Mycobacterium avium Subsp. hominissuis Interactions with Macrophage Killing Mechanisms

Phenothiazines boost host control of Mycobacterium avium infection in primary human macrophages

Mycobacterium avium (Mav) complex is the leading cause of pulmonary diseases associated with non-tuberculous mycobacterial (NTM) infections worldwide. The inherent and increasing acquired antibiotic resistance of Mav hampers the treatment of Mav infections and emphasizes the urgent need for alternative treatment strategies. A promising approach is host-directed therapy (HDT), which aims to boost the host's immune defenses to combat infections. In this study, we show that phenothiazines, particularly trifluoperazine (TFP) and chlorproethazine (CPE), restricted Mav survival in primary human macrophages. Notably, TFP and CPE did not directly inhibit mycobacterial growth at used concentrations, confirming these drugs function through host-dependent mechanisms. TFP and CPE induced a mild, albeit not statistically significant, increase in autophagic flux along with the nuclear intensity of transcription factor EB (TFEB), the master transcriptional regulator of autophagy. Inhibition of autophagic flux with bafilomycin, however, did not impair the improved host infection control by TFP and CPE, suggesting that the host (auto)phagolysosomal pathway is not causally involved in the mechanism of action of TFP and CPE. Additionally, TFP and CPE increased the production of both cellular and mitochondrial reactive oxygen species (ROS). Scavenging mitochondrial ROS did not impact, whereas inhibition of NADPH oxidase (NOX)-mediated ROS production partially impaired the HDT activity of TFP and CPE, indicating that oxidative burst may play a limited role in the improved host control of Mav infection by these drugs. Overall, our study demonstrates that phenothiazines are promising HDT candidates that enhance the antimicrobial response of macrophages against Mav, through mechanism(s) that were partially elucidated.

Genetic variations underlying aminoglycoside resistance in antibiotic-induced Mycobacterium intracellulare mutants

Mycobacterium avium complex (MAC) is an emerging pathogen leading to public health concerns in developing and developed countries, particularly among immunocompromised individuals and patients with structural lung diseases. Current clinical guidelines recommend combination antibiotic therapy for treating MAC pulmonary disease (MAC-PD). However, the rising prevalence of antibiotic resistance poses significant challenges, including treatment failure and clinical recurrence. A deeper understanding of the mechanisms underlying MAC antibiotic resistance is essential to improve treatment outcomes. This study investigates the genetic variations associated with aminoglycoside resistance in an antibiotic-induced Mycobacterium intracellulare mutant derived from a clinical strain. Whole-genome analysis identified seven mutations in the aminoglycoside-resistant mutant, including single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Key genetic alterations included a frameshift variant in a gene encoding a secreted protein antigen, missense mutations in rpsL and rsmG, and synonymous and in-frame deletion variants in srfAB and mtrB, respectively. These findings highlight the complex genetic landscape of aminoglycoside resistance in M. intracellulare. Understanding these resistance determinants provides valuable insights for developing diagnostic tools to detect drug-resistant MAC strains and optimizing therapeutic strategies for managing MAC infections in clinical practice.

Stealth in non-tuberculous mycobacteria: clever challengers to the immune system

Non-tuberculous Mycobacteria (NTM) are found extensively in various environments, yet most are non-pathogenic. Only a limited number of these organisms can cause various infections, including those affecting the lungs, skin, and central nervous system, particularly when the host's autoimmune function is compromised. Among these, Non-tuberculous Mycobacteria Pulmonary Diseases (NTM-PD) are the most prevalent. Currently, there is a lack of effective treatments and preventive measures for NTM infections. This article aims to deepen the comprehension of the pathogenic mechanisms linked to NTM and to formulate new intervention strategies by synthesizing current research and detailing the different tactics used by NTM to avoid elimination by the host's immune response. These intricate mechanisms not only affect the innate immune response but also successfully oppose the adaptive immune response, establishing persistent infections within the host. This includes effects on the functions of macrophages, neutrophils, dendritic cells, and T lymphocytes, as well as modulation of cytokine production. The article particularly emphasizes the survival strategies of NTM within macrophages, such as inhibiting phagosome maturation and acidification, resisting intracellular killing mechanisms, and interfering with autophagy and cell death pathways. This review aims to deepen the understanding of NTM's immune evasion mechanisms, thereby facilitating efforts to inhibit its proliferation and spread within the host, ultimately providing new methods and strategies for NTM-related treatments.

Amoebae as training grounds for microbial pathogens

Grazing of amoebae on microorganisms represents one of the oldest predator-prey dynamic relationships in nature. It represents a genetic "melting pot" for an ancient and continuous multi-directional inter- and intra-kingdom horizontal gene transfer between amoebae and its preys, intracellular microbial residents, endosymbionts, and giant viruses, which has shaped the evolution, selection, and adaptation of microbes that evade degradation by predatory amoeba. Unicellular phagocytic amoebae are thought to be the ancient ancestors of macrophages with highly conserved eukaryotic processes. Selection and evolution of microbes within amoeba through their evolution to target highly conserved eukaryotic processes have facilitated the expansion of their host range to mammals, causing various infectious diseases. Legionella and environmental Chlamydia harbor an immense number of eukaryotic-like proteins that are involved in ubiquitin-related processes or are tandem repeats-containing proteins involved in protein-protein and protein-chromatin interactions. Some of these eukaryotic-like proteins exhibit novel domain architecture and novel enzymatic functions absent in mammalian cells, such as ubiquitin ligases, likely acquired from amoebae. Mammalian cells and amoebae may respond similarly to microbial factors that target highly conserved eukaryotic processes, but mammalian cells may undergo an accidental response to amoeba-adapted microbial factors. We discuss specific examples of microbes that have evolved to evade amoeba predation, including the bacterial pathogens- Legionella, Chlamydia, Coxiella, Rickettssia, Francisella, Mycobacteria, Salmonella, Bartonella, Rhodococcus, Pseudomonas, Vibrio, Helicobacter, Campylobacter, and Aliarcobacter. We also discuss the fungi Cryptococcus, and Asperigillus, as well as amoebae mimiviruses/giant viruses. We propose that amoeba-microbe interactions will continue to be a major "training ground" for the evolution, selection, adaptation, and emergence of microbial pathogens equipped with unique pathogenic tools to infect mammalian hosts. However, our progress will continue to be highly dependent on additional genomic, biochemical, and cellular data of unicellular eukaryotes.

E3 ubiquitin ligase CBLB regulates innate immune responses and bacterial dissemination during nontuberculous mycobacteria infection

Nontuberculous mycobacteria (NTM) are emerging opportunistic pathogens causing pulmonary infection to fatal disseminated disease. NTM infections are steadily increasing in children and adults, and immune-compromised individuals are at a greater risk of fatal infections. The NTM disease's adverse pathology and resistance to antibiotics have further worsened the therapeutic measures. Innate immune regulators are potential targets for therapeutics to NTM, especially in a T cell-suppressed population, and many ubiquitin ligases modulate pathogenesis and innate immunity during infections, including mycobacterial infections. Here, we investigated the role of an E3 ubiquitin ligase, Casitas B-lineage lymphoma proto-oncogene B (CBLB), in immunocompromised mouse models of NTM infection. We found that CBLB is essential to prevent bacterial growth and dissemination. Cblb deficiency debilitated natural killer cells, inflammatory monocytes, and macrophages in vivo. However, Cblb deficiency in macrophages did not wane its ability to inhibit bacterial growth or production of reactive oxygen species or interferon γ production by natural killer cells in vitro. CBLB restricted NTM growth and dissemination by promoting early granuloma formation in vivo. Our study shows that CBLB bolsters innate immune responses and helps prevent the dissemination of NTM during compromised T cell immunity.

MptpB Inhibitor Improves the Action of Antibiotics against Mycobacterium tuberculosis and Nontuberculous Mycobacterium avium Infections

Treatment of Mycobacterium tuberculosis and Mycobacterium avium infections requires multiple drugs for long time periods. Mycobacterium protein-tyrosine-phosphatase B (MptpB) is a key M. tuberculosis virulence factor that subverts host antimicrobial activity to promote intracellular survival. Inhibition of MptpB reduces the infection burden in vivo and offers new opportunities to improve current treatments. Here, we demonstrate that M. avium produces an MptpB orthologue and that the MptpB inhibitor C13 reduces the M. avium infection burden in macrophages. Combining C13 with the antibiotics rifampicin or bedaquiline showed an additive effect, reducing intracellular infection of both M. tuberculosis and M. avium by 50%, compared to monotreatment with antibiotics alone. This additive effect was not observed with pretomanid. Combining C13 with the minor groove-binding compounds S-MGB-362 and S-MGB-363 also reduced the M. tuberculosis intracellular burden. Similar additive effects of C13 and antibiotics were confirmed in vivo using Galleria mellonella infections. We demonstrate that the reduced mycobacterial burden in macrophages observed with C13 treatments is due to the increased trafficking to lysosomes.

Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in ORF1 and ORF2, respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in Mycobacterium avium complex members, but SSR1-based modulation of ORF1 reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne's disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of Mycobacterium avium subsp. paratuberculosis (MAP) with Crohn's disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.

Metabolic pathways that permit Mycobacterium avium subsp. hominissuis to transition to different environments encountered within the host during infection

Introduction

M. avium subsp. hominissuis (M. avium) is an intracellular, facultative bacterium known to colonize and infect the human host through ingestion or respiratory inhalation. The majority of pulmonary infections occur in association with pre- existing lung diseases, such as bronchiectasis, cystic fibrosis, or chronic obstructive pulmonary disease. M. avium is also acquired by the gastrointestinal route in immunocompromised individuals such as human immunodeficiency virus HIV-1 patients leading to disseminated disease. A hallmark of M. avium pulmonary infections is the ability of pathogen to form biofilms. In addition, M. avium can reside within granulomas of low oxygen and limited nutrient conditions while establishing a persistent niche through metabolic adaptations.

Methods

Bacterial metabolic pathways used by M. avium within the host environment, however, are poorly understood. In this study, we analyzed M. avium proteome with a focus on core metabolic pathways expressed in the anaerobic, biofilm and aerobic conditions and that can be used by the pathogen to transition from one environment to another.

Results

Overall, 3,715 common proteins were identified between all studied conditions and proteins with increased synthesis over the of the level of expression in aerobic condition were selected for analysis of in specific metabolic pathways. The data obtained from the M. avium proteome of biofilm phenotype demonstrates in enrichment of metabolic pathways involved in the fatty acid metabolism and biosynthesis of aromatic amino acid and cofactors. Here, we also highlight the importance of chloroalkene degradation pathway and anaerobic fermentationthat enhance during the transition of M. avium from aerobic to anaerobic condition. It was also found that the production of fumarate and succinate by MAV_0927, a conserved hypothetical protein, is essential for M. avium survival and for withstanding the stress condition in biofilm. In addition, the participation of regulatory genes/proteins such as the TetR family MAV_5151 appear to be necessary for M. avium survival under biofilm and anaerobic conditions.

Conclusion

Collectively, our data reveal important core metabolic pathways that M. avium utilize under different stress conditions that allow the pathogen to survive in diverse host environments.