In vitro and in vivo studies of a rapid and selective breath test for tuberculosis based upon mycobacterial CO dehydrogenase

Microbial oxidation of atmospheric trace gases

The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H₂), carbon monoxide (CO) and methane (CH₄). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H₂ and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH₄, H₂ and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.

Biodiagnostics in an era of global pandemics-From biosensing materials to data management

The novel corona virus SARS-CoV-2 (COVID-19) has exposed the world to challenges never before seen in fast diagnostics, monitoring, and prevention of the outbreak. As a result, different approaches for fast diagnostic and screening are made and yet to find the ideal way. The current mini-review provides and examines evidence-based innovative and rapid chemical sensing and related biodiagnostic solutions to deal with infectious disease and related pandemic emergencies, which could offer the best possible care for the general population and improve the approachability of the pandemic information, insights, and surrounding contexts. The review discusses how integration of sensing devices with big data analysis, artificial Intelligence or machine learning, and clinical decision support system, could improve the accuracy of the recorded patterns of the disease conditions within an ocean of information. At the end, the mini-review provides a prospective on the requirements to improve our coping of the pandemic-related biodiagnostics as well as future opportunities.

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists

Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.

A Review of Analytical Techniques and Their Application in Disease Diagnosis in Breathomics and Salivaomics Research

The application of metabolomics to biological samples has been a key focus in systems biology research, which is aimed at the development of rapid diagnostic methods and the creation of personalized medicine. More recently, there has been a strong focus towards this approach applied to non-invasively acquired samples, such as saliva and exhaled breath. The analysis of these biological samples, in conjunction with other sample types and traditional diagnostic tests, has resulted in faster and more reliable characterization of a range of health disorders and diseases. As the sampling process involved in collecting exhaled breath and saliva is non-intrusive as well as comparatively low-cost and uses a series of widely accepted methods, it provides researchers with easy access to the metabolites secreted by the human body. Owing to its accuracy and rapid nature, metabolomic analysis of saliva and breath (known as salivaomics and breathomics, respectively) is a rapidly growing field and has shown potential to be effective in detecting and diagnosing the early stages of numerous diseases and infections in preclinical studies. This review discusses the various collection and analyses methods currently applied in two of the least used non-invasive sample types in metabolomics, specifically their application in salivaomics and breathomics research. Some of the salient research completed in this field to date is also assessed and discussed in order to provide a basis to advocate their use and possible future scientific directions.

Detecting virulence and drug-resistance mycobacterial phenotypes in vivo

Bacterial phenotypes are predominantly studied in culture because detection of their specific metabolic pathways in the host is challenging. Development of stable-isotope breath tests, allowing in situ phenotype analyses, may endow diagnostics with new modalities based upon direct monitoring of in vivo microbial metabolism and host-pathogen phenotypic interactions.

Rapid in vivo detection of isoniazid-sensitive Mycobacterium tuberculosis by breath test

There is urgent need for rapid, point of care diagnostic tools for tuberculosis (TB) and drug sensitivity. Current methods based on in vitro growth take weeks, while DNA amplification can neither differentiate live from dead organisms nor determine phenotypic drug resistance. Here we show the development and evaluation of a rapid breath test for isoniazid (INH)-sensitive TB based on detection of labeled N₂ gas formed specifically from labeled INH by mycobacterial KatG enzyme. In vitro data shows the assay is specific, dependent on mycobacterial abundance, and discriminates between INH-sensitive and resistant (S315T mutant KatG) TB. In vivo, the assay is rapid with maximal detection of ¹⁵N₂ in exhaled breath of infected rabbits within five to ten minutes. No increase in ¹⁵N₂ is detected in un-infected animals, and the increases in ¹⁵N₂ are dependent on infection dose. This test may allow rapid detection of INH-sensitive TB.