Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape

First time whole genome sequencing of Mycobacterium bovis from the environment supports transmission at the animal-environment interface

Spreading of Mycobacterium bovis causing animal tuberculosis (TB) at livestock-wildlife-environment interfaces remains a significant problem. Recently, we provided evidence of widespread environmental contamination of an endemic animal TB setting with viable and dormant M. bovis cells able to recover metabolic activity, making indirect transmission via environmental contamination plausible. We now report the first whole genome sequences of M. bovis recovered from the environment. We establish epidemiological links at the environment-animal interface by phylogenomic comparison of these M. bovis genomes with those isolated from livestock and wild ungulates from the same area. Environmental and animal genomes are highly intertwined and distribute similarly into the same M. bovis lineages, supporting several instances of environmental contamination. This study provides compelling evidence of M. bovis excretion into the environment and viability maintenance, supporting the environment as a potential source of new infection. These insights have clear implications for policy formulation, advocating environmental surveillance and an ecosystem perspective in TB control programs. ENVIRONMENTAL IMPLICATION: We report the first whole genome sequences of M. bovis from the environment and establish epidemiological links at the environment-animal interface, demonstrating close phylogenomic relatedness of animal and environmental M. bovis. Definitive evidence of M. bovis excretion into the environment with viability maintenance is provided, supporting the environment as a potential source of new infection. Implications of this work include methodological innovations offering a tool to resolve indirect transmission chains and support customized biosecurity measures. Policy formulation aiming at the control of animal tuberculosis and cost mitigation should consider these findings, encouraging environmental surveillance in official eradication programmes.

Spatial spillover effect of environmental factors on the tuberculosis occurrence among the elderly: a surveillance analysis for nearly a dozen years in eastern China

BACKGROUND

In many areas of China, over 30% of tuberculosis cases occur among the elderly. We aimed to investigate the spatial distribution and environmental factors that predicted the occurence of tuberculosis in this group.

METHODS

Data were collected on notified pulmonary tuberculosis (PTB) cases aged ≥ 65 years in Zhejiang Province from 2010 to 2021. We performed spatial autocorrelation and spatial-temporal scan statistics to determine the clusters of epidemics. Spatial Durbin Model (SDM) analysis was used to identify significant environmental factors and their spatial spillover effects.

RESULTS

77,405 cases of PTB among the elderly were notified, showing a decreasing trend in the notification rate. Spatial-temporal analysis showed clustering of epidemics in the western area of Zhejiang Province. The results of the SDM indicated that a one-unit increase in PM2.5 led to a 0.396% increase in the local notification rate. The annual mean temperature and precipitation had direct effects and spatial spillover effects on the rate, while complexity of the shape of the greenspace (SHAPE_AM) and SO2 had negative spatial spillover effects.

CONCLUSION

Targeted interventions among the elderly in Western Zhejiang may be more efficient than broad, province-wide interventions. Low annual mean temperature and high annual mean precipitation in local and neighboring areas tend to have higher PTB onset among the elderly.

Assessing risks for bovine and zoonotic tuberculosis through spatial analysis and a questionnaire survey in Fiji - A pilot study

Mycobacterium bovis causes tuberculosis in cattle and when transmitted to humans typically causes extra-pulmonary tuberculosis (EPTB). Bovine tuberculosis (bTB) has a global distribution and is controlled in most countries to protect animal and public health. Recent studies revealed that bTB is established on dairy farms in Fiji where EPTB cases have been reported in people. The aims of this pilot investigation were to look for putative zoonotic TB (EPTB) cases in people and to evaluate practices that might contribute to the persistence and transmission of M. bovis between cattle and to humans. Existing data sets were shared between the Fiji Ministry of Agriculture and Ministry of Health and a questionnaire-based survey was implemented using One Health principles. Statistically significant co-location and close proximity of EPTB cases and bovine TB affected farms were identified. The bTB infection status of farms was significantly associated with unfenced water sources where cattle grazed. Of 247 households, 65 % shared drinking water sources with cattle and 36 % consumed raw milk without boiling, while 62 % of participants reported backyard slaughter of cattle. Several participants reported current symptoms potentially suggestive of TB (chronic cough) but the impact of smoking and history of previous TB treatment could not be evaluated. Farmers had limited understanding of the practices required to prevent bTB at farm level. Further study is recommended and should include an assessment of lifetime EPTB diagnoses, classification of farms based on more recent bTB test data and molecular typing of mycobacterial isolates from humans, cattle and the environment. A targeted awareness and education approach is required to reduce the future risk of zoonotic TB and to help ensure uptake of recommendations and practices aimed at controlling and preventing bTB.

Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review

Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.

Vacuoles in the Breast: A Histologic Clue for an Unusual Presentation of an Atypical Organism

Infections with nontuberculous mycobacteria (NTM) are increasing in prevalence worldwide, and this group of organisms is emerging as significant clinical pathogens. We present a case of a 58-year-old female with persistent furuncles of the breast who was found to have an NTM infection. This case is unique for the lack of risk factors for NTM in the patient's history, the location of the infection in the breast, and the close cooperation needed across disciplines to arrive at the diagnosis. This multi-disciplinary discussion considers the classic clinical presentation of NTM, it is a characteristic morphological appearance on histopathology, the differential diagnosis, treatment, and the ultimate outcome of the case. This case report and discussion will assist both clinicians and pathologists in the diagnosis of this important infectious disease.

Mycobacterial cavity on chest computed tomography: clinical implications and deep learning-based automatic detection with quantification

Background

This study aimed (I) to investigate the clinical implication of computed tomography (CT) cavity volume in tuberculosis (TB) and non-tuberculous mycobacterial pulmonary disease (NTM-PD), and (II) to develop a three-dimensional (3D) nnU-Net model to automatically detect and quantify cavity volume on CT images.

Methods

We retrospectively included conveniently sampled 206 TB and 186 NTM-PD patients in a tertiary referral hospital, who underwent thin-section chest CT scans from 2012 through 2019. TB was microbiologically confirmed, and NTM-PD was diagnosed by 2007 Infectious Diseases Society of America/American Thoracic Society guideline. The reference cavities were semi-automatically segmented on CT images and a 3D nnU-Net model was built with 298 cases (240 cases for training, 20 for tuning, and 38 for internal validation). Receiver operating characteristic curves were used to evaluate the accuracy of the CT cavity volume for two clinically relevant parameters: sputum smear positivity in TB and treatment in NTM-PD. The sensitivity and false-positive rate were calculated to assess the cavity detection of nnU-Net using radiologist-detected cavities as references, and the intraclass correlation coefficient (ICC) between the reference and the U-Net-derived cavity volumes was analyzed.

Results

The mean CT cavity volumes in TB and NTM-PD patients were 11.3 and 16.4 cm³, respectively, and were significantly greater in smear-positive TB (P<0.001) and NTM-PD necessitating treatment (P=0.020). The CT cavity volume provided areas under the curve of 0.701 [95% confidence interval (CI): 0.620-0.782] for TB sputum positivity and 0.834 (95% CI: 0.773-0.894) for necessity of NTM-PD treatment. The nnU-Net provided per-patient sensitivity of 100% (19/19) and per-lesion sensitivity of 83.7% (41/49) in the validation dataset, with an average of 0.47 false-positive small cavities per patient (median volume, 0.26 cm³). The mean Dice similarity coefficient between the manually segmented cavities and the U-Net-derived cavities was 78.9. The ICCs between the reference and U-Net-derived volumes were 0.991 (95% CI: 0.983-0.995) and 0.933 (95% CI: 0.897-0.957) on a per-patient and per-lesion basis, respectively.

Conclusions

CT cavity volume was associated with sputum positivity in TB and necessity of treatment in NTM-PD. The 3D nnU-Net model could automatically detect and quantify mycobacterial cavities on chest CT, helping assess TB infectivity and initiate NTM-TB treatment.

Genomic, Metabolic, and Immunological Characterization of GMP-Grade Mycobacterium phlei

Mycobacterium phlei (M. phlei) is an understudied microbe with medical values as an immunomodulating agent. Here, we establish an industrial strain of M. phlei, CUD, and characterize its genomic, metabolic, and immunological profiles. The established strain has been stably passed for more than a decade, indicated by next-generation sequencing of its 5.3 Mb genome. We show that the intramuscular inoculation of heat-inactivated CUD in immunocompetent mice is well tolerated, and can mount immunological responses. Immunophenotyping demonstrates induced innate and adaptive immune responses in peripheral blood, spleen, and inguinal lymph nodes of CUD-treated mice. Using GC-TOF-MS, we find that the metabolomic profiles of different batches are highly concordant. These results demonstrate a highly reproducible production of M. phlei under GMP conditions.

IMPORTANCE Heat-inactivated M. phlei demonstrates promising efficacy to treat BCG-unresponsive non-muscle-invasive bladder cancer patients in clinical trials. However, lack of GMP-grade heat-inactivated M. phlei hampers further clinical investigations. Here, we described a GMP-grade, heat-inactivated M. phlei product, and presented initial characterization of its safety and immunomodulating properties. This product will serve as a starting point for further preclinical studies as well as clinical trials such as in combination with immune checkpoint inhibitors to treat bladder cancer.

Non-tuberculous mycobacteria, not Mycobacterium bovis, are a significant cause of TB-like lesions observed in slaughtered cattle in Ghana

Objectives

The aim was to isolate and identify the species of mycobacteria causing tuberculous-like (TB-like) lesions in cattle in Ghana.

Methods

Between 2019 and 2020, 68 bovine tissue samples with TB-like lesions, identified during post slaughter examination, were obtained from four major abattoirs close to border towns in Ghana. The samples were cultured on Lowenstein-Jensen medium. Isolated bacteria were characterized by Ziehl-Neelsen staining and observation for acid-fast bacilli (AFB) under a microscope. DNA was extracted from AFB-positive isolates, and mycobacterial speciation was performed by line probe assay using GenoType Mycobacterium CM and also with mycobacterial 16S rRNA gene amplification and sequencing.

Results

No Mycobacterium bovis was identified; however 53 bacterial isolates were obtained, of which 41 were non-tuberculous mycobacteria (NTM) strains and 12 were gram-positive bacteria. The predominant NTM species was M. fortuitum (43.9%, 18/41), with the rest being M. novocastrense, M. terrae, M. flavescens, M. holsaticum, M. cosmeticum, M. virginiense, M. intracellulare, M. mageritense, M. minnesotensis, M. duvalii, M. lehmannii, and M. koreense.

Conclusions

In cattle, NTM contribute significantly to lesions observed during slaughter examination and may be an important cause of zoonotic tuberculosis. A One Health surveillance of NTM in Ghana would provide insights into their clinical significance.

Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense

Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense, a related bacillus, is being increasingly isolated from human clinical cases with tuberculosis-like symptoms in various parts of the world. To elucidate the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the M. tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologs with M. tuberculosis and shows the expansion of toxin/antitoxin pairs, PE/PPE family proteins compared with other non-tuberculous mycobacteria. We observed M. riyadhense lacks wecE gene which may result in the absence of lipooligosaccharides (LOS) IV. Comparative transcriptomic analysis of infected macrophages reveals genes encoding inducers of Type I IFN responses, such as cytosolic DNA sensors, were relatively less expressed by macrophages infected with M. riyadhense or M. kansasii, compared to BCG or M. tuberculosis. Overall, our work sheds new light on the evolution of M. riyadhense, its relationship to the MTBC, and its potential as a system for the study of mycobacterial virulence and pathogenesis.

Human Pathogenic Bacteria Detected in Rainwater: Risk Assessment and Correlation to Microbial Source Tracking Markers and Traditional Indicators

Roof-harvested rainwater (RHRW) was investigated for the presence of the human pathogenic bacteria Mycobacterium tuberculosis (M. tuberculosis), Yersinia spp. and Listeria monocytogenes (L. monocytogenes). While Yersinia spp. were detected in 92% (n = 25) of the RHRW samples, and L. monocytogenes and M. tuberculosis were detected in 100% (n = 25) of the samples, a significantly higher mean concentration (1.4 × 10³ cells/100 mL) was recorded for L. monocytogenes over the sampling period. As the identification of appropriate water quality indicators is crucial to ensure access to safe water sources, correlation of the pathogens to traditional indicator organisms [Escherichia coli (E. coli) and Enterococcus spp.] and microbial source tracking (MST) markers (Bacteroides HF183, adenovirus and Lachnospiraceae) was conducted. A significant positive correlation was then recorded for E. coli versus L. monocytogenes (r = 0.6738; p = 0.000), and Enterococcus spp. versus the Bacteroides HF183 marker (r = 0.4071; p = 0.043), while a significant negative correlation was observed for M. tuberculosis versus the Bacteroides HF183 marker (r = −0.4558; p = 0.022). Quantitative microbial risk assessment indicated that the mean annual risk of infection posed by L. monocytogenes in the RHRW samples exceeded the annual infection risk benchmark limit (1 × 10^–4 infections per person per year) for intentional drinking (∼10^–4). In comparison, the mean annual risk of infection posed by E. coli was exceeded for intentional drinking (∼10^–1), accidental consumption (∼10^–3) and cleaning of the home (∼10^–3). However, while the risk posed by M. tuberculosis for the two relevant exposure scenarios [garden hosing (∼10^–5) and washing laundry by hand (∼10^–5)] was below the benchmark limit, the risk posed by adenovirus for garden hosing (∼10^–3) and washing laundry by hand (∼10^–3) exceeded the benchmark limit. Thus, while the correlation analysis confirms that traditional indicators and MST markers should be used in combination to accurately monitor the pathogen-associated risk linked to the utilisation of RHRW, the integration of QMRA offers a more site-specific approach to monitor and estimate the human health risks associated with the use of RHRW.

PLAN-M; Mycobacteriophage Endolysins Fused to Biodegradable Nanobeads Mitigate Mycobacterial Growth in Liquid and on Surfaces

The Mycobacteria are a genus of Actinobacteria that include human pathogens such as Mycobacterium tuberculosis (TB). Active TB disease can spread by airborne transmission to healthcare workers and to their community. The HHMI SEA-PHAGES program has contributed to discovering bacteriophages that are able to infect M. smegmatis MC² 155, a close relative of M. tuberculosis. This collection of diverse Mycobacteriophages is an excellent resource for trialling bacteriophage-sourced enzymes in novel applications. Herein we measured the ability Mycobacteriophage endolysins to lyse their host strain when functionally fused to biodegradable polyhydroxyalkanoate (PHA) nanobeads. PHA nanobeads facilitate both the expression and the application of enzymes to surfaces and have been demonstrated to stabilize a wide array of proteins for practical applications whilst eliminating the challenges of traditional protein purification. We selected two Lysin A and six Lysin B homologs to be functionally fused to the polyhydroxyalkanoate synthase C (PhaC). Expression of these constructs resulted in functional lysins displayed on the surface of PHA nanobeads. The lysins thus directionally displayed on nanobeads lysed up to 79% of the M. smegmatis MC² 155 population using 80 mg/mL of nanobeads in pure culture. In order to determine whether the nanobeads would be effective as a protective layer in PPE we adapted a fabric-based test and observed a maximum of 1 log loss of the cell population after 5 h of exposure on a textile (91% cell lysis). Lysin B enzymes performed better than the Lysin A enzymes as a protective barrier on textiles surface assays. These results suggest that bacterial endolysins are efficient in their action when displayed on PHA nanobeads and can cause significant population mortality in as little as 45 min. Our results provide the proof-of-principle that Mycobacteriophage endolysins can be used on functionalized nanobeads where they can protect surfaces such as personal protective equipment (PPE) that routinely come into contact with aerosolised bacteria.

Does Mycobacterium tuberculosis var. bovis Survival in the Environment Confound Bovine Tuberculosis Control and Eradication? A Literature Review

Bovine tuberculosis (bTB) is one of the globe's most common, multihost zoonoses and results in substantial socioeconomic costs for governments, farming industries, and tax payers. Despite decades of surveillance and research, surprisingly, little is known about the exact mechanisms of transmission. In particular, as a facultative intracellular pathogen, to what extent does survival of the causative agent, Mycobacterium tuberculosis var. bovis (M. bovis), in the environment constitute an epidemiological risk for livestock and wildlife? Due largely to the classical pathology of cattle cases, the received wisdom was that bTB was spread by direct inhalation and exchange of bioaerosols containing droplets laden with bacteria. Other members of the Mycobacterium tuberculosis complex (MTBC) exhibit differing host ranges, an apparent capacity to persist in environmental fomites, and they favour a range of different transmission routes. It is possible, therefore, that infection from environmental sources of M. bovis could be a disease transmission risk. Recent evidence from GPS-collared cattle and badgers in Britain and Ireland suggests that direct transmission by infectious droplets or aerosols may not be the main mechanism for interspecies transmission, raising the possibility of indirect transmission involving a contaminated, shared environment. The possibility that classical pulmonary TB can be simulated and recapitulated in laboratory animal models by ingestion of contaminated feed is a further intriguing indication of potential environmental risk. Livestock and wildlife are known to shed M. bovis onto pasture, soil, feedstuffs, water, and other fomites; field and laboratory studies have indicated that persistence is possible, but variable, under differing environmental conditions. Given the potential infection risk, it is timely to review the available evidence, experimental approaches, and methodologies that could be deployed to address this potential blind spot and control point. Although we focus on evidence from Western Europe, the concepts are widely applicable to other multihost bTB episystems.

Correlation of Conservation of Sequence and Structures of Mycobacterial Hemerythrin-like Proteins with Evolutionary Relationship and Host Pathogenicity

The Rv2633c gene of Mycobacterium tuberculosis, which plays a role in infection, encodes a hemerythrin-like protein (HLP). The crystal structure of an orthologue of Rv2633c, the HLP from Mycobacterium kansasii, revealed that it possessed structural features that were distinct from other hemerythrins and HLPs. These and other orthologous proteins comprise a distinct class of non-heme di-iron HLPs that are only found in mycobacteria. This study presents an analysis and comparison of protein sequences, putative structures, and evolutionary relationship of HLPs from 20 mycobacterial species that are known to cause tuberculosis or pulmonary disorders in humans. The results of this analysis allowed correlation of the physicochemical characteristics of amino acid residues that are substituted in these highly conserved sequences with their position in structures, possible effects on function, and evolutionary relationships. The sequences of the proteins from M. tuberculosis, Mycobacterium bovis, and other members of the M. tuberculosis complex, which cause tuberculosis, have substitutions not seen in the other non-tuberculous mycobacteria. Furthermore, groups of species that are closely related, based on phylogenetic analysis, possess substitutions of otherwise conserved residues not seen in other species that are less related. This information is correlated with the occurrence and clinical presentations of these groups of mycobacterial species. The results of this study provide a framework for structure-function studies to determine how subtle differences in the primary sequences of members of this family of proteins correlate with their structures and activities and how this may influence the infectious properties of the host species.

The Best of All Worlds: Streptococcus pneumoniae Conjunctivitis through the Lens of Community Ecology and Microbial Biogeography

The study of the forces which govern the geographical distributions of life is known as biogeography, a subject which has fascinated zoologists, botanists and ecologists for centuries. Advances in our understanding of community ecology and biogeography—supported by rapid improvements in next generation sequencing technology—have now made it possible to identify and explain where and why life exists as it does, including within the microbial world. In this review, we highlight how a unified model of microbial biogeography, one which incorporates the classic ecological principles of selection, diversification, dispersion and ecological drift, can be used to explain community dynamics in the settings of both health and disease. These concepts operate on a multiplicity of temporal and spatial scales, and together form a powerful lens through which to study microbial population structures even at the finest anatomical resolutions. When applied specifically to curious strains of conjunctivitis-causing, nonencapsulated Streptococcus pneumoniae, we show how this conceptual framework can be used to explain the possible evolutionary and disease-causing mechanisms which allowed these lineages to colonize and invade a separate biogeography. An intimate knowledge of this radical bifurcation in phylogeny, still the only known niche subspecialization for S. pneumoniae to date, is critical to understanding the pathogenesis of ocular surface infections, nature of host-pathogen interactions, and developing strategies to curb disease transmission.

Tuberculosis: Current Status, Diagnosis, Treatment and Development of Novel Vaccines

Tuberculosis (TB) is an infectious disease that mainly affects the lungs and spreads to other organs of the body through the haematogenous route. It is one of the ten major causes of mortality worldwide. India has the highest incidence of new- and multidrug-resistant (MDR) - TB cases in the world. Bacille Calmette-Guerin (BCG) is the vaccine commonly available against TB. BCG does offer some protection against serious forms of TB in childhood but its protective effect wanes with age. Many new innovative strategies are being trailed for the development of effective and potent vaccines like mucosal- and epitope-based vaccines, which may replace BCG or boost BCG responses. The use of nanotechnology for diagnosis and treatment of TB is also in the pipeline along with many other vaccines, which are under clinical trials. Further, in-silico models were developed for finding new drug targets and designing drugs against Mycobacterium tuberculosis (Mtb). These models offer the benefit of computational experiments which are easy, inexpensive and give quick results. This review will focus on the available treatments and new approaches to develop potent vaccines for the treatment of TB.

Endocrine disruption and commensal bacteria alteration associated with gaseous and soil PAH contamination among daycare children

Polycyclic aromatic hydrocarbons (PAHs) are priority environmental pollutants that cause adverse health effects. PAHs belong to endocrine signaling disruptors to which children are sensitive to. Recent evidence suggests that PAH pollution alters the abundance of environmental bacteria that is associated with health outcomes. The alteration of environmental and commensal microbiota by PAH pollution has never been connected to endocrine signaling pathways. To estimate the risk of endocrine disruption in daycare children, we measured PAHs from soil and air of eleven urban daycare centres in Finland. We analyzed daycare yards' soil and children's gut and skin bacterial communities with 16S rRNA gene metabarcoding and used Kyoto Encyclopaedia of Genes and Genomes database to categorize endocrine signaling pathways. We also assessed the PAH hazard to children's health based on the current risk assesments. We observed associations between signaling pathways in endocrine system and gaseous PAH levels in ambient air. Peroxisome proliferator-activated receptor and adipocytokine signaling pathway decreased with higher chrysene concentration in the air. Soil PAH contamination was associated with altered Actinobacteria, Bacteoridetes and Proteobacteria communities on children's skin and in daycare yard soil. However, adjusted genera were not the same in soil and on skin, with the exception of Mycobacterium that was associated with higher PAH concentrations both in soil and on the skin. Even though fluoranhtene levels were above the current threshold values, total PAHs were below safety threshold values and based on current risk assessments there is a minor risk for child health. Our findings indicate that PAH concentrations that are considered safe may interfere with endocrine signaling by commensal microbiota and alter both environmental and commensal bacterial communities. The imbalance in human microbiota and the decrease in signaling pathways may contribute to emerging public health problems, including inflammatory disorders, obesity and diabetes. Therefore, the optimal risk assessments of PAHs and theoretically also other contaminants shaping commensal microbiota may need to take into account the possibility of the disruption of endocrine signaling pathways.

Distribution of reactive oxygen species defense mechanisms across domain bacteria

Bacteria are the most diverse and numerous organisms on the planet, inhabiting environments from the deep subsurface to particles in clouds. Across this range of conditions, bacteria have evolved a diverse suite of enzymes to mitigate cellular damage from reactive oxygen species (ROS). Here, we review the diversity and distribution of ROS enzymatic defense mechanisms across the domain Bacteria, using both peer-reviewed literature and publicly available genome databases. We describe the specific strategies used by well-characterized organisms in order to highlight differences in oxidative stress responses between aerobic, facultatively anaerobic, and anaerobic lifestyles. We present evidence from genome minimization experiments to suggest that ROS defenses are obligately required for life. This review clarifies the variability in ROS defenses across Bacteria, including the novel diversity found in currently uncharacterized Candidate Phyla.

Preliminary evaluation of the positively and negatively charge effects of tetra-substituted porphyrins on photoinactivation of rapidly growing mycobacteria

This manuscript reports, at the first time, the photoinactivation evaluation of tetra-cationic and anionic porphyrins as photosensitizers (PS) for the photodynamic inactivation (PDI) of rapidly growing mycobacteria strains. Two different charged porphyrin groups were obtained commercially. PDI experiments in the strains Mycobacterium massiliense e Mycobacterium fortuitum conducted with adequate concentration (without aggregation) of photosensitizer under white light at a fluence rate of 50 mW/cm² over 90 min showed that the most effective PS caused a 100 times reduction in the concentration of viable mycobacteria. The present results show that porphyrin with positively charge are more efficient PS than anionic porphyrin (negatively charged) against M. massiliense e M. fortuitum. It is also clear that the effectiveness of the molecule as PS for PDI studies with mycobacteria is strongly related with the porphyrin peripheral charge, and consequently their solubility in physiological media. Cationic PSs might be promising anti-mycobacteria PDI agents with potential applications in medical clinical cases and bioremediation.

Engineering the microbiome for animal health and conservation

IMPACT STATEMENT

Considering the clear effects of microbiota on important aspects of animal biology and development (including in humans), this topic is timely and broadly appealing, as it compels us to consider the possibilities of altering the microbiome (without antibiotics) to positively affect animal health. In this review, we highlight three general approaches to manipulating the microbiome that have demonstrated success and promise for use in animal health. We also point out knowledge gaps where further inquiry would most benefit the field. Our paper not only provides a short and digestible overview of the current state of application, but also calls for further exploration of the microbial diversity at hand to expand our toolkit, while also leveraging the diversity and flexibility of animal systems to better understand mechanisms of efficacy.

Carbonic Anhydrase Inhibitors as Novel Drugs against Mycobacterial β-Carbonic Anhydrases: An Update on In Vitro and In Vivo Studies

Mycobacteria cause a variety of diseases, such as tuberculosis, leprosy, and opportunistic diseases in immunocompromised people. The treatment of these diseases is problematic, necessitating the development of novel treatment strategies. Recently, β-carbonic anhydrases (β-CAs) have emerged as potential drug targets in mycobacteria. The genomes of mycobacteria encode for three β-CAs that have been cloned and characterized from Mycobacterium tuberculosis (Mtb) and the crystal structures of two of the enzymes have been determined. Different classes of inhibitor molecules against Mtb β-CAs have subsequently been designed and have been shown to inhibit these mycobacterial enzymes in vitro. The inhibition of these centrally important mycobacterial enzymes leads to reduced growth of mycobacteria, lower virulence, and impaired biofilm formation. Thus, the inhibition of β-CAs could be a novel approach for developing drugs against the severe diseases caused by pathogenic mycobacteria. In the present article, we review the data related to in vitro and in vivo inhibition studies in the field.

Inflammasome in the Pathogenesis of Pulmonary Diseases

Lung diseases are common and significant causes of illness and death around the world. Inflammasomes have emerged as an important regulator of lung diseases. The important role of IL-1 beta and IL-18 in the inflammatory response of many lung diseases has been elucidated. The cleavage to turn IL-1 beta and IL-18 from their precursors into the active forms is tightly regulated by inflammasomes. In this chapter, we structurally review current evidence of inflammasome-related components in the pathogenesis of acute and chronic lung diseases, focusing on the "inflammasome-caspase-1-IL-1 beta/IL-18" axis.