Whole-genome sequence analysis of multidrug-resistant uropathogenic strains of Escherichia coli from Mexico

Background: Escherichia coli is the main bacterium associated with urinary tract infections (UTIs), including cystitis and pyelonephritis. Uropathogenic E. coli (UPEC) harbors numerous genes that encode diverse virulence factors contributing to its pathogenicity. The treatment of UTIs has become complicated due to the natural selection of E. coli strains that are multiresistant to several groups of antibiotics regularly used in clinical settings such as hospitals. Genomic reports of the global composition and distribution of the antibiotic resistance and virulence genes of these pathogenic strains are lacking in the Mexican population.

Purpose and methods: The aim of this study was to globally characterize the genomes of a group of UPEC strains by massive parallel sequencing to determine the prevalence and distribution of virulence and antibiotic resistance genes associated with different serotypes and phylogenetic groups.

Results: The strains exhibited 138-197 virulence genes and 29 antibiotic resistance genes related to antibiotics that are commonly used in clinical practice. 

Conclusions: These findings are relevant to the definition of new strategies for treating urinary tract infections in public hospitals and private practice. To further define the epidemiological distribution and composition of these virulence and antibiotic resistance genes, larger studies are needed.

Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods

This data article describes a controlled, spiked proteomic dataset for which the “ground truth” of variant proteins is known. It is based on the LC-MS analysis of samples composed of a fixed background of yeast lysate and different spiked amounts of the UPS1 mixture of 48 recombinant proteins. It can be used to objectively evaluate bioinformatic pipelines for label-free quantitative analysis, and their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. More specifically, it can be useful for tuning software tools parameters, but also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. The raw MS files can be downloaded from ProteomeXchange with identifier PXD001819. Starting from some raw files of this dataset, we also provide here some processed data obtained through various bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, to exemplify the use of such data in the context of software benchmarking, as discussed in details in the accompanying manuscript [1]. The experimental design used here for data processing takes advantage of the different spike levels introduced in the samples composing the dataset, and processed data are merged in a single file to facilitate the evaluation and illustration of software tools results for the detection of variant proteins with different absolute expression levels and fold change values.

Isolation of Actinobacillus pleuropneumoniae from layer hens showing clinical signs of infectious coryza

Actinobacillus pleuropneumoniae is the causal agent of porcine pleuropneumonia, which is a highly contagious respiratory disease that affects swine nearly exclusively. An isolate with characteristics of some Pasteurellaceae family members (Gram-negative bacterium, pleomorphic, and NAD-dependent) was isolated from layer hens showing clinical signs of infectious coryza. This bacterium presented hemolysis on rabbit red blood cell agar plates, and PCR amplification and sequencing of its 16S rDNA gene indicated 99% identity with A. pleuropneumoniae serotypes 3 and 7. The presence of a putative apxIIA gene was also determined by PCR. A single, smooth colony of this bacterium inoculated in five, 7-day-old chicken embryos via the yolk sac route induced 100% mortality. However, inoculation into 10-wk-old, specific-pathogen-free chickens induced only light facial swelling, and reisolation of the inoculated bacterium was negative.

Bacterial protein signals are associated with Crohn's disease

OBJECTIVE

No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls.

DESIGN

We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions.

RESULTS

Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins.

CONCLUSIONS

This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis.

Gallibacterium anatis-secreted metalloproteases degrade chicken IgG

Gallibacterium anatis (previously named Pasteurella haemolytica-like) is considered a normal inhabitant of genital and upper respiratory tracts of healthy chickens, but it is also associated with different pathological conditions. Secreted metalloproteases from field and reference G. anatis cultures were obtained by methanol precipitation and were characterized. Proteins of molecular mass higher than 100 kDa showing proteolytic activity were observed in 10% polyacrylamide gels copolymerized with 1% bovine casein. They were active at alkaline pH, and inhibited by ethylenediamine tetraacetic acid. Their activity was stable at 50 degrees C, but partially inhibited at 60 degrees C, and totally inhibited at higher temperatures. Secreted proteins were able to degrade chicken IgG after 24 h of incubation, and cross-reacted with a polyclonal antibody against purified protease from Actinobacillus pleuropneumoniae. Secreted metalloproteases could play a role in infections caused by G. anatis.

Haemophilus paragallinarumsecretes metalloproteases

Haemophilus paragallinarum secretes metalloproteases into different culture media lacking serum. Secreted proteins, concentrated by precipitation with 70% ammonium sulphate ((NH4)2SO4) or methanol, displayed proteolytic activity at >100 kDa molecular mass in 10% polyacrylamide gels co-polymerized with porcine gelatin (0.1%). They were active in a broad pH range (4–9); pH 7.5 being the optimum. Protease activity was inhibited by 20 mmol EDTA/L and reactivated by calcium. The proteolytic activity was heat-stable at 40, 50, and 60 °C, but its activity diminished at 70 °C or higher. Secreted proteins partially degraded chicken immunoglobulin G (IgG) and cross-reacted with a polyclonal serum against a high molecular mass protease secreted by Actinobacillus pleuropneumoniae. Extracellular proteases could play a role in infectious coryza caused by H. paragallinarum.Key words: pathogenicity, secreted protein, infectious coryza.

Effect of beta-lactamase inhibitors on minimum inhibitory concentration of ampicillin and amoxicillin for Staphylococcus aureus strains

Seventy strains of Staphylococcus aureus isolated from the nasopharynx (80%), urinary tract (16%), skin (1 strain) and eyes (2 strains) of patients at the clinical laboratory "El eritrocito" were analyzed. Susceptibility to 12 antibiotics was tested by the method of Kirby-Bauer. Minimal inhibitory concentration (MIC) of ampicillin, ampicillin + sulbactam, amoxicillin and amoxicillin + clavulanic acid were determined by plate dilution. Percentages of resistance were: Penicillin and ampicillin (100%), ceftazidime (81.4%), erythromycin (68.6%), tetracycline (31.4%) trimethoprim-sulphametoxasol (25.7%), dicloxacillin and pefloxacin (12.8%), cefuroxime and cefotaxime (4.3%), gentamicin (2.8%), cephalothin (0%). All strains were resistant to three or more antibiotics, with higher percentages of resistance to four (31.4%), three (27.1%), five (21.4%) and six (12.9%) drugs. One strain was resistant to nine antibiotics and 5.9% were resistant to seven. 97.5% of the strains were beta-lactamase-positive. The MIC50 of ampicillin and amoxicillin was 500 micrograms/ml and the MIC90 were 1727 micrograms/ml and 2000 micrograms/ml, respectively. beta-lactamase inhibitors sulbactam and clavulanic acid reduced these values eightfold, except for the MIC50 of ampicillin + sulbactam whose reduction was sixteen fold. These results show that the combination of beta-lactamic + beta-lactamase inhibitor was more efficient than cephalosporins for killing these beta-lactamase-positive strains.

Osmoregulation in Pseudomonas aeruginosa under hyperosmotic shock

Pseudomonas aeruginosa PAO1 strain was found to be able to tolerate 700 mM NaCl. 0.5 mM of the osmoprotectant betaine restablished the growth of this strain in 1200 mM NaCl. Intracellular K+ and glutamate concentrations of P. aeruginosa PAO1 after an hyperosmotic shock (400 mM NaCl) showed a permanent increase. Adition of betaine (0.5 mM) to the medium with NaCl had an inhibitory effect on the intracellular accumulation of glutamate. The results indicate that P. aeruginosa PAO1 resists high NaCl concentrations, K+ accumulation and glutamate synthesis probably being the first mechanisms involved in adaptation to osmotic stress. Also is is demonstrated that betaine modulates intracellular glutamate levels in osmotically stressed P. aeruginosa PAO1.

[Restoration of transcription antitermination of N- bacteriophages in Escherichia coli with a mutant RNA polymerase]

The N protein of bacteriophage lambda modifies Escherichia coli RNA polymerase in such a way that it transcribes through termination signals, in a process called antitermination. In general N-mutants are not able to perform transcription antitermination. In this paper we report the suppression of N7 and Nmar3 mutations by Escherichia coli ron-lon strain. The lon mutation causes the N protein half-life to raise, suggesting that excess of N7 fragment or Nmar3 protein overcome the defect in antitermination. Under these conditions the lambda N-phages produced a titer similar to lambda wild type, although the plaques were smaller. These observations highlight the relevance of N half life in the regulation of transcription antitermination.

Partial genetic characterization of FIZ15 bacteriophage of Pseudomonas aeruginosa

FIZ15 phage of Pseudomonas aeruginosa causes lysogenic conversion in PAO1 strain. Lysogen shows increased adhesion to human buccal epithelial cells, increased resistance to 75 percent human serum bactericidal effect, and streptomycin resistant. These phenotypes apparently are due to a phage-induced superficial change on its own bacterial receptor, which probably is the O-antigen. In order to begin FIZ15 characterization, nitrous acid-induced clear-plaque mutants were obtained. They belonged to three complementation groups and mapping by two factor crosses revealed that they were closely linked. In a search for phage mutants that do not cause lysogenic conversion, two streptomycin-sensitive mutants were obtained by ethyl methane sulphonate mutagenesis of PAO1 lysogenic for FIZ15 (PIZ15 strain). One mutant (con1) showed and adhesion value similar to that of PAO1 and the other (con2) had an adhesion twofold and 1.3 times greater than PAO1 and PIZ15, respectively. con1 did not show increased serum resistance, whereas con2 was as resistant as PIZ15. Phages were isolated from the streptomycin sensitive mutants and used to relisogenize PAO1 to obtain the con1d and con2d lysogens. Adhesion and serum sensitivity of con1d was identical to that of PAO1 but con2d behaves like PIZ15. FIZ15 phage was unable to adsorb to PIZ15, con2 and con2d. On the other hand, FIZ15 phage adsorbs well to con1 and con1d but not to PIZ15. These results suggest that con1 mutation lies on the phage chromosome and con2 on the bacterial one. Finally, adhesion of all lysogens and PAO1 was stimulated 2-3 times by KCl and this effect was suppressed by and oxidative phosphorylation uncoupler.

[Mechanisms of bacterial resistance to heavy metals]

Resistance to toxic heavy metals has been found in bacteria from clinical and environmental origins. The genetic determinants of resistance are frequently located on plasmids or transposons. Several heavy metal resistance genes have been cloned and sequenced. The mechanisms of resistance to heavy metals are commonly based on novel membrane transport systems that expel the toxic ions (including cobalt, nickel, zinc, and probably copper and chromium) from the bacterial cytoplasm. Arsenic and cadmium ions are effluxed from the cells by specific membrane ATPases encoded by resistance plasmids. Reduction of mercuric ions to the volatile metallic form by a plasmid-coded enzyme is responsible for mercury resistance. Studies on other resistance determinants (e.g., antimony, bismuth, boron, lead, silver, tin, tellurium) have been reported but the mechanisms of resistance are still unknown.

[Chromates: resistance and detoxification in bacteria]

Derivatives of hexavalent chromium (chromates and dichromates) are highly toxic and have been shown to be mutagens and carcinogens. These compounds are often disposed to the environment as a result of diverse industrial procedures. The presence of chromates selects bacterial strains possessing chromate resistance determinants, commonly carried by plasmids. Some bacteria are able to reduce hexavalent chromium to trivalent chromium which is much less toxic. Bacterial strains combining both properties, resistance to and reduction of chromate, are potentially useful for decontamination of sewage or other refuse contaminated by chromates.