Identification of Yersinia pestis and Escherichia coli strains by whole cell and outer membrane protein extracts with mass spectrometry-based proteomics.

Whole cell protein and outer membrane protein (OMP) extracts were compared for their ability to differentiate and delineate the correct database organism to an experimental sample and for the degree of dissimilarity to the nearest neighbor database organism strains. These extracts were isolated from pathogenic and nonpathogenic strains of Yersinia pestis and Escherichia coli using ultracentrifugation and a sarkosyl extraction method followed by protein digestion and analysis using liquid chromatography tandem mass spectrometry (MS). Whole cell protein extracts contain many different types of proteins resident in an organism at a given phase in its growth cycle. OMPs, however, are often associated with virulence in Gram-negative pathogens and could prove to be model biomarkers for strain differentiation among bacteria. The mass spectra of bacterial peptides were searched, using the SEQUEST algorithm, against a constructed proteome database of microorganisms in order to determine the identity and number of unique peptides for each bacterial sample. Data analysis was performed with the in-house BACid software. It calculated the probabilities that a peptide sequence assignment to a product ion mass spectrum was correct and used accepted spectrum-to-sequence matches to generate a sequence-to-bacterium (STB) binary matrix of assignments. Validated peptide sequences, either present or absent in various strains (STB matrices), were visualized as assignment bitmaps and analyzed by the BACid module that used phylogenetic relationships among bacterial species as part of a decision tree process. The bacterial classification and identification algorithm used assignments of organisms to taxonomic groups (phylogenetic classification) based on an organized scheme that begins at the phylum level and follows through the class, order, family, genus, and species to the strain level. For both Gram-negative organisms, the number of unique distinguishing proteins arrived at by the whole cell method was less than that of the OMP method. However, the degree of differentiation measured in linkage distance units on a dendrogram with the OMP extract showed similar or significantly better separation than the whole cell protein extract method between the sample and correct database match compared to the next nearest neighbor. The nonpathogenic Y. pestis A1122 strain used does not have its genome available, and thus, data analysis resulted in an equal similarity index to the nonpathogenic 91001 and pathogenic Antiqua and Nepal 516 strains for both extraction methods. Pathogenic and nonpathogenic strains of E. coli were correctly identified with both protein extraction methods, and the pathogenic Y. pestis CO92 strain was correctly identified with the OMP procedure. Overall, proteomic MS proved useful in the analysis of unique protein assignments for strain differentiation of E. coli and Y. pestis. The power of bacterial protein capture by the whole cell protein and OMP extraction methods was highlighted by the data analysis techniques and revealed differentiation and similarities between the two protein extraction approaches for bacterial delineation capability.

Double-blind characterization of non-genome-sequenced bacteria by mass spectrometry-based proteomics.

Due to the possibility of a biothreat attack on civilian or military installations, a need exists for technologies that can detect and accurately identify pathogens in a near-real-time approach. One technology potentially capable of meeting these needs is a high-throughput mass spectrometry (MS)-based proteomic approach. This approach utilizes the knowledge of amino acid sequences of peptides derived from the proteolysis of proteins as a basis for reliable bacterial identification. To evaluate this approach, the tryptic digest peptides generated from double-blind biological samples containing either a single bacterium or a mixture of bacteria were analyzed using liquid chromatography-tandem mass spectrometry. Bioinformatic tools that provide bacterial classification were used to evaluate the proteomic approach. Results showed that bacteria in all of the double-blind samples were accurately identified with no false-positive assignment. The MS proteomic approach showed strain-level discrimination for the various bacteria employed. The approach also characterized double-blind bacterial samples to the respective genus, species, and strain levels when the experimental organism was not in the database due to its genome not having been sequenced. One experimental sample did not have its genome sequenced, and the peptide experimental record was added to the virtual bacterial proteome database. A replicate analysis identified the sample to the peptide experimental record stored in the database. The MS proteomic approach proved capable of identifying and classifying organisms within a microbial mixture.

Identification of genes involved in biosynthesis of Actinobacillus pleuropneumoniae serotype 1 O-antigen and biological properties of rough mutants.

Actinobacillus pleuropneumoniae is an important pathogen of swine. Lipopolysaccharide (LPS) has been identified as the major adhesin of A. pleuropneumoniae and it is involved in adherence to porcine respiratory tract cells. We previously generated seven rough LPS mutants of A. pleuropneumoniae serotype 1 by using a mini-Tn10 transposon mutagenesis system [Rioux S, Galarneau C, Harel J et al. Isolation and characterization of mini-Tn10 lipopolysaccharide mutants of Actinobacillus pleuropneumoniae serotype 1. Can J Microbiol 1999; 45: 1017-1026]. The purpose of the present study was to characterize these mutants in order to learn more about LPS O-antigen biosynthesis genes and their organization in A. pleuropneumoniae, and to determine the surface properties and virulence in pigs of these isogenic mutants. By mini-Tn10 insertions in rough mutants, four putative genes (ORF12, ORF16, ORF17, and ORF18) involved in O-antigen biosynthesis in A. pleuropneumoniae serotype 1 were found within a region of 18 ORFs. This region is homologous to the gene cluster of serotype-specific O-polysaccharide biosynthesis from A. actinomycetemcomitans strain Y4 (serotype b). Two mutants showed homology to a protein with identity to glycosyltransferases (ORF12); two others had the mini-Tn10 insertion localized in genes encoding for two distinct proteins with identity to rhamnosyltransferases (ORF16 and ORF17) and three showed homology to a protein which is known to initiate polysaccharide synthesis (ORF18). These four ORFs were also present in A. pleuropneumoniae serotypes 9 and 11 that express an O-antigen that serologically cross-reacts with serotype 1. Evaluation of some biological properties of rough mutants seems to indicate that the absence of O-chains does not appear to have an influence on the virulence of the bacteria in pigs and on the overall surface hydrophobicity, charge and hemoglobin-binding activity, or on LAL activation. An acapsular mutant was included in the present study in order to compare the influence of O-chains and capsule polysaccharides on different cell surface properties. Our data suggest that capsular polysaccharides and not O-chains polysaccharides have a major influence on surface properties of A. pleuropneumoniae serotype 1 and its virulence in pigs.

Mechanisms of drug resistance in Mycobacterium tuberculosis.

Tuberculosis is a worldwide health problem posing increasing threat with the spread of HIV infection and drug resistant Mycobacterium tuberculosis strains. Consequently, control of this disease has become a significant challenge despite the availability of chemotherapy and BCG vaccine. Drug resistance for all first-line anti-tuberculosis agents and some second-line agents has been observed. Moreover, the occurrence of strains of M. tuberculosis resistant to multiple anti-tuberculosis drugs is increasing. Mechanisms of action and resistance of major anti-tuberculosis drugs are reviewed. In addition, the phenotypic drug resistance such as dormant or persistent tubercle bacilli and its importance are also emphasized. In order to combat the threat of drug resistant tuberculosis and to more effectively control the disease, an understanding of the mechanisms underlying drug resistance is necessary. This knowledge could be used for the development of molecular tests for rapid detection of drug resistant bacilli and future anti-tuberculosis drugs.

Accurate mapping of mutations of pyrazinamide-resistant Mycobacterium tuberculosis strains with a scanning-frame oligonucleotide microarray.

The increasing emergence of drug-resistant Mycobacterium tuberculosis poses significant threat to the treatment of tuberculosis. Conventional susceptibility testing for the front-line tuberculosis drug pyrazinamide (PZA) is difficult, because of the requirement for acid pH for the drug to show activity. Resistance to PZA in M. tuberculosis is caused by mutations in the pncA gene, and detection of pncA mutations can be an indicator of PZA resistance. In this study, we examined the feasibility of a microarray-based approach exploiting short overlapping oligonucleotides (sliding-frame array) to rapidly detect pncA mutations (substitutions, deletions, and insertions) in multiple strains of PZA-resistant M. tuberculosis. The genetic mapping of these mutations is necessary to link the gene sequence to the protein function defined by mutant phenotype. Microarray analysis was performed in a blind manner using 57 isolates of M. tuberculosis for which the sequence of the pncA gene was previously determined. Our results showed that all mutations could be unambiguously detected, suggesting that microarray can be a routine and valuable tool for rapid identification of drug-resistant M. tuberculosis isolates. We expect that mutation mapping with a sliding-frame microarray will accelerate the molecular analysis of drug-resistant M. tuberculosis bacteria and the microorganism populations.

Anaerobic incubation conditions enhance pyrazinamide activity against Mycobacterium tuberculosis.

Pyrazinamide (PZA) is an unconventional front line tuberculosis drug characterized by high in vivo sterilizing activity, but poor in vitro activity. This disparity in PZA activity may reflect differences between the in vivo tissue environment and in vitro culture conditions. This study examined the effect of anaerobic conditions, which exist in granulomatous lesions in vivo, on PZA activity in vitro. Low oxygen enhanced the activity of PZA against Mycobacterium tuberculosis, with anaerobic conditions resulting in greater enhancement than microaerobic conditions. ATPase and respiratory chain enzyme inhibitors enhanced PZA activity under normal atmospheric conditions, but not under anaerobic conditions. Furthermore, the inhibitors did not enhance isoniazid or rifampicin activity. Nitrate as an alternative electron acceptor antagonized PZA activity under anaerobic conditions. These findings provide further support for a proposed mechanism of action of PZA in which the active form of PZA (pyrazinoic acid) depletes the membrane energy reserve. They also provide another explanation for the higher sterilizing activity of PZA within in vivo lesions with low oxygen than under in vitro drug susceptibility testing conditions with ambient oxygen.

Extracellular protein biomarkers for the characterization of enterohemorrhagic and enteroaggregative Escherichia coli strains.

The extracellular proteins (ECPs) of enterohemorrhagic Escherichia coli (EHEC) can cause hemorrhagic colitis which may cause life threatening hemolytic-uremic syndrome, while that of enteroaggregative E. coli (EAEC) can clump to intestinal membranes. Liquid chromatography-electrospray ionization-tandem mass spectrometry based proteomics is used to evaluate a preliminary study on the extracellular and whole cell protein extracts associated with E. coli strain pathogenicity. Proteomics analysis, which is independent of genomic sequencing, of EAEC O104:H4 (unsequenced genome) identified a number of proteins. Proteomics of EHEC O104:H4, causative agent of the Germany outbreak, showed a closest match with E. coli E55989, in agreement with genomic studies. Dendrogram analysis separated EHEC O157:H7 and EHEC/EAEC O104:H4. ECP analysis compared to that of whole cell processing entails few steps and convenient experimental extraction procedures. Bacterial characterization results are promising in exploring the impact of environmental conditions on E. coli ECP biomarkers with a few relatively straightforward protein extraction steps.

Pulsed UV-C disinfection of Escherichia coli with light-emitting diodes, emitted at various repetition rates and duty cycles.

A 2010 study exposed Staphylococcus aureus to ultraviolet (UV) radiation and thermal heating from pulsed xenon flash lamps. The results suggested that disinfection could be caused not only by photochemical changes from UV radiation, but also by photophysical stress damage caused by the disturbance from incoming pulses. The study called for more research in this area. The recent advances in light-emitting diode (LED) technology include the development of LEDs that emit in narrow bands in the ultraviolet-C (UV-C) range (100-280 nm), which is highly effective for UV disinfection of organisms. Further, LEDs would use less power, and allow more flexibility than other sources of UV energy in that the user may select various pulse repetition frequencies (PRFs), pulse irradiances, pulse widths, duty cycles and types of waveform output (e.g. square waves, sine waves, triangular waves, etc.). Our study exposed Escherichia coli samples to square pulses of 272 nm radiation at various PRFs and duty cycles. A statistically significant correlation was found between E. coli's disinfection sensitivity and these parameters. Although our sample size was small, these results show promise and are worthy of further investigation. Comparisons are also made with pulsed disinfection by LEDs emitting at 365 nm, and pulsed disinfection by xenon flash lamps.

Evaluation of handheld assays for the detection of ricin and staphylococcal enterotoxin B in disinfected waters.

Development of a rapid field test is needed capable of determining if field supplies of water are safe to drink by the warfighter during a military operation. The present study sought to assess the effectiveness of handheld assays (HHAs) in detecting ricin and Staphylococcal Enterotoxin B (SEB) in water. Performance of HHAs was evaluated in formulated tap water with and without chlorine, reverse osmosis water (RO) with chlorine, and RO with bromine. Each matrix was prepared, spiked with ricin or SEB at multiple concentrations, and then loaded onto HHAs. HHAs were allowed to develop and then read visually. Limits of detection (LOD) were determined for all HHAs in each water type. Both ricin and SEB were detected by HHAs in formulated tap water at or below the suggested health effect levels of 455 ng/mL and 4.55 ng/mL, respectively. However, in brominated or chlorinated waters, LODs for SEB increased to approximately 2,500 ng/mL. LODs for ricin increased in chlorinated water, but still remained below the suggested health effect level. In brominated water, the LOD for ricin increased to approximately 2,500 ng/mL. In conclusion, the HHAs tested were less effective at detecting ricin and SEB in disinfected water, as currently configured.

Survival of viral biowarfare agents in disinfected waters.

Protecting civilian and military water supplies has received more attention since the United States began its war on terror in 2001. Both chlorine and bromine are used by branches of the U.S. military for disinfecting water supplies; however, limited data exists as to the effectiveness of these additives when used against viral biowarfare agents. The present study sought to evaluate the survival of selected viral biothreat agents in disinfected water. Disinfected water samples were spiked with vaccinia virus strain WR and Venezuelan equine encephalitis (VEE) virus strain TC-83 each separately to a final concentration of approximately 1 × 10(6) PFU/mL, and survival was assessed by plaque assay. Both viruses were inactivated by 1 mg/L free available chlorine (FAC) and 2mg/L total bromine within one hour. In conclusion, these results demonstrate that both chlorine and bromine are effective disinfectants against vaccinia virus and VEE strain TC-83 at the concentrations tested.

Effects of weak acids, UV and proton motive force inhibitors on pyrazinamide activity against Mycobacterium tuberculosis in vitro.

BACKGROUND: Pyrazinamide is a paradoxical frontline tuberculosis drug characterized by high sterilizing in vivo activity but poor in vitro activity. Pyrazinamide is thought to act by the entrapment of pyrazinoic acid in the bacterial cell, leading to acidification and membrane damage. Consequently, the effects of weak acids and molecules affecting membranes added to pyrazinamide were studied. OBJECTIVES: To examine the effects of weak acids, UV, oxidative stress and additional energy inhibitors on pyrazinamide activity in vitro against Mycobacterium tuberculosis as well as the effect of pyrazinamide on Escherichia coli ampicillin persisters. METHODS: Drug exposure experiments followed by cfu counts were performed to determine the effects of the above various factors on pyrazinamide activity in vitro against M. tuberculosis. RESULTS: Some weak acids such as benzoic acid, sorbic acid and propyl hydroxybenzoic acid could enhance the activity of pyrazinamide in vitro against old tubercle bacilli but not young bacilli whereas other weak acids such as salicylic acid and lactic acid did not appear to enhance pyrazinamide activity. While energy inhibitors carbonylcyanide m-chlorophenylhydrazone and dinitrophenol enhanced pyrazinamide activity for old tubercle bacilli but not young bacilli, valinomycin and KCN increased pyrazinamide activity for both young and old bacilli. Oxidative stresses due to H2O2 and menadione did not have a significant effect on pyrazinamide activity. UV, which presumably damages the membrane, enhanced the activity of pyrazinamide. Pyrazinamide, which otherwise has no activity against actively growing E. coli bacteria, could kill non-growing starved E. coli and also ampicillin-tolerant persisters. CONCLUSIONS: Some weak acids, UV and various energy inhibitors were found to enhance the activity of pyrazinamide in vitro against M. tuberculosis. Pyrazinamide shows preferential activity against both M. tuberculosis and E. coli persisters over the growing forms.

Iron enhances the antituberculous activity of pyrazinamide.

BACKGROUND: Pyrazinamide is a paradoxical frontline tuberculosis drug characterized by high in vivo sterilizing activity but poor in vitro activity. This separation in pyrazinamide activity reflects differences between the in vivo tissue environment and in vitro culture conditions. The well-known acid pH requirement for pyrazinamide activity was discovered previously based on such reasoning but does not completely explain the discrepancy between in vivo and in vitro activity of pyrazinamide. This study examined the effect of iron, which could potentially be elevated in local inflammatory lesions, on pyrazinamide activity in vitro. MATERIALS AND METHODS: The effect of iron on the activity of pyrazinamide or its active derivative pyrazinoic acid against Mycobacterium tuberculosis was assessed in liquid medium in a drug exposure assay or in solid medium with pyrazinamide plus iron or pyrazinamide alone. The effect of iron on pyrazinamide or pyrazinoic acid was expressed as percentage of growth inhibition. RESULTS: We have shown that iron enhances the activity of pyrazinamide and pyrazinoic acid against M. tuberculosis in both liquid and solid media at acid pH 5.6. Iron enhanced the activity of pyrazinoic acid but not pyrazinamide against the naturally pyrazinamide-resistant Mycobacterium bovis BCG. Other metal ions such as magnesium, calcium and zinc did not enhance the activity of pyrazinamide or pyrazinoic acid. CONCLUSIONS: Iron increased the activity of pyrazinamide or pyrazinoic acid against M. tuberculosis in vitro. These findings may have implications for the study of mechanism of action of pyrazinamide and possible iron supplement for improving the activity of pyrazinamide.

Mode of action of pyrazinamide: disruption of Mycobacterium tuberculosis membrane transport and energetics by pyrazinoic acid.

Pyrazinamide is an important sterilizing drug that shortens tuberculosis (TB) therapy. However, the mechanism of action of pyrazinamide is poorly understood because of its unusual properties. Here we show that pyrazinoic acid, the active moiety of pyrazinamide, disrupted membrane energetics and inhibited membrane transport function in Mycobacterium tuberculosis. The preferential activity of pyrazinamide against old non-replicating bacilli correlated with their low membrane potential and the disruption of membrane potential by pyrazinoic acid and acid pH. Inhibitors of membrane energetics increased the antituberculous activity of pyrazinamide. These findings shed new light on the mode of action of pyrazinamide and may help in the design of new drugs that shorten therapy.