BacterAI maps microbial metabolism without prior knowledge

Training artificial intelligence (AI) systems to perform autonomous experiments would vastly increase the throughput of microbiology; however, few microbes have large enough datasets for training such a system. In the present study, we introduce BacterAI, an automated science platform that maps microbial metabolism but requires no prior knowledge. BacterAI learns by converting scientific questions into simple games that it plays with laboratory robots. The agent then distils its findings into logical rules that can be interpreted by human scientists. We use BacterAI to learn the amino acid requirements for two oral streptococci: Streptococcus gordonii and Streptococcus sanguinis. We then show how transfer learning can accelerate BacterAI when investigating new environments or larger media with up to 39 ingredients. Scientific gameplay and BacterAI enable the unbiased, autonomous study of organisms for which no training data exist.

A reinforcement learning framework for pooled oligonucleotide design

MOTIVATION

The goal of oligonucleotide (oligo) design is to select oligos that optimize a set of design criteria. Oligo design problems are combinatorial in nature and require computationally intensive models to evaluate design criteria. Even relatively small problems can be intractable for brute-force approaches that test every possible combination of oligos, so heuristic approaches must be used to find near-optimal solutions.

RESULTS

We present a general reinforcement learning (RL) framework, called OligoRL, to solve oligo design problems with complex constraints. OligoRL allows 'black-box' design criteria and can be adapted to solve many oligo design problems. We highlight the flexibility of OligoRL by building tools to solve three distinct design problems: (i) finding pools of random DNA barcodes that lack restriction enzyme recognition sequences (CutFreeRL); (ii) compressing large, non-degenerate oligo pools into smaller degenerate ones (OligoCompressor) and (iii) finding Not-So-Random hexamer primer pools that avoid rRNA and other unwanted transcripts during RNA-seq library preparation (NSR-RL). OligoRL demonstrates how RL offers a general solution for complex oligo design problems.

AVAILABILITY AND IMPLEMENTATION

OligoRL and all simulation codes are available as a Julia package at http://jensenlab.net/tools and archived at https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://github.com/bmdavid2/OligoRL.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A Novel Competence Pathway in the Oral Pathogen Streptococcus sobrinus

Streptococcus sobrinus is an etiologic cause of dental caries (tooth decay) in humans. Our knowledge of S. sobrinus is scant despite the organism's important role in oral health. It is widely believed that S. sobrinus lacks the natural competence pathways that are used by other streptococci to regulate growth, virulence, and quorum sensing. The lack of natural competence has also prevented genetic manipulation of S. sobrinus, limiting our knowledge of its pathogenicity. We discovered that most strains of S. sobrinus contain a new class of the ComRS competence system. Although S. sobrinus is typically placed among the mutans group streptococci, the S. sobrinus ComRS system is most similar to the competence pathways in the salivarius group. Unlike all other ComRS systems, the S. sobrinus pathway contains 2 copies of the transcriptional regulator ComR and has a peptide pheromone (XIP) that lacks any aromatic amino acids. Synthetic XIP enables transformation of S. sobrinus with plasmid or linear DNA, and we leverage this newfound genetic tractability to confirm that only 1 of the ComR homologs is required for induced competence while the other appears to suppress competence. Exogenous XIP increases the expression of bacteriocin gene clusters and produces an antimicrobial response that inhibits growth of S. mutans. We also identified 2 strains of S. sobrinus that appear to be "cheaters" by either not responding to or not producing XIP. We show how a recombination event in the nonresponsive strain could restore function of the ComRS pathway but delete the gene encoding XIP. Thus, the S. sobrinus ComRS pathway provides new tools for studying this pathogen and offers a lens into the evolution of ecological cheaters.

Gapsplit: efficient random sampling for non-convex constraint-based models

SUMMARY

Gapsplit generates random samples from convex and non-convex constraint-based models by targeting under-sampled regions of the solution space. Gapsplit provides uniform coverage of linear, mixed-integer and general non-linear models.

AVAILABILITY AND IMPLEMENTATION

Python and Matlab source code are freely available at http://jensenlab.net/tools.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes

While Tn-Seq is a powerful tool to determine genome-wide bacterial fitness in high-throughput, culturing transposon-mutant libraries in pools can mask community or other complex single-cell phenotypes. Droplet Tn-Seq (dTn-Seq) solves this problem by microfluidics facilitated encapsulation of individual transposon mutants into growth medium-in-oil droplets, thereby enabling isolated growth, free from the influence of the population. Here we describe and validate microfluidic chip design, production, encapsulation, and dTn-Seq sample preparation. We determine that 1-3% of mutants in Streptococcus pneumoniae have a different fitness when grown in isolation and show how dTn-Seq can help identify leads for gene function, including those involved in hyper-competence, processing of alpha-1-acid glycoprotein, sensitivity against the human leukocyte elastase and microcolony formation. Additionally, we show dTn-Seq compatibility with microscopy, FACS and investigations of bacterial cell-to-cell and bacteria-host cell interactions. dTn-Seq reduces costs and retains the advantages of Tn-Seq, while expanding the method's original applicability.

The bare necessities: Uncovering essential and condition-critical genes with transposon sequencing

Querying gene function in bacteria has been greatly accelerated by the advent of transposon sequencing (Tn-seq) technologies (related Tn-seq strategies are known as TraDIS, INSeq, RB-TnSeq, and HITS). Pooled populations of transposon mutants are cultured in an environment and next-generation sequencing tools are used to determine areas of the genome that are important for bacterial fitness. In this review we provide an overview of Tn-seq methodologies and discuss how Tn-seq has been applied, or could be applied, to the study of oral microbiology. These applications include studying the essential genome as a means to rationally design therapeutic agents. Tn-seq has also contributed to our understanding of well-studied biological processes in oral bacteria. Other important applications include in vivo pathogenesis studies and use of Tn-seq to probe the molecular basis of microbial interactions. We also highlight recent advancements in techniques that act in synergy with Tn-seq such as clustered regularly interspaced short palindromic repeats (CRISPR) interference and microfluidic chip platforms.

Evaluation of the Tuberculosis Infection Control Training Center, Tajikistan, 2014-2015

SETTING

Training center on tuberculosis (TB) infection control (IC) for health care workers in the Central Asian Republics region.

OBJECTIVE

To assess the effects of TB IC training courses conducted at the Tuberculosis Infection Control Training Center in Machiton, Tajikistan.

DESIGN

Participants who participated in training (n = 89) during the first year of operation (April 2014-February 2015) were invited to participate in a post-training interview.

RESULTS

Of the 89 participants, 84 (94%) completed the interview and expressed satisfaction with the training. Eighty (95%) participants reported meeting with workplace leadership to discuss the training. Of these, 69 (85%) reported discussing changes required to meet TB IC standards. Self-reported changes in TB IC practices at work facilities post training included the creation of TB IC committees, designation of a TB IC focal person, TB IC planning, policies to separate infectious patients in waiting rooms, provision of masks for infectious patients, development of cough etiquette policies, improved glove availability, hand hygiene programs, and TB IC posters in waiting rooms.

CONCLUSIONS

Participant satisfaction and reported changes in TB IC activities illustrate the potential of these training courses to improve TB IC in the region. Future training courses may be tailored to specific audiences using a structured conceptual framework to impact administration, budgeting, and facilities management of TB IC practices.

Designing Randomized DNA Sequences Free of Restriction Enzyme Recognition Sites

DNA libraries containing random "barcodes" complicate synthetic biology workflows that utilize restriction enzymes since restriction sites can appear inside some barcodes. By removing bases at particular sites in the barcodes, it is possible to create semi-random pools of barcodes that do not contain any restriction sites. The challenge is to remove as few bases as possible to maximize the number of sequences in the pool while ensuring all sequences are free of restriction sites. The authors present CutFree, a computational approach to create pools of random DNA barcodes that lack a pre-defined set of restriction sites. The resulting pools can be inexpensively produced en masse with standard DNA synthesis techniques. CutFree is experimentally validated by blocking digestion of pools of barcodes designed to frequently contain restriction sites. Using CutFree, a pool of 1.3 billion barcodes that are free from recognition sites for 182 commercially available restriction enzymes is designed. CutFree is available as a software package and an online tool (http://jensenlab.net/tools).

Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria

Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude. Moreover, a gene expression meta-analysis reveals that genes with large fitness changes during stress have low transcriptional variation across hundreds of other conditions, and vice versa. Our work suggests that cellular responses can be understood through network models that incorporate regulatory and genetic relationships, which could aid drug target predictions and genetic network engineering.

Hands-On Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics

The scale of genomic sequencing data and the complexity of bioinformatic algorithms make it difficult for students to develop a concrete understanding of assembling complete genomes from millions of short DNA sequences. We present a hands-on activity where students explore the genome assembly process using short DNA sequences printed on paper. Topics highlighted during the lesson include overlap identification, reference sequences, and the challenges arising from sequencing errors, low-frequency mutations, and repetitive regions. Sample materials provide reads and solutions for assembling clinically relevant regions of the S. gordonii penicillin binding protein and the human HTT gene. An online tool allows instructors to generate custom read sets from other DNA sequences.

Institutional Tuberculosis Transmission. Controlled Trial of Upper Room Ultraviolet Air Disinfection: A Basis for New Dosing Guidelines

RATIONALE

Transmission is driving the global tuberculosis epidemic, especially in congregate settings. Worldwide, natural ventilation is the most common means of air disinfection, but it is inherently unreliable and of limited use in cold climates. Upper room germicidal ultraviolet (UV) air disinfection with air mixing has been shown to be highly effective, but improved evidence-based dosing guidelines are needed.

OBJECTIVES

To test the efficacy of upper room germicidal air disinfection with air mixing to reduce tuberculosis transmission under real hospital conditions, and to define the application parameters responsible as a basis for proposed new dosing guidelines.

METHODS

Over an exposure period of 7 months, 90 guinea pigs breathed only untreated exhaust ward air, and another 90 guinea pigs breathed only air from the same six-bed tuberculosis ward on alternate days when upper room germicidal air disinfection was turned on throughout the ward.

MEASUREMENTS AND MAIN RESULTS

The tuberculin skin test conversion rates (>6 mm) of the two chambers were compared. The hazard ratio for guinea pigs in the control chamber converting their skin test to positive was 4.9 (95% confidence interval, 2.8-8.6), with an efficacy of approximately 80%.

CONCLUSIONS

Upper room germicidal UV air disinfection with air mixing was highly effective in reducing tuberculosis transmission under hospital conditions. These data support using either a total fixture output (rather than electrical or UV lamp wattage) of 15-20 mW/m(3) total room volume, or an average whole-room UV irradiance (fluence rate) of 5-7 μW/cm(2), calculated by a lighting computer-assisted design program modified for UV use.

Miniaturized plate readers for low-cost, high-throughput phenotypic screening

We present a miniaturized plate reader for measuring optical density in 96-well plates. Our standalone reader fits in most incubators, environmental chambers, or biological containment suites, allowing users to leverage their existing laboratory infrastructure. The device contains no moving parts, allowing an entire 96-well plate to be read several times per second. We demonstrate how the fast sampling rate allows our reader to detect small changes in optical density, even when the device is placed in a shaking incubator. A wireless communication module allows remote monitoring of multiple devices in real time. These features allow easy assembly of multiple readers to create a scalable, accurate solution for high-throughput phenotypic screening.

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data

MOTIVATION

Metabolic reaction maps allow visualization of genome-scale models and high-throughput data in a format familiar to many biologists. However, creating a map of a large metabolic model is a difficult and time-consuming process. MetDraw fully automates the map-drawing process for metabolic models containing hundreds to thousands of reactions. MetDraw can also overlay high-throughput 'omics' data directly on the generated maps.

Performance evaluation of selected n95 respirators and surgical masks when challenged with aerosolized endospores and inert particles

The objective of this study was to assess how the relative efficiency of N95 respirators and surgical masks might vary with different challenge aerosols, utilizing a standardized manikin head form as a surrogate to human participation. A Collision nebulizer aerosolized B. anthracis Sterne strain endospores and polystyrene latex (PSL) particles to evaluate 11 models of N95 respirators and surgical masks. An automated breathing simulator, calibrated to normal tidal volume and active breathing rate, mimicked human respiration. A manikin head form with N95 respirators or surgical masks, and manikin head form without N95 respirators or surgical masks were placed in the bioaerosol chamber. An AGI-30 sampler filled with phosphate buffered water was fitted behind the mouth of each manikin head form to collect endospore bioaerosol samples. PSL aerosols concentrations were quantified by an ARTI Hand Held Particle Counter. Geometric Mean (GM) relative efficiency of N95 respirators and surgical masks challenged with endospore bioaerosol ranged from 34-65%. In PSL aerosol experiments, GM relative efficiency ranged from 35-64% for 1.3 μm particles. GM filtration efficiency of all N95 and surgical N95 respirators filter media evaluated was ≥99% when challenged with particles ≥0.1 μm. GM filtration efficiency of surgical mask filter media ranged from 70-83% with particles ≥0.1 μm and 74-92% with 1.3 μm PSL particles. Relative efficiencies of N95 respirators and surgical masks challenged with aerosolized B. anthracis endospores and PSL were similar. Relative efficiency was similar between N95 respirators and surgical masks on a manikin head form despite clear differences in filtration efficiency. This study further highlights the importance of face seal leakage in the respiratory protection provided by N95 respirators, and demonstrates it on a human surrogate.

Surgical face masks worn by patients with multidrug-resistant tuberculosis: impact on infectivity of air on a hospital ward

RATIONALE

Drug-resistant tuberculosis transmission in hospitals threatens staff and patient health. Surgical face masks used by patients with tuberculosis (TB) are believed to reduce transmission but have not been rigorously tested.

OBJECTIVES

We sought to quantify the efficacy of surgical face masks when worn by patients with multidrug-resistant TB (MDR-TB).

METHODS

Over 3 months, 17 patients with pulmonary MDR-TB occupied an MDR-TB ward in South Africa and wore face masks on alternate days. Ward air was exhausted to two identical chambers, each housing 90 pathogen-free guinea pigs that breathed ward air either when patients wore surgical face masks (intervention group) or when patients did not wear masks (control group). Efficacy was based on differences in guinea pig infections in each chamber.

MEASUREMENTS AND MAIN RESULTS

Sixty-nine of 90 control guinea pigs (76.6%; 95% confidence interval [CI], 68-85%) became infected, compared with 36 of 90 intervention guinea pigs (40%; 95% CI, 31-51%), representing a 56% (95% CI, 33-70.5%) decreased risk of TB transmission when patients used masks.

CONCLUSIONS

Surgical face masks on patients with MDR-TB significantly reduced transmission and offer an adjunct measure for reducing TB transmission from infectious patients.

Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease

Background

Systems biology holds promise as a new approach to drug target identification and drug discovery against neglected tropical diseases. Genome-scale metabolic reconstructions, assembled from annotated genomes and a vast array of bioinformatics/biochemical resources, provide a framework for the interrogation of human pathogens and serve as a platform for generation of future experimental hypotheses. In this article, with the application of selection criteria for both Leishmania major targets (e.g. in silico gene lethality) and drugs (e.g. toxicity), a method (MetDP) to rationally focus on a subset of low-toxic Food and Drug Administration (FDA)-approved drugs is introduced.

Results

This metabolic network-driven approach identified 15 L. major genes as high-priority targets, 8 high-priority synthetic lethal targets, and 254 FDA-approved drugs. Results were compared to previous literature findings and existing high-throughput screens. Halofantrine, an antimalarial agent that was prioritized using MetDP, showed noticeable antileishmanial activity when experimentally evaluated in vitro against L. major promastigotes. Furthermore, synthetic lethality predictions also aided in the prediction of superadditive drug combinations. For proof-of-concept, double-drug combinations were evaluated in vitro against L. major and four combinations involving the drug disulfiram that showed superadditivity are presented.

Conclusions

A direct metabolic network-driven method that incorporates single gene essentiality and synthetic lethality predictions is proposed that generates a set of high-priority L. major targets, which are in turn associated with a select number of FDA-approved drugs that are candidate antileishmanials. Additionally, selection of high-priority double-drug combinations might provide for an attractive and alternative avenue for drug discovery against leishmaniasis.

Effectiveness of selected surgical masks in arresting vegetative cells and endospores when worn by simulated contagious patients

OBJECTIVE

The objective of this study was to quantify the effectiveness of selected surgical masks in arresting vegetative cells and endospores in an experimental model that simulated contagious patients.

SETTING

Laboratory.

METHODS

Five commercially available surgical masks were tested for their ability to arrest infectious agents. Surgical masks were placed over the nose and mouth of mannequin head forms (Simulaids adult model Brad CPR torso). The mannequins were retrofitted with a nebulizer attached to an automated breathing simulator calibrated to a tidal volume of 500 mL/breath and a breathing rate of 20 breaths/min, for a minute respiratory volume of 10 L/min. Aerosols of endospores or vegetative cells were generated with a modified microbiological research establishment-type 6-jet collision nebulizer, while air samples were taken with all-glass impinger (AGI-30) samplers downstream of the point source. All experiments were conducted in a horizontal bioaerosol chamber.

RESULTS

Mean arrestance of bioaerosols by the surgical masks ranged from 48% to 68% when the masks were challenged with endospores and from 66% to 76% when they were challenged with vegetative cells. When the arrestance of endospores was evaluated, statistical differences were observed between some pairs, though not all, of the models evaluated. There were no statistically significant differences in arrestance observed between models of surgical masks challenged with vegetative cells.

CONCLUSIONS

The arrestance of airborne vegetative cells and endospores by surgical masks worn by simulated contagious patients supports surgical mask use as one of the recommended cough etiquette interventions to limit the transmission of airborne infectious agents.

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

Background

Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR) relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model.

Results

We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae.

Conclusion

The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.

Feasibility of selected prophylactic barriers in arrestance of airborne bacterial vegetative cells and endospores

BACKGROUND

Transmission of infection by airborne agents is a risk for health care personnel, patients, and visitors. This risk is heightened in regions without access to environmental controls and personal protective equipment. The ability of 2 prophylactic barriers (ie, semitransparent netting for insect control) to arrest bioaerosols was assessed for potential use within the malarial zones.

METHODS

Barriers (pore sizes of 0.8 mm and 0.25 mm) were challenged with bioaerosols of vegetative cells and endospores of Bacillus anthracis strain Sterne 34F2 using a bioaerosol chamber. Barriers were also challenged with airborne inert polystyrene latex particles of known diameters (0.1, 0.43, 0.6, 1.3, 3.2, and 8.0 μm), and the arrestance provided by barrier with the 0.25 mm pore size was expressed as a function of aerodynamic diameter of challenge aerosols.

RESULTS

Barrier with the 0.8 mm pore size provided no significant arrestance of aerosols, whereas the barrier with the 0.25 mm pore size provided an 8% arrestance of vegetative cells and a 13% arrestance of endospores. No arrestance at or below the 0.6 μm particle size was observed.

CONCLUSION

The level of arrestance provided by these prophylactic barriers does not justify their use as a sole method of preventing transmission.

Functional integration of a metabolic network model and expression data without arbitrary thresholding

MOTIVATION

Flux balance analysis (FBA) has been used extensively to analyze genome-scale, constraint-based models of metabolism in a variety of organisms. The predictive accuracy of such models has recently been improved through the integration of high-throughput expression profiles of metabolic genes and proteins. However, extensions of FBA often require that such data be discretized a priori into sets of genes or proteins that are either 'on' or 'off'. This procedure requires selecting relatively subjective expression thresholds, often requiring several iterations and refinements to capture the expression dynamics and retain model functionality.

RESULTS

We present a method for mapping expression data from a set of environmental, genetic or temporal conditions onto a metabolic network model without the need for arbitrary expression thresholds. Metabolic Adjustment by Differential Expression (MADE) uses the statistical significance of changes in gene or protein expression to create a functional metabolic model that most accurately recapitulates the expression dynamics. MADE was used to generate a series of models that reflect the metabolic adjustments seen in the transition from fermentative- to glycerol-based respiration in Saccharomyces cerevisiae. The calculated gene states match 98.7% of possible changes in expression, and the resulting models capture functional characteristics of the metabolic shift.

AVAILABILITY

MADE is implemented in Matlab and requires a mixed-integer linear program solver. Source code is freely available at http://www.bme.virginia.edu/csbl/downloads/.

A scalable systems analysis approach for regulated metabolic networks

High-throughput data such as genome sequencing and genome expression profiling have enabled the reconstruction of cellular networks. These networks have been represented in computational frameworks that can be used to make testable predictions concerning phenotypes under a variety of experimental conditions and multiple molecular perturbations. This presentation will detail several recent advances in the analysis of these networks as well as provide an outlook of remaining challenges.

Tuberculosis infection control in resource-limited settings in the era of expanding HIV care and treatment

The opportunities for human immunodeficiency virus (HIV) care and treatment created by new treatment initiatives promoting universal access are also creating unprecedented opportunities for persons with HIV-associated immunosuppression to be exposed to patients with infectious tuberculosis (TB) within health care facilities, with the attendant risks of acquiring TB infection and developing TB disease. Infection control measures can reduce the risk of Mycobacterium tuberculosis transmission even in settings with limited resources, on the basis of a 3-level hierarchy of controls, including administrative or work practice, environmental controls, and respiratory protection. Further research is needed to define the most efficient interventions. The importance of preventing transmission of M. tuberculosis in the era of expanding HIV care and treatment in resource-limited settings must be recognized and addressed.

Development of an empirical model to aid in designing airborne infection isolation rooms

Airborne infection isolation rooms (AIIRs) house patients with tuberculosis, severe acute respiratory syndrome (SARS), and many other airborne infectious diseases. Currently, facility engineers and designers of heating, ventilation, and air-conditioning (HVAC) systems have few analytical tools to estimate a room's leakage area and establish an appropriate flow differential (DeltaQ) in hospitals, shelters, and other facilities where communicable diseases are present. An accurate estimate of leakage area and selection of DeltaQ is essential for ensuring that there is negative pressure (i.e., pressure differential [DeltaP]) between an AIIR and adjoining areas. National Institute for Occupational Safety and Health (NIOSH) researchers evaluated the relationship between DeltaQ and DeltaP in 67 AIIRs across the United States and in simulated AIIR. Data gathered in the simulated AIIR was used to develop an empirical model describing the relationship between DeltaQ, DeltaP, and leakage area. Data collected in health care facilities showed that the model accurately predicted the leakage area 44 of 48 times. Statistical analysis of the model and experimental validation showed that the model effectively estimated the actual leakage area from -39% to +22% with 90% confidence. The NIOSH model is an effective, cost-cutting tool that can be used by HVAC engineers and designers to estimate leakage area and select an appropriate DeltaQ in AIIRs to reduce the airborne transmission of disease.

Guidelines for preventing the transmission of Mycobacterium tuberculosis in health-care settings, 2005

In 1994, CDC published the Guidelines for Preventing the Transmission of Mycobacterium tuberculosis in HealthCare Facilities, 1994. The guidelines were issued in response to 1) a resurgence of tuberculosis (TB) disease that occurred in the United States in the mid-1980s and early 1990s, 2) the documentation of several high-profile health-care--associated (previously termed "nosocomial") outbreaks related to an increase in the prevalence of TB disease and human immunodeficiency virus (HIV) coinfection, 3) lapses in infection control practices, 4) delays in the diagnosis and treatment of persons with infectious TB disease, and 5) the appearance and transmission of multidrug-resistant (MDR) TB strains. The 1994 guidelines, which followed statements issued in 1982 and 1990, presented recommendations for TB infection control based on a risk assessment process that classified health-care facilities according to categories of TB risk, with a corresponding series of administrative, environmental, and respiratory protection control measures. The TB infection control measures recommended by CDC in 1994 were implemented widely in health-care facilities in the United States. The result has been a decrease in the number of TB outbreaks in health-care settings reported to CDC and a reduction in health-care-associated transmission of Mycobacterium tuberculosis to patients and health-care workers (HCWs). Concurrent with this success, mobilization of the nation's TB control programs succeeded in reversing the upsurge in reported cases of TB disease, and case rates have declined in the subsequent 10 years. Findings indicate that although the 2004 TB rate was the lowest recorded in the United States since national reporting began in 1953, the declines in rates for 2003 (2.3%) and 2004 (3.2%) were the smallest since 1993. In addition, TB infection rates greater than the U.S. average continue to be reported in certain racial/ethnic populations. The threat of MDR TB is decreasing, and the transmission of M. tuberculosis in health-care settings continues to decrease because of implementation of infection-control measures and reductions in community rates of TB. Given the changes in epidemiology and a request by the Advisory Council for the Elimination of Tuberculosis (ACET) for review and update of the 1994 TB infection control document, CDC has reassessed the TB infection control guidelines for health-care settings. This report updates TB control recommendations reflecting shifts in the epidemiology of TB, advances in scientific understanding, and changes in health-care practice that have occurred in the United States during the preceding decade. In the context of diminished risk for health-care-associated transmission of M. tuberculosis, this document places emphasis on actions to maintain momentum and expertise needed to avert another TB resurgence and to eliminate the lingering threat to HCWs, which is mainly from patients or others with unsuspected and undiagnosed infectious TB disease. CDC prepared the current guidelines in consultation with experts in TB, infection control, environmental control, respiratory protection, and occupational health. The new guidelines have been expanded to address a broader concept; health-care--associated settings go beyond the previously defined facilities. The term "health-care setting" includes many types, such as inpatient settings, outpatient settings, TB clinics, settings in correctional facilities in which health care is delivered, settings in which home-based health-care and emergency medical services are provided, and laboratories handling clinical specimens that might contain M. tuberculosis. The term "setting" has been chosen over the term "facility," used in the previous guidelines, to broaden the potential places for which these guidelines apply.

Test for the integrity of environmental tractor cab filtration systems

Cab filtration systems can be used to protect vehicle operators from hazardous air contaminants. In a cab filtration system, a fan draws air through filters and pressurizes the cab with this filtered air. This article describes the application of a low-cost, optical particle counter to evaluate the performance of tractor cab filtration systems. The tractors were equipped with environmental enclosures to protect the operators from pesticide exposures that occur during air blast spraying in orchards. Prior to testing, all environmental tractor cabs underwent a complete maintenance overhaul followed by a careful inspection by the manufacturer's field representative. As part of this maintenance effort, 13 tractors with cab filtration systems were tested in an enclosure. A Met One model 227B two-channel optical particle counter was used to measure the aerosol concentration outside and inside the cab. Ambient aerosol and/or aerosol generated by burning incense sticks were used to challenge the stationary cab filtration system in an enclosure. The ratio of the outside to inside concentration (Co/Ci) is the exposure reduction attained by the cab system. Alternatively, the inside concentration divided by the outside concentration times 100 (Ci/Co x 100) gives the percent penetration. All 13 tractors were tested for leak sites. Leak sites were identified and sealed. This process was repeated until each cab showed an exposure reduction ratio Co/Ci of at least 50 (aerosol penetration into the cab Ci/Co x 100 was less than 2%) at the 0.3-0.5 microm particle size interval.

Reducing respirator fit test errors: a multi-donning approach

As a continuation of recent studies to assess the accuracy of existing fit test methods, a multi-donning approach to fit testing is presented. As an example of that approach, a multi-donning quantitative fit test for filtering-facepiece respirators is presented and analyzed by comparing its error rates with those of the single-donning approach of current fit test methods. That analysis indicates the multi-donning fit test has the potential to reduce both the alpha error and the beta error to half that of single-donning fit tests. The alpha error is the error of failing a respirator that should pass; the beta error is the error of passing a respirator that should fail. Lowering fit test error rates for filtering-facepiece respirators is important because fit testing is an essential means of helping assure that an individual has selected an adequately fitting respirator. To reduce the alpha and beta error inherent in current fit test methods, the proposed fit test for filtering-facepiece respirators incorporates five donnings of the facepiece, unlike the single donning of existing fit test methods. The analysis presented here indicates that the multiple-donning approach reduces the element of chance in the fit test result and thereby increases the consistency and accuracy of the fit tests. The time to conduct the multi-donning test can approximate the time for current, single-donning tests by shortening the time the respirator is worn after each donning to about 10 sec. And, unlike current fit tests for filtering-facepieces that measure only faceseal leakage, the example multiple-donning fit test considered here is based on a measurement of total leakage (faceseal plus filter). Utilizing total respirator leakage can result in simpler quantitative fit test instrumentation and a fit test that is more relevant to the workplace. Further trials with human subjects are recommended in order to validate the proposed multi-donning approach.

Fitting characteristics of eighteen N95 filtering-facepiece respirators

Four performance measures were used to evaluate the fitting characteristics of 18 models of N95 filtering-facepiece respirators: (1) the 5th percentile simulated workplace protection factor (SWPF) value, (2) the shift average SWPF value, (3) the h-value, and (4) the assignment error. The effect of fit-testing on the level of protection provided by the respirators was also evaluated. The respirators were tested on a panel of 25 subjects with various face sizes. Simulated workplace protection factor values, determined from six total penetration (face-seal leakage plus filter penetration) tests with re-donning between each test, were used to indicate respirator performance. Five fit-tests were used: Bitrex, saccharin, generated aerosol corrected for filter penetration, PortaCount Plus corrected for filter penetration, and the PortaCount Plus with the N95-Companion accessory. Without fit-testing, the 5th percentile SWPF for all models combined was 2.9 with individual model values ranging from 1.3 to 48.0. Passing a fit-test generally resulted in an increase in protection. In addition, the h-value of each respirator was computed. The h-value has been determined to be the population fraction of individuals who will obtain an adequate level of protection (i.e., SWPF >/=10, which is the expected level of protection for half-facepiece respirators) when a respirator is selected and donned (including a user seal check) in accordance with the manufacturer's instructions without fit-testing. The h-value for all models combined was 0.74 (i.e., 74% of all donnings resulted in an adequate level of protection), with individual model h-values ranging from 0.31 to 0.99. Only three models had h-values above 0.95. Higher SWPF values were achieved by excluding SWPF values determined for test subject/respirator combinations that failed a fit-test. The improvement was greatest for respirator models with lower h-values. Using the concepts of shift average and assignment error to measure respirator performance yielded similar results. The highest level of protection was provided by passing a fit-test with a respirator having good fitting characteristics.

Correlation between quantitative fit factors and workplace protection factors measured in actual workplace environments at a steel foundry

Past studies have found little or no correlation between workplace protection factors (WPFs) and quantitative fit factors (FFs). This study investigated the effect of good- and poor-fitting half-facepiece, air-purifying respirators on protection in actual workplace environments at a steel foundry and the correlation between WPFs and FFs. Fifteen burners and welders, who wore respirators voluntarily, and chippers participated in this study. Each subject was fit-tested with two respirator models each with three sizes, for a total of six fit-tests. Models and sizes were assigned this way to provide a wide range of FFs among study participants. Each worker donned the respirator twice per day (at the beginning of the shift and following the lunch break) for 2 days. Quantitative FFs were first obtained for each donning using the PortaCount Plus trade mark in a separate room. Without redonning the respirators, workers performed normal work for 1 to 2 hours, and WPFs were measured by collecting ambient and in-facepiece samples simultaneously. A second fit-test was conducted without disturbing the respirator. FFs were obtained by averaging the results from the first and second fit-tests. The resulting FFs had a geometric mean (GM) of 400 (range=10-6010) and a geometric standard deviation (GSD) of 6.1. Of the 55 valid donnings, 43 were good fitting (FFs> or =100) and 12 were poor fitting (FFs<100). The WPFs had a GM of 920 (range=13-230,000) and a GSD of 17.8. The WPFs were found to be significantly correlated with the FFs (R(2)=.55 and p-value=.0001). Therefore, FF was shown to be a meaningful indicator of respirator performance in actual workplace environments.

Environmental agricultural tractor cab filter efficiency and field evaluation

To evaluate filter efficiency and performance of environmental enclosures for tractors, 3- to 4-year-old tractor enclosure combinations (cabs retrofitted to tractors after manufacturing) were studied at a custom pesticide applicators facility. Optical particle counters were used to measure the aerosol number concentration inside and outside the cab. The ratio of these concentrations multiplied by 100 is termed percentage penetration, the amount of the aerosol that penetrates into the enclosure. For particles in the 0.3 to 0.4 microm range, penetration into the cab was reduced from 11 to 0.4% in the following sequential steps. First, manufacturing mistakes were corrected by fixing a bowed flange and inappropriate sealing of the sheet metal used to separate incoming air from air that had passed through the filter. This reduced aerosol penetration from 11 to 4.8%. Replacing gasket material on the used filter reduced penetration from 4.8 to 0.65%. This suggests that the filter gaskets are deforming and allowing leakage. Also, the filter media were evaluated for aerosol penetration as a function of particle size and were tested per the criteria stipulated in 42 CFR 84 for negative pressure air-purifying particulate respirators. These results showed penetration through the filter media of less than 0.03%, indicating that filter media were not a major source of aerosol leakage into the cab. The results suggest that the manufacturer should implement a quality control program to ensure that minimal aerosol penetration criteria into the cabs are met and an acceptable maintenance program exists to ensure compliance. Furthermore, the degradation of filter gasket material over time needs to be minimized to ensure that the environmental cabs continue to provide acceptable performance.

Comparison of five methods for fit-testing N95 filtering-facepiece respirators

Five fit-testing methods (Bitrex, ambient aerosol condensation nuclei counter using the TSI PortaCount Plus, saccharin, modified ambient aerosol condensation nuclei counter using the TSI PortaCount Plus with the N95-Companion, and generated aerosol using corn oil) were evaluated for their ability to identify poorly fitting N95 filtering-facepiece respirators. Eighteen models of NIOSH-certified, N95 filtering-facepiece respirators were tested by a panel of 25 subjects using each fit-testing method. The penetration of the corn oil and the ambient aerosols through the filter media of each respirator was measured in order to adjust the corresponding generated and ambient aerosol overall fit factors, reflecting only face-seal leakage. Fit-testing results were compared to 5th percentiles of simulated workplace protection factors. Beta errors (the chance of passing a fit-test in error) ranged from 3 percent to 11 percent. Alpha errors (the chance of failing a fit-test in error) ranged from 51 percent to 84 percent. The ambient aerosol using the TSI PortaCount Plus and the generated aerosol methods identified poorly fitting respirators better than the saccharin, the Companion, and Bitrex methods. These errors rates should be considered when selecting a fit-testing method for fitting N95 filtering-facepieces. When both types of errors were combined as an assignment error, the ambient aerosol method using the TSI PortaCount Plus had the lowest percentage of wearers being assigned a poor-fitting respirator.

Comparison of five methods for fit-testing N95 filtering-facepiece respirators

Five fit-testing methods (Bitrex, ambient aerosol condensation nuclei counter using the TSI PortaCount Plus, saccharin, modified ambient aerosol condensation nuclei counter using the TSI PortaCount Plus with the N95-Companion, and generated aerosol using corn oil) were evaluated for their ability to identify poorly fitting N95 filtering-facepiece respirators. Eighteen models of NIOSH-certified, N95 filtering-facepiece respirators were tested by a panel of 25 subjects using each fit-testing method. The penetration of the corn oil and the ambient aerosols through the filter media of each respirator was measured in order to adjust the corresponding generated and ambient aerosol overall fit factors, reflecting only face-seal leakage. Fit-testing results were compared to 5th percentiles of simulated workplace protection factors. Beta errors (the chance of passing a fit-test in error) ranged from 3 percent to 11 percent. Alpha errors (the chance of failing a fit-test in error) ranged from 51 percent to 84 percent. The ambient aerosol using the TSI PortaCount Plus and the generated aerosol methods identified poorly fitting respirators better than the saccharin, the Companion, and Bitrex methods. These errors rates should be considered when selecting a fit-testing method for fitting N95 filtering-facepieces. When both types of errors were combined as an assignment error, the ambient aerosol method using the TSI PortaCount Plus had the lowest percentage of wearers being assigned a poor-fitting respirator.

Improving the health of workers in indoor environments: priority research needs for a national occupational research agenda

Indoor nonindustrial work environments were designated a priority research area through the nationwide stakeholder process that created the National Occupational Research Agenda. A multidisciplinary research team used member consensus and quantitative estimates, with extensive external review, to develop a specific research agenda. The team outlined the following priority research topics: building-influenced communicable respiratory infections, building-related asthma/allergic diseases, and nonspecific building-related symptoms; indoor environmental science; and methods for increasing implementation of healthful building practices. Available data suggest that improving building environments may result in health benefits for more than 15 million of the 89 million US indoor workers, with estimated economic benefits of $5 to $75 billion annually. Research on these topics, requiring new collaborations and resources, offers enormous potential health and economic returns.

Sampling and analytical method development for qualitative assessment of airborne mycobacterial species of the Mycobacterium tuberculosis complex

This article presents a novel, qualitative approach for detecting airborne M. tuberculosis. Culturing or sample purification is not required. A DNA diagnostic method involving the polymerase chain reaction (PCR) coupled to an enzymatically generated color reaction was used for direct detection of M. bovis BCG (Bacillus of Calmette-Guérin), a surrogate for pathogenic M. tuberculosis. Fewer than 10 mycobacteria were detected with no culturing using this bioanalytical method. Analysis was completed in 1 to 1.5 days, in contrast to traditional culturing methods requiring a minimum of 2-3 weeks. To evaluate an air sampling method coupled to a PCR bioanalytical method, liquid cultures of the surrogate were aerosolized and collected for PCR analyses using 37-mm filter cassettes containing polytetrafluoroethylene filters. An Andersen six-stage (viable) particle sizing sampler was employed as a reference sampler. Aerosolized BCG impacted onto Andersen agar plates required incubation periods of 6-8 weeks before small colony forming units could be detected and enumerated. Although the BCG mean length of the rod-shaped particles was 8.3 microns, the airborne BCG particles were collected predominantly on the Andersen 4-6 stages, representing aerodynamic diameters 0.7 to 3.3 microns. Approximately 25 mycobacteria were detected without culturing using the PCR-filter cassette method. This approach could be used to detect airborne mycobacterial species of the M. tuberculosis complex and could permit the early detection of contaminated indoor air. Also, the efficacy of environmental controls could be evaluated and monitored. This approach could also be used to study the expulsion of infectious particles from patients and may permit risk assessment in regard to personal respiratory protection.

Method for Evaluating Germicidal Ultraviolet Inactivation of Biocontaminated Surfaces

Safety issues related to work-site conditions often deal with potential worker exposure to infectious airborne microorganisms due to their dissemination in indoor air and contamination of surfaces. Germicidal ultraviolet (GUV) radiation is used in health-care settings and other occupational environments for microbial inactivation. In this study, a new methodology for determining the efficiency of GUV microbial inactivation of surfaces was developed and evaluated. The method utilizes identical chambers in which test microorganisms are irradiated on agar surfaces at different humidity and irradiation intensity levels. The effects of GUV intensity and exposure time on microbial inactivation were examined for Micrococcus luteus and Serratia marcescens. It was found that at low humidity levels (20-25%) both organisms can be inactivated with at least 95% efficiency if the GUV intensity exceeds 50 μW/cm² for at least 3-5 min (corresponding to a dose of ~ 10 mJ/cm²). The radiation dose needed for effective inactivation of S. marcescens, as measured by a UV meter near the microbial sample, was found not to be affected by the humidity level, whereas that of M. luteus increased at higher humidities. The findings of this study can be used to determine sufficient GUV inactivation doses for occupational environments with various microbial contaminations.

Evaluation of standard and modified sampling heads for the International PBI Surface Air System bioaerosol samplers

This study substituted sampling heads with smaller holes to collect small particles with the International PBI Surface Air System (SAS) battery-powered, bioaerosol air samplers, which have proved inefficient in collecting small airborne particles such as free bacteria (e.g., < 2 microns). An Andersen six-stage (6-STG) sampler was used simultaneously with two SAS samplers (SAS high flow [SAS-HF] and Compact SAS [SAS-C]) to sample indoor air in two office environments. Discrepancies were observed in the flow rate results obtained using the manufacturer's Pitot Validation Kit (PVK). Air sampling results suggested no significant difference in the concentration of bacteria and fungi collected among the four sampling heads using either sampler model in a small sample (n = 5) at either site. However, with an additional 15 samples at Site B (n = 5 + 15 = 20), three of the four sampling heads statistically undersampled the 6-STG and the other sampling head. The field data were variable (geometric standard deviation [GSD] = 1.25-1.94 for bacteria; GSD = 1.18-3.51 for fungi), but within ranges previously observed. The manufacturer increased particle collection efficiency by decreasing the hole size; however, this increase was only noticeable after many replicates. The PVK may be used as an accurate flow rate measurement device with the SAS-HF sampler, though the Pitot tube measures only centerline velocity pressure. Because of the 10% decrease in flow rate resulting from the pressure drop across the PVK, the equation in the manufacturer's literature for calculation of average velocities (VAVG) provides a reasonable estimate of flow rate through the SAS-C sampler.

Evaluation and control of worker exposure to fungi in a beet sugar refinery

A study of worker exposure to airborne fungi was undertaken in a sugar beet refinery to evaluate the level of exposure and to determine if controls could be implemented that would lower these exposures. A previous study at this refinery identified one worker who reacted on challenge testing to the moldy but not the fresh sugar beet pulp, had specific Immunoglobulin G to Aspergillus niger, and specific Immunoglobulin E to Aspergillus. Also, two employees were diagnosed with occupational asthma. In the study reported here, two field surveys were conducted, the first during the sugar production campaign (January) and the second during postproduction cleanup and maintenance (June). Approximately 65 personal and area air samples were collected on polycarbonate filters and the culturable fungal spores were identified and enumerated. This study showed high exposure of pellet loaders and pellet silo workers to various species of Aspergillus. Other fungal species that might pose a health hazard were detected. Exposures to fungi during the postproduction cleanup and maintenance phase were much higher than those measured during the production campaign. Engineering controls that would reduce employee exposure are discussed.

Evaluation of eight bioaerosol samplers challenged with aerosols of free bacteria

The need to quantify airborne microorganisms in the commercial microbiology industry (biotechnology) and during evaluations of indoor air quality, infectious disease outbreaks, and agriculture health investigations has shown there is a major technological void in bioaerosol sampling techniques to measure and identify viable and nonviable aerosols. As commercialization of microbiology increases and diversifies, it is increasingly necessary to assess occupational exposure to bioaerosols. Meaningful exposure estimates, by using area or environmental samplers, can only be ensured by the generation of data that are both precise and accurate. The Andersen six-stage viable (microbial) particle sizing sampler (6-STG) and the Ace Glass all-glass impinger-30 (AGI-30) have been suggested as the samplers of choice for the collection of viable microorganisms by the International Aerobiology Symposium and the American Conference of Governmental Industrial Hygienists. Some researchers consider these samplers inconvenient for evaluating industrial bioprocesses and indoor or outdoor environments. Alternative samplers for the collection of bioaerosols are available; however, limited information has been reported on their collection efficiencies. A study of the relative sampling efficiencies of eight bioaerosol samplers has been completed. Eight samplers were individually challenged with a bioaerosol, created with a Collison nebulizer, of either Bacillus subtilis or Escherichia coli. The samplers were evaluated under controlled conditions in a horizontal bioaerosol chamber. During each experimental run, simultaneous samples were collected with a reference AGI-30 to verify the concentration of microorganisms in the chamber from run to run and day to day.(ABSTRACT TRUNCATED AT 250 WORDS)

Phase I alternate-day dose study of chromomycin A3

Chromomycin A3 was given to 43 patients with metastatic cancer in order to determine the tolerable dose when the drug was administered on an every-other-day dose schedule for a total of five iv push injections, with the course of therapy being repeated every 4 weeks. At least three patients were entered at each dose level, graduated in 0.1-mg/m2 increments between 0.7 and 1.6 mg/m2. The most common (19 patients) side effect was nausea and/or vomiting, but this was usually mild, lasted for a few hours, and diminished in severity with repeated injections. Skin necrosis due to drug extravasation was a problem early in the study, but was eliminated by injecting the drug through iv tubing. Transient elevations in SGOT and alkaline phosphatase levels were observed, but proved not to be of serious consequence. Renal toxicity proved to be the limiting factor in therapy. However, a dose level of 1.3 mg/m2 was found to be a tolerable level of drug administration in previously untreated patients. Objective tumor responses were noted in four patients (Hodgkin's disease, embryonal rhabdomyosarcoma, adenocarcinoma of the lung, and malignant melanoma).