Whole genome identification of Mycobacterium tuberculosis vaccine candidates by comprehensive data mining and bioinformatic analyses

<p>Abstract</p> <p>Background</p> <p><it>Mycobacterium tuberculosis</it>, the causative agent of tuberculosis (TB), infects ~8 million annually culminating in ~2 million deaths. Moreover, about one third of the population is latently infected, 10% of which develop disease during lifetime. Current approved prophylactic TB vaccines (BCG and derivatives thereof) are of variable efficiency in adult protection against pulmonary TB (0%–80%), and directed essentially against early phase infection.</p> <p>Methods</p> <p>A genome-scale dataset was constructed by analyzing published data of: (1) global gene expression studies under conditions which simulate intra-macrophage stress, dormancy, persistence and/or reactivation; (2) cellular and humoral immunity, and vaccine potential. This information was compiled along with revised annotation/bioinformatic characterization of selected gene products and <it>in silico </it>mapping of T-cell epitopes. Protocols for scoring, ranking and prioritization of the antigens were developed and applied.</p> <p>Results</p> <p>Cross-matching of literature and <it>in silico</it>-derived data, in conjunction with the prioritization scheme and biological rationale, allowed for selection of 189 putative vaccine candidates from the entire genome. Within the 189 set, the relative distribution of antigens in 3 functional categories differs significantly from their distribution in the whole genome, with reduction in the Conserved hypothetical category (due to improved annotation) and enrichment in Lipid and in Virulence categories. Other prominent representatives in the 189 set are the PE/PPE proteins; iron sequestration, nitroreductases and proteases, all within the Intermediary metabolism and respiration category; ESX secretion systems, resuscitation promoting factors and lipoproteins, all within the Cell wall category. Application of a ranking scheme based on qualitative and quantitative scores, resulted in a list of 45 best-scoring antigens, of which: 74% belong to the dormancy/reactivation/resuscitation classes; 30% belong to the Cell wall category; 13% are classical vaccine candidates; 9% are categorized Conserved hypotheticals, all potentially very potent T-cell antigens.</p> <p>Conclusion</p> <p>The comprehensive literature and <it>in silico</it>-based analyses allowed for the selection of a repertoire of 189 vaccine candidates, out of the whole-genome 3989 ORF products. This repertoire, which was ranked to generate a list of 45 top-hits antigens, is a platform for selection of genes covering all stages of <it>M. tuberculosis </it>infection, to be incorporated in rBCG or subunit-based vaccines.</p

National Market Cow and Bull Beef Quality Audit - 1999

The National Non-Fed Beef Quality Audit – 1994 (NNFBQA-94) was conducted to benchmark the quality characteristics of market cows and bulls in the beef and dairy industries for purposes of encouraging implementation of quality management practices within the beef industry. From this audit, it was determined that producers were losing $69.90 for each market cow and bull harvested due to quality defects. As a means of recovering the lost value, producers were provided three means by which they could begin to recapture the lost value: 1) Manage market cows and bulls to minimize defects and quality deficiencies, 2) Monitor the health and condition of market cows and bulls, and 3) Market cows and bulls in a timely manner. The audit, now referred to as the National Market Cow and Bull Beef Quality Audit – 1999 (NMCBBQA-99), was conducted again in 1999 to determine the quality and consistency of market cows and bulls and to measure improvement in quality and consistency since 1994. Specifically, objectives of NMCBBQA-99 were to 1) identify and quantify, numerically and monetarily, the incidence of quality defects in U.S. market cows and bulls, their carcasses and offal items; 2) characterize as many as possible of the causes of quality defects in market cows and bulls; 3) compare the results of the NMCBBQA-99 to the NNFBQA-94; and 4) identify strategies and tactics to pursue and employ efforts to reduce/eliminate specific defects in the quality and consistency of market cow and bull beef

Modeling the Growth/No-Growth Boundaries of Postprocessing Listeria monocytogenes Contamination on Frankfurters and Bologna Treated with Lactic Acid▿

This study developed models to predict lactic acid concentration, dipping time, and storage temperature combinations determining growth/no-growth interfaces of Listeria monocytogenes at desired probabilities on bologna and frankfurters. L. monocytogenes was inoculated on bologna and frankfurters, and 75 combinations of lactic acid concentrations, dipping times, and storage temperatures were tested. Samples were stored in vacuum packages for up to 60 days, and bacterial populations were enumerated on tryptic soy agar plus 0.6% yeast extract and Palcam agar on day zero and at the end point of storage. The combinations that allowed L. monocytogenes increases of ≥1 log CFU/cm2 were assigned the value of 1 (growth), and the combinations that had increases of <l log CFU/cm2 were given the value of 0 (no growth). These binary growth response data were fitted to logistic regression to develop a model predicting probabilities of growth. Validation with existing data and various indices showed acceptable model performance. Thus, the models developed in this study may be useful in determining probabilities of growth and in selecting lactic acid concentrations and dipping times to control L. monocytogenes growth on bologna and frankfurters, while the procedures followed may also be used to develop models for other products, conditions, or pathogens

Impact of Inoculum Preparation and Storage Conditions on the Response of Escherichia coli O157:H7 Populations to Undercooking and Simulated Exposure to Gastric Fluid

This study evaluated the impact of inoculum preparation and storage conditions on the response of Escherichia coli O157:H7 exposed to consumer-induced stresses simulating undercooking and digestion. Lean beef tissue samples were inoculated with E. coli O157:H7 cultures prepared in tryptic soy broth or meat decontamination runoff fluids (WASH) or detached from moist biofilms or dried biofilms formed on stainless steel coupons immersed in inoculated WASH. After inoculation, the samples were left untreated or dipped for 30 s each in hot (75°C) water followed by lactic acid (2%, 55°C), vacuum packaged, stored at 4 (28 days) or 12°C (16 days), and periodically transferred to aerobic storage (7°C for 5 days). During storage, samples were exposed to sequential heat (55°C; 20 min) and simulated gastric fluid (adjusted to pH 1.0 with HCl; 90 min) stresses simulating consumption of undercooked beef. Under the conditions of this study, cells originating from inocula of planktonic cells were, in general, more resistant to heat and acid than cells from cultures grown as biofilms and detached prior to meat inoculation. Heat and acid tolerance of cells on meat stored at 4°C was lower than that of cells on nondecontaminated meat stored at 12°C, where growth occurred during storage. Decontamination of fresh beef resulted in injury that inhibited subsequent growth of surviving cells at 12°C, as well as in decreases in resistance to subsequent heat and acid stresses. The shift of pathogen cells on beef stored under vacuum at 4°C to aerobic storage did not affect cell populations or subsequent survival after sequential exposure to heat and simulated gastric fluid. However, the transfer of meat stored under vacuum at 12°C to aerobic storage resulted in reduction in pathogen counts during aerobic storage and sensitization of survivors to the effects of sequential heat and acid exposure

Localized Chemical Decont- amination of Cattle Hides to Reduce Microbial Loads and Prevalence of Foodborne Pathogens

ABSTRACT hides of cattle have been shown to be the principal source of E. coli O157:h7 at slaughter. This project was conducted to determine if localized interventions are a viable option for cattle hide decontamination. Localized decontaminant treatments consisting of negative control (CT), warm water (h 2 O), 6.0% lactic acid (LA), 5.0% acetic acid (AA), and 2.7% sodium hydroxide (NaOh) were applied to the pattern lines of beef hides. Samples were collected before and after treatment application and from dressed carcass surfaces and were analyzed for aerobic bacterial plate counts (APC), total coliform count (TCC), biotype I E. coli count (ECC), E. coli O157:h7, and Salmonella. APCs on cattle hides were reduced by 0.11, 2.62, 2.30 and 1.66, TCCs were reduced by -0.09, 3.82, 3.76 and 3.63, and ECCs were reduced by -0.03, 3.77, 3.83 and 3.54 log CFu/400 cm 2 following application of h 2 O, LA, AA and NaOh, respectively. Prevalence of E. coli O157:h7 was reduced by -6.0%, 46.0%, 28.0% and 53.2% and Salmonella was reduced by -20.0%, 0% (none detected), 24.0% and 17.1% following application of h 2 O, LA, AA and NaOh, respectively. use of localized chemical interventions on cattle hides is an effective mechanism for reducing incoming loads of bacteria on hide surfaces and reducing foodborne pathogen prevalence on dressed carcasses