there is no uniform selection pressure leading to a single fitter clone during an infection. We discuss a possible mechanism and a mathematical model that explains these unexpected results. Our data suggest that the evolution of diversity in the course of an infection and in in vitro experimental evolution in the absence of host immune selective pressure may have many parallels. Whatever the mechanisms leading to diversity, our results have strong medical implications in terms of the need for more extensive isolate testing before deciding on antibiotic therapies.

In this work we analyze the physiological state of cells after lethal-UV dose disinfection using independent metabolic markers. Through the detection of some metabolic activities we proved that cell lysis does not immediately follow death in UV-irradiated Escherichia coli K12 cells.

The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome., Author Summary Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.

In Xanthomonas campestris pv. campestris, fructose is transported and phosphorylated into fructose 1-phosphate through a phosphoenolpyruvate-dependent phosphotransferase system. The nucleotide sequence of the fruA gene encoding the phosphotransferase system permease specific of fructose (EIIFru) was determined. The fructose 1-phosphate produced by the phosphotransferase system is phosphorylated into fructose 1,6-bisphosphate by a 1-phosphofructokinase. This enzyme was characterized and the corresponding gene (fruK) was sequenced. Sequence comparisons revealed that FruK is a member of a new family of ATP-binding proteins composed of sugar (or sugar-phosphate) kinases. In phosphotransferase system-deficient strains, fructose can still be transported by an unidentified permease. The intracellular fructose is then phosphorylated by a multimeric fructokinase of 135 kDa specific for fructose and inhibited by fructose, fructose 1,6-bisphosphate, and mannose. Several other enzymes of fructose metabolism were assayed and a potential pathway for fructose catabolism is presented.

Fructose was shown to be phosphorylated by a specific phosphoenolpyruvate-dependent phosphotransferase system (PTS) in Xanthomonas campestris pv. campestris. Transposon mutagenesis of X. campestris was performed and two mutants affected in growth on fructose were isolated. Both mutants were deficient in PTS activity. Comparison of the rate of uptake and phosphorylation of fructose in the wild-type and in the mutant strains revealed the presence of a second fructose permeation and phosphorylation pathway in this bacterium: an unidentified permease coupled to an ATP-dependent fructokinase. One of the two mutants was also deficient in fructokinase activity. Chromosomal DNA fragments containing the regions flanking the transposon insertion site were cloned from both mutant strains. Their physical study revealed that the insertion sites were separated by 1.4 kb, allowing the reconstruction of a wild-type DNA fragment which complemented one of the two mutants. The region flanking the transposon insertion site was sequenced in one of the mutants, showing that the transposon had interrupted the gene encoding the fructose EII. The mutant strains also failed to utilize mannose, sucrose and mannitol, suggesting the existence of a branch point between the metabolism of fructose and of these latter carbohydrates.

The diffusely adhering Escherichia coli (Afa/Dr DAEC) are associated with recurrent urinary tract infections in adults as well as with diarrheal disease in infants. We previously demonstrated that in wild-type strain IH11128, the Dr fimbriae is released in the extracellular medium in response to multiple environmental signals such as temperature, low aeration and rich medium. A number of molecules of eukaryotic origin, such as catecholamines, have been reported to stimulate bacterial growth and virulence factor production. We show that norepinephrine affects the production and release of Dr fimbriae in Afa/Dr DAEC WT-IH11128 bacteria. The regulatory mechanism involved with norepinephrine-induced Dr fimbriae liberation was apparently due to a differential induction of genes draC, encoding the usher, and draE, encoding the major fimbrial subunit. In addition, we show that the released Dr fimbriae induces the phosphorylation of the mitogen-activated protein kinase, extracellular signal-regulated kinase 1/2 (ERK1/2) and the production of the pro-inflammatory cytokine, IL-8 in fully differentiated cultured human intestinal Caco-2/TC7 cells.

Afa/Dr diffusely adhering Escherichia coli have been shown to cause urinary tract infections and enteric infections. Virulence of Dr-positive IH11128 bacteria is associated with the presence of Dr fimbriae. In this report, we show for the first time that the Dr fimbriae are released in the extracellular medium in response to multiple environmental signals. Production and secretion of Dr fimbriae are clearly thermoregulated. A comparison of the amounts of secreted fimbriae showed that the secretion is drastically increased during anaerobic growth in minimal medium. The effect of anaerobiosis on secretion seemed to depend on both the growth phase and the culture medium. The secretion was maximal during the logarithmic-phase growth and corresponded to 27 and 57% of total Dr fimbriae produced by bacteria grown in mineral medium+glucose and LB broth, respectively. Thus, the anaerobic environment of the colon would favour the secretion of Dr fimbriae during bacterial multiplication. The controlled release of the Dr fimbriae, which is carried out in the absence of cellular lysis, appears independent of the action of proteases or a process of maturation. The mechanism employed in the liberation of Dr fimbriae thus seems different from that described for the adhesins FHA and Hap of Bordetella pertussis and Haemophilus influenzae.

Cells that have lost the ability to grow in culture could be defined operationally as either alive or dead depending on the method used to determine cell viability. As a consequence, the interpretation of the state of ‘nonculturable’ cells is often ambiguous. Escherichia coli K12 cells inactivated by UV-irradiation with a low (UV1) and a high (UV2) dose were used as a model of nonculturable cells. Cells inactivated by the UV1 dose lost ‘culturability’ but they were not lysed and maintained the capacity to respond to nutrient addition by protein synthesis and cell wall synthesis. The cells also retained both a high level of glucose transport and the capacity for metabolizing glucose. Moreover, during glucose incorporation, UV1-treated cells showed the capacity to respond to aeration conditions modifying their metabolic flux through the Embden–Meyerhof and pentose-phosphate pathways. However, nonculturable cells obtained by irradiation with the high UV2 dose showed several levels of metabolic imbalance and retained only residual metabolic activities. Nonculturable cells obtained by irradiation with UV1 and UV2 doses were diagnosed as active and inactive (dying) cells, respectively.

The addition of exogenous pyrophosphate increases the growth yield and cAMP synthesis in stationary phase when Escherichia coli is grown in minimal medium. Pyrophosphate increases the yield by altering the enterobactin uptake system. We studied the physiological effects and examined how the E. coli transcriptome was modified when two structural analogs of pyrophosphate were added to the growth medium. Methylenediphosphonic acid or a high concentration of iron had the same positive effects as pyrophosphate on growth yield, cAMP synthesis and the repression of Fur-regulated genes. In contrast, imidodiphosphate did not affect these cellular processes significantly. The transcriptome modifications generated by pyrophosphate or methylenediphosphonic acid were more similar than those generated by imidodiphosphate or excess iron. The transcriptome data also indicated that processes other than iron uptake might be involved in the cellular response to exogenous pyrophosphate or methylenediphosphonic acid.

Summary It is admitted that one of the characteristics of pseudomonads is their inability to accumulate poly(3-hydroxybutyrate). In this paper, we show that poly(3-hydroxyoctanoate) synthesis is restricted to Pseudomonas rRNA homology group I, which includes both fluorescent and nonfluorescent species. However, within the genus Pseudomonas, the P. aeruginosa complex can be subdivided into two groups : the “P. aeruginosa group”, which includes P. aeruginosa, P. alcaligenes, P. citronellolis, P. mendocina, produce poly(3-hydroxyoctanoate) from octanoate and the “P. oleovorans group” which includes the type strain of P. oleovorans, P. pseudoalcaligenes and two Pseudomonas sp., produce poly(3-hydroxybutyrate) during cultivation on octanoate. Strain GPo1 (ATCC 29347) formely identified as P. oleovorans and known to produce various mediumside-chain PHAs such as poly(3-hydroxyoctanoate) has been reclassified in the P. putida complex.

The metabolism of mannose was examined in resting cells in vivo using 13C-NMR and 31P-NMR spectroscopy, in cell-free extracts in vitro using 31P-NMR spectroscopy, and by enzyme assays. Plesiomonas shigelloides was shown to transport mannose by a phosphoenolpyruvate-dependent phosphotransferase system producing mannose 6-phosphate. However, a toxic effect was observed when P. shigelloides was grown in the presence of mannose. Investigation of mannose metabolism using in vivo13C NMR showed mannose 6-phosphate accumulation without further metabolism. In contrast, glucose was quickly metabolized under the same conditions to lactate, ethanol, acetate and succinate. Extracts of P. shigelloides exhibited no mannose-6-phosphate isomerase activity whereas the key enzyme of the Embden–Meyerhof pathway (6-phosphofructokinase) was found. This result explains the mannose 6-phosphate accumulation observed in cells grown on mannose. The levels of phosphoenolpyruvate and Pi were estimated by in vivo31P-NMR spectroscopy. The intracellular concentrations of phosphoenolpyruvate and Pi were relatively constant in both starved cells and mannose-metabolizing cells. In glucose-metabolizing cells, the phosphoenolpyruvate concentration was lower, and about 80% of the Pi was used during the first 10 min. It thus appears that the toxic effect of mannose on growth is not due to energy depletion but probably to a toxic effect of mannose 6-phosphate.

A number of methods have been proposed to assess the viability of cells without culture. Each method is based on criteria that reflect different levels of cellular integrity or functionality. As a consequence, the interpretation of viability is often ambiguous. The purposes of this work were to evaluate the capacity of current viability markers to distinguish between live and dead Escherichia coli K-12 cells. Methods that assess ‘viability’ by the demonstration of metabolic activities (esterase activity, active electron transport chain, transport of glucose), cellular integrity (membrane integrity, presence of nucleic acids) or the building up of cellular material (cell elongation) have been evaluated in live and UV- or heat-killed cells. With live cells, viability markers detected cells in counts similar to the colony count. However, these so-called viability markers could stain dead cells for some time after the lethal treatment. For the UV-killed cells, residual activities were detected even after 48 h of storage at 20 °C. However, for heat-treated cells, these activities disappeared within hours after heat treatment. Only a combination of fluorescence in situ hybridization with rRNA probes and cell elongation in response to nutrients (in the presence of an inhibitor of cell division) had the ability to differentiate live from dead cells. Problems in the definition of a viable but nonculturable state are in part due to the lack of a clear definition of bacterial death. We consider death as an irreversible state where no growth, cell elongation or protein synthesis may occur.

Glucose metabolism of Pasteurella multocida was examined in resting cells in vivo using 13C NMR spectroscopy, in cell-free extracts in vitro using 31P NMR spectroscopy and using enzyme assays. The NMR data indicate that glucose is converted by the Embden-Meyerhof and pentose phosphate pathways. The P. multocida fructose 6-phosphate phosphotransferase activity (the key enzyme of the Embden-Meyerhof pathway) was similar to that of Escherichia coli. Nevertheless, and in contrast to that of E. coli, its activity was inhibited by alpha glycerophosphate. This inhibition is consistent with the very low fructose 6-phosphate phosphotransferase activity found in cell-free extracts of P. multocida using a spectrophotometric method. The dominant end products of glucose metabolism were mannitol, acetate and succinate. Under anaerobic conditions, P. multocida was able to constitutively produce mannitol from glucose, mannose, fructose, sucrose, glucose 6-phosphate and fructose 6-phosphate. We propose a new metabolic pathway in P. multocida where fructose 6-phosphate is reduced to mannitol 1-phosphate by fructose 6-phosphate reductase. Mannitol 1-phosphate produced is then converted to mannitol by mannitol 1-phosphatase.

Pasteurella multicida was examined for glucose and mannose transport. P. multocida was shown to possess a phosphoenolpyruvate (PEP):mannose phosphotransferase system (PTS) that transports glucose as well as mannose and was functionally similar to the Escherichia coli mannose PTS. Phosphorylated proteins with molecular masses similar to those of E. coli mannose PTS proteins were visualized when incubated with 32 P-PEP. The presence of an enzyme IIA Glc which could play an important role in regulation, as described in other Gram-negative bacteria, was detected. The enzymes of the pentose-phosphate pathway were present in P. multocida grown on glucose. The activity of 6-phosphofructokinase (the key enzyme of the Embden-Meyerhof pathway (EMP)), was very low in cell extracts, suggesting that EMP is not the major pathway for glucose catabolism.

Aeromonas hydrophila was examined for fructose and mannose transport systems. A. hydrophila was shown to possess a phosphoenolpyruvate (PEP): fructose phosphotransferase system (fructose-PTS) and a mannose-specific PTS, both induced by fructose and mannose. The mannose-PTS of A. hydrophila exhibited cross-reactivity with Escherichia coli mannose-PTS proteins. The fructose-PTS proteins exhibited cross-reactivities with E. coli and Xanthomonas campestris fructose-PTS proteins. In A. hydrophila grown on mannose as well as on fructose, the phosphorylated derivative accumulated from fructose was fructose 1-phosphate. Identification of fructose 1-phosphate was confirmed by 13C-NMR spectroscopy. 1-Phosphofructokinase (1-PFK), which converts the product of the PTS reaction to fructose 1,6-diphosphate, was present in A. hydrophila grown with fructose but not on mannose. An inducible phosphofructomutase (PFM) activity, an unusual enzyme converting fructose 1-phosphate to fructose 6-phosphate, was detected in extracts induced by mannose or fructose. These results suggest that in cells grown on fructose, fructose 1-phosphate could be converted to fructose 1,6-diphosphate either directly by the 1-PFK activity or via fructose 6-phosphate by the PFM and 6-phosphofructokinase activities. In cells grown on mannose, the degradation of fructose 1-phosphate via PFM and the Embden-Meyerhof pathway appeared to be a unique route.

Serratia marcescens bacteria were encapsulated in silica gels containing glycerol. In agreement with previous studies on Escherichia coli, entrapped cells showed a ca. 50% viability rate after one month. Nutrients were provided to the bacteria, allowing the production of prodigiosin, a red pigment exhibiting some promising therapeutic properties. Addition of “quorum sensing” molecules involved in intercellular communication leads to an enhanced prodigiosin production after four subsequent recyclings of the bacteria-containing gels over one month. Moreover, at the end of this period, nearly 100% of the initial cell population remain viable within the gels. These results suggest that, in the presence of “quorum sensing” molecules, S. marcescens bacteria can enter a stationary state where their metabolism is modified, enhancing their resistance to the stresses induced by encapsulation.

One of the purposes of bacterial taxonomy is to delineate groups (taxa) about which one can generalize knowledge obtained by the study of a few strains in these groups. The delineation of taxa is now achieved using molecular methods such as DNA-DNA hybridization, rRNA-DNA hybridization or rRNA sequencing. However, the description of these carefully delineated taxa rests on empirical 'biochemical' tests. Obviously, the fantastic diversity of metabolic pathways in bacteria is insufficiently used in taxonomy. Our group is engaged in taxonomic research and we want to define bacterial taxa on a sound biochemical and physiological basis. Our first project in that area concerned glucose entry routes in the Enterobacteriaceae. There are currently about a hundred genomic species (i.e. species defined by DNA relatedness, whether named or not) in the family Enterobacteriaceae. Most of our knowledge concerning the physiology and genetics of this family is limited to Escherichia coli K-12 and Salmonella typhimuri

A study of D-glucose oxidation by Acinetobacter species was carried out. Glucose-oxidizing strains were found distributed among almost all Acinetobacter species. 14C-glucose oxidation kinetics by non-proliferating cells with separation of oxidation products (14C-gluconate) by DEAE-cellulose paper chromatography was studied. Inhibition of glucose dehydrogenase (GDH) activity by 11 carbohydrates (mono- and disaccharides) and determination of the kinetic parameters showed that glucose oxidation was due to the action of membrane-bound GDH (inactive in vivo on disaccharides). On the basis of GDH inhibition patterns obtained, two groups were individualized. The first group of strains (identified as A. calcoaceticus, A. baumannii, A. lwoffii, A. johnsonii and Acinetobacter species 3, 9, 10 and 11) showed a greater affinity for glucose than the second group (A. haemolyticus, A. junii and Acinetobacter species 6 and 12). Restoration of GDH activity after addition of pyrroloquinoline quinone (PQQ) was studied in 187 strains previously found unable to oxidize glucose. GDH activity of 150 out of 166 strains identified as A. baumannii, A. johnsonii, A. lwoffii and Acinetobacter species 11 and 12 was restored. Eighteen of 21 strains identified as A. haemolyticus and Acinetobacter species 6 were unable to produce acid from glucose after addition of PQQ. Our results confirm that the former taxonomic scheme for the genus Acinetobacter (2 species differing only by glucose oxidation) is untenable and that, accordingly, identification of Acinetobacter strains at the species level must be performed using more modern methods, i.e. carbon source utilization tests.

Tests allowing the screening of large numbers of enterobacterial strains for the presence of the glucose oxidation pathway (glucose, gluconate, and 2-ketogluconate dehydrogenases) were devised or adapted. A total of 506 strains representing 111 taxa (named species or subspecies and unnamed genomic groups) were studied. The members of the genera Budvicia, Edwardsiella, Leminorella, Providencia, and Xenorhabdus and the species Citrobacter freundii, Erwinia carnegeana, Erwinia carotovora, Erwinia chrysanthemi, Erwinia nigrifluens, Erwinia salicis, Moellerella wisconsensis, Proteus penneri, Proteus vulgaris, Yersinia intermedia, Yersinia pestis, Yersinia pseudotuberculosis, and Yersinia ruckeri were negative in all tests. Five species, Erwinia cypripedii, Ewingella americana, Rahnella aquatilis, Serratia marcescens (at 20°), and Tatumella ptyseos produced 2,5-diketogluconate from glucose without a requirement for pyrroloquinoline quinone (PQQ). When PQQ was provided (required for glucose oxidation), Serratia grimesii and Serratia liquefaciens produced 2,5-diketogluconate from glucose at 20°. Escherichia blattae had gluconate- and 2-ketogluconate dehydrogenases without glucose dehydrogenase. The members of the genera Hafnia, Obesumbacterium, and Pragia had only gluconate dehydrogenase. Other species had glucose dehydrogenase (with or without a requirement for PQQ) with or without gluconate dehydrogenase. Classification and identification may take advantage of tests exploring the glucose oxidation pathway.

The DNA relatedness of 64 enterobacterial species to Escherichia coli genes ptsI, ptsH, crr, ptsG, and ptsLPM, was determined by quantitative filter hybridization. DNA relatedness was expressed relative to E. coli K-12 DNA. Enterobacterial DNAs were 0 to 100% related to E. coli genes and the level of relatedness (except for crr data) reflected the known taxonomic (phylogenetic) position of species with respect to E. coli. When ptsI relatedness data were plotted against ptsH data, correlation was excellent. In ptsG versus ptsLPM plots, the data points (species) were scattered along the diagonal with a large gap separating E. coli strains (80–100% relatedness to both probes) from the 63 other species (1 to 40% relatedness to E. coli genes). Serratia (9 species), Buttiauxella agrestis, and Klebsiella planticola gave higher relatedness values with crr probe than with the other probes tested.

The sol-gel process opens new possibilities in the field of biotechnologies. Sol-gel glasses are formed at room temperature via the polymerization of molecular precursors. Enzymes can be added to the solution of precursors and trapped within the growing silica network. Small substrate molecules can diffuse through the pores allowing reactions to be performed in-situ, within the silica gels. Enzyme are encased by the hydrated silica in a cage tailored to their size, they retain their biocatalytic activity and may even be stabilized within the sol-gel matrix.Whole cell bacteria have also been immobilized within sol-gel glasses. They behave as a "bag of enzymes" and their membrane protects enzymes against denaturation and leaching. The cellular organization of bacteria cells is preserved upon encapsulation. Experiments performed with Escherichia coli induced to β-galactosidase show that they still exhibit noticeable enzymatic activity. Some degradation of the cell walls may even occur increasing the “measured” activity. However silica gels made from aqueous precursors seem to prevent bacteria from natural degradation upon ageing.Antibody-antigen recognition has been shown to be feasible within sol-gel matrices. Trapped antibodies bind specifically the corresponding haptens and can be used for the detection of traces of chemicals. Even whole cell protozoa have been encapsulated without any alteration of their cellular organization. For medical applications, trapped parasitic protozoa have been used as antigens for blood tests with human sera. Antigen-antibody interactions were followed by the so-called Enzyme Linked ImmunoSorbent Assays (ELISA).

Background Uropathogenic strains of Escherichia coli cause symptomatic infections whereas asymptomatic bacteriuria (ABU) strains are well adapted for growth in the human urinary tract, where they establish long-term bacteriuria. Human urine is a very complex growth medium that could be perceived by certain bacteria as a stressful environment. To investigate a possible imbalance between endogenous oxidative response and antioxidant mechanisms, lipid oxidative damage estimated as thiobarbituric acid reactive substances (TBARS) content was evaluated in twenty-one E. coli belonging to various pathovars and phylogenetic groups. Antioxidant defense mechanisms were also analysed. Results During exponential growth in urine, TBARS level differs between strains, without correlation with the ability to grow in urine which was similarly limited for commensal, ABU and uropathogenic strains. In addition, no correlation between TBARS level and the phylogroup or pathogenic group is apparent. The growth of ABU strain 83972 was associated with a high level of TBARS and more active antioxidant defenses that reduce the imbalance. Conclusions Our results indicate that growth capacity in urine is not a property of ABU strains. However, E. coli isolates respond very differently to this stressful environment. In strain ABU 83972, on one hand, the increased level of endogenous reactive oxygen species may be responsible for adaptive mutations. On the other hand, a more active antioxidant defense system could increase the capacity to colonize the bladder.