Computational Identification of the Proteins Associated With Quorum Sensing and Biofilm Formation in Mycobacterium tuberculosis

Mycobacterial biofilms: Understanding the genetic factors playing significant role in pathogenesis, resistance and diagnosis

Even though the genus Mycobacterium is a diverse group consisting of a majority of environmental bacteria known as non-tuberculous mycobacteria (NTM), it also contains some of the deadliest pathogens (Mycobacterium tuberculosis) in history associated with chronic disease called tuberculosis (TB). Formation of biofilm is one of the unique strategies employed by mycobacteria to enhance their ability to survive in hostile conditions. Biofilm formation by Mycobacterium species is an emerging area of research with significant implications for understanding its pathogenesis and treatment of related infections, specifically TB. This review provides an overview of the biofilm-forming abilities of different species of Mycobacterium and the genetic factors influencing biofilm formation with a detailed focus on M. tuberculosis. Biofilm-mediated resistance is a significant challenge as it can limit antibiotic penetration and promote the survival of dormant mycobacterial cells. Key genetic factors promoting biofilm formation have been explored such as the mmpL genes involved in lipid transport and cell wall integrity as well as the groEL gene essential for mature biofilm formation. Additionally, biofilm-mediated antibiotic resistance and pathogenesis highlighting the specific niches, sites of infection along with the possible mechanisms of biofilm dissemination have been discussed. Furthermore, drug targets within mycobacterial biofilm and their role as potential biomarkers in the development of rapid diagnostic tools have been highlighted. The review summarises the current understanding of the complex nature of Mycobacterium biofilm and its clinical implications, paving the way for advancements in the field of disease diagnosis, management and treatment against its multi-drug resistant species.

Mycobacterial Biofilm: Mechanisms, Clinical Problems, and Treatments

Tuberculosis (TB) remains a threat to human health worldwide. Mycobacterium tuberculosis (Mtb) and other nontuberculous mycobacteria (NTM) can form biofilms, and in vitro and animal experiments have shown that biofilms cause serious drug resistance and mycobacterial persistence. Deeper investigations into the mechanisms of mycobacterial biofilm formation and, consequently, the exploration of appropriate antibiofilm treatments to improve the efficiency of current anti-TB drugs will be useful for curing TB. In this review, the genes and molecules that have been recently reported to be involved in mycobacterial biofilm development, such as ABC transporter, Pks1, PpiB, GroEL1, MprB, (p)ppGpp, poly(P), and c-di-GMP, are summarized. Biofilm-induced clinical problems, including biofilm-related infections and enhanced virulence, as well as their possible mechanisms, are also discussed in detail. Moreover, we also illustrate newly synthesized anti-TB agents that target mycobacterial biofilm, as well as some assistant methods with high efficiency in reducing biofilms in hosts, such as the use of nanoparticles.

Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.

Computational tools for exploring peptide-membrane interactions in gram-positive bacteria

The vital cellular functions in Gram-positive bacteria are controlled by signaling molecules known as quorum sensing peptides (QSPs), considered promising therapeutic interventions for bacterial infections. In the bacterial system QSPs bind to membrane-coupled receptors, which then auto-phosphorylate and activate intracellular response regulators. These response regulators induce target gene expression in bacteria. One of the most reliable trends in drug discovery research for virulence-associated molecular targets is the use of peptide drugs or new functionalities. In this perspective, computational methods act as auxiliary aids for biologists, where methodologies based on machine learning and in silico analysis are developed as suitable tools for target peptide identification. Therefore, the development of quick and reliable computational resources to identify or predict these QSPs along with their receptors and inhibitors is receiving considerable attention. The databases such as Quorumpeps and Quorum Sensing of Human Gut Microbes (QSHGM) provide a detailed overview of the structures and functions of QSPs. The tools and algorithms such as QSPpred, QSPred-FL, iQSP, EnsembleQS and PEPred-Suite have been used for the generic prediction of QSPs and feature representation. The availability of compiled key resources for utilizing peptide features based on amino acid composition, positional preferences, and motifs as well as structural and physicochemical properties, including biofilm inhibitory peptides, can aid in elucidating the QSP and membrane receptor interactions in infectious Gram-positive pathogens. Herein, we present a comprehensive survey of diverse computational approaches that are suitable for detecting QSPs and QS interference molecules. This review highlights the utility of these methods for developing potential biomarkers against infectious Gram-positive pathogens.

A systematic computational analysis of Mycobacterium tuberculosis H37Rv and human CD34+ genomic expression reveals crucial molecular entities involved in infection progression

The co-evolution of Mycobacterium tuberculosis H37Rv along with its host systems enables the pathogenic bacterium to emerge as a multi-drug resistant form. This creates challenges for a more efficacious treatment strategy that can mitigate the infection. Working towards the same, our study followed a mathematical and statistical approach proposing that mycobacterial transcription factors regulating virulence and adaptation, host cell cytoplasmic component metabolism, oxidoreductase activity and respiratory ETC would be targets for antibiotics against Mycobacterium tuberculosis. Simultaneously, extending the statistical study on Mycobacterium-infected human cord blood CD34+ cells revealed that the human CD34+ genes, S100A8 and FGR (tyrosine-protein kinase, Src2), might be affected in the infection pathogenesis by Mycobacterium. Further, the deduced Mycobacterium-human gene interaction network proposed that mycobacterial coregulators Rv0452 (MarR family regulator) and Rv3862c (WhiB6) triggered genes controlling bacterial metabolism, which influences human immunological pathways involving TLR2 and CXCL8/MAPK8.Communicated by Ramaswamy H. Sarma.

Transcriptional Changes in Bifidobacterium bifidum Involved in Synergistic Multispecies Biofilms

Bifidobacterium bifidum is part of the core microbiota of healthy infant guts where it may form biofilms on epithelial cells, mucosa, and food particles in the gut lumen. Little is known about transcriptional changes in B. bifidum engaged in synergistic multispecies biofilms with ecologically relevant species of the human gut. Recently, we reported prevalence of synergism in mixed-species biofilms formed by the human gut microbiota. This study represents a comparative gene expression analysis of B. bifidum when grown in a single-species biofilm and in two multispecies biofilm consortia with Bifidobacterium longum subsp. infantis, Bacteroides ovatus, and Parabacteroides distasonis in order to identify genes involved in this adaptive process in mixed biofilms and the influence on its metabolic and functional traits. Changes up to 58% and 43% in its genome were found when it grew in three- and four-species biofilm consortia, respectively. Upregulation of genes of B. bifidum involved in carbohydrate metabolism (particularly the galE gene), quorum sensing (luxS and pfs), and amino acid metabolism (especially branched chain amino acids) in both multispecies biofilms, compared to single-species biofilms, suggest that they may be contributing factors for the observed synergistic biofilm production when B. bifidum coexists with other species in a biofilm.

Intercellular communication and social behaviors in mycobacteria

Cell-to-cell communication is a fundamental process of bacteria to exert communal behaviors. Sputum samples of patients with cystic fibrosis have often been observed with extensive mycobacterial genetic diversity. The emergence of heterogenic mycobacterial populations is observed due to subtle changes in their morphology, gene expression level, and distributive conjugal transfer (DCT). Since each subgroup of mycobacteria has different hetero-resistance, they are refractory against several antibiotics. Such genetically diverse mycobacteria have to communicate with each other to subvert the host immune system. However, it is still a mystery how such heterogeneous strains exhibit synchronous behaviors for the production of quorum sensing (QS) traits, such as biofilms, siderophores, and virulence proteins. Mycobacteria are characterized by division of labor, where distinct sub-clonal populations contribute to the production of QS traits while exchanging complimentary products at the community level. Thus, active mycobacterial cells ensure the persistence of other heterogenic clonal populations through cooperative behaviors. Additionally, mycobacteria are likely to establish communication with neighboring cells in a contact-independent manner through QS signals. Hence, this review is intended to discuss our current knowledge of mycobacterial communication. Understanding mycobacterial communication could provide a promising opportunity to develop drugs to target key pathways of mycobacteria.

Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits, including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.

The source and fate of Mycobacterium tuberculosis complex in wastewater and possible routes of transmission

BACKGROUND

The Mycobacterium tuberculosis complex (MTBC) consists of causative agents of both human and animal tuberculosis and is responsible for over 10 million annual infections globally. Infections occur mainly through airborne transmission, however, there are possible indirect transmissions through a faecal-oral route which is poorly reported. This faecal-oral transmission could be through the occurrence of the microbe in environments such as wastewater. This manuscript, therefore, reviews the source and fate of MTBC in the wastewater environment, including the current methods in use and the possible risks of infections.

RESULTS

The reviewed literature indicates that about 20% of patients with pulmonary TB may have extra-pulmonary manifestations such as GITB, resulting in shedding in feaces and urine. This could potentially be the reason for the detection of MTBC in wastewater. MTBC concentrations of up to 5.5 × 105 (±3.9 × 105) copies/L of untreated wastewater have been reported. Studies have indicated that wastewater may provide these bacteria with the required nutrients for their growth and could potentially result in environmental transmission. However, 98.6 (± 2.7) %, removal during wastewater treatment, through physical-chemical decantation (primary treatment) and biofiltration (secondary treatment) has been reported. Despite these reports, several studies observed the presence of MTBC in treated wastewater via both culture-dependent and molecular techniques.

CONCLUSION

The detection of viable MTBC cells in either treated or untreated wastewater, highlights the potential risks of infection for wastewater workers and communities close to these wastewater treatment plants. The generation of aerosols during wastewater treatment could be the main route of transmission. Additionally, direct exposure to the wastewater containing MTBC could potentially contribute to indirect transmissions which may lead to pulmonary or extra-pulmonary infections. This calls for the implementation of risk reduction measures aimed at protecting the exposed populations.

Bactericidal efficacy of slightly acidic electrolyzed water (SAEW) against Listeria monocytogenes planktonic cells and biofilm on food-contact surfaces

In the present study, the bactericidal efficacy of slightly acidic electrolyzed water (SAEW) against L. monocytogenes planktonic cells and biofilm on food-contact surfaces including stainless steel and glass was systematically evaluated. The results showed that SAEW (pH of 5.09 and available chlorine concentration (ACC) of 60.33 mg/L) could kill L. monocytogenes on food-contact surfaces completely in 30 s, whose disinfection efficacy is equal to that of NaClO solutions (pH of 9.23 and ACC of 253.53 mg/L). The results showed that long exposure time and high ACC contributed to the enhancement of the disinfection efficacy of SAEW on L. monocytogenes on food-contact surfaces. Moreover, the log reduction of SAEW treatment presented an increasing tendency within the prolonging of treatment time when SAEW was used to remove the L. monocytogenes biofilm formed on stainless steel and glass surfaces, which suggested that SAEW could remove L. monocytogenes biofilm effectively and its disinfection efficacy is equal to (in case of stainless steel) or higher than (in case of glass) that of high ACC of NaClO solutions. In addition, the results of the crystal violet staining and scanning electron microscopy (SEM) also demonstrated that SAEW treatment could remove the L. monocytogenes biofilm on food-contact surfaces.

Imidazole-Thiosemicarbazide Derivatives as Potent Anti-Mycobacterium tuberculosis Compounds with Antibiofilm Activity

Mycobacterium tuberculosis (Mtb) is an intracellular pathogenic bacterium and the causative agent of tuberculosis. This disease is one of the most ancient and deadliest bacterial infections, as it poses major health, social and economic challenges at a global level, primarily in low- and middle-income countries. The lack of an effective vaccine, the long and expensive drug therapy, and the rapid spread of drug-resistant strains of Mtb have led to the re-emergence of tuberculosis as a global pandemic. Here, we assessed the in vitro activity of new imidazole-thiosemicarbazide derivatives (ITDs) against Mtb infection and their effects on mycobacterial biofilm formation. Cytotoxicity studies of the new compounds in cell lines and human monocyte-derived macrophages (MDMs) were performed. The anti-Mtb activity of ITDs was evaluated by determining minimal inhibitory concentrations of resazurin, time-kill curves, bacterial intracellular growth and the effect on biofilm formation. Mutation frequency and whole-genome sequencing of mutants that were resistant to ITDs were performed. The antimycobacterial potential of ITDs with the ability to penetrate Mtb-infected human macrophages and significantly inhibit the intracellular growth of tubercle bacilli and suppress Mtb biofilm formation was observed.

Role of the kdpDE Regulatory Operon of Mycobacterium tuberculosis in Modulating Bacterial Growth in vitro

Bacteria use K⁺-uptake transporters differentially for adaptation in varying growth conditions. In Mycobacterium tuberculosis, two K⁺-uptake systems, the Trk comprising the CeoB and CeoC proteins and the Kdp consisting of the two-component system (TCS), KdpDE and KdpFABC, have been characterized, but their selective utilization during bacterial growth has not been completely explored. In the current study, the roles of the M. tuberculosis KdpDE regulatory system alone and in association with the Trk transporters in bacterial growth were investigated by evaluating the growth of M. tuberculosis KdpDE-deletion and KdpDE/Trk (KT)-double knockout mutant strains in planktonic culture under standard growth conditions. The KT-double knockout mutant strain was first constructed using homologous recombination procedures and was evaluated together with the KdpDE-deletion mutant and the wild-type (WT) strains with respect to their rates of growth, K⁺-uptake efficiencies, and K⁺-transporter gene expression during planktonic growth. During growth at optimal K⁺ concentrations and pH levels, selective deletion of the TCS KdpDE (KdpDE-deletion mutant) led to attenuation of bacterial growth and an increase in bacterial K⁺-uptake efficiency, as well as dysregulated expression of the kdpFABC and trk genes. Deletion of both the KdpDE and the Trk systems (KT-double knockout) also led to severely attenuated bacterial growth, as well as an increase in bacterial K⁺-uptake efficiency. These results demonstrate that the KdpDE regulatory system plays a key role during bacterial growth by regulating K⁺ uptake via modulation of the expression and activities of both the KdpFABC and Trk systems and is important for bacterial growth possibly by preventing cytoplasmic K⁺ overload.

Host-directed therapy to combat mycobacterial infections

Upon infection, mycobacteria, such as Mycobacterium tuberculosis (Mtb) and nontuberculous mycobacteria (NTM), are recognized by host innate immune cells, triggering a series of intracellular processes that promote mycobacterial killing. Mycobacteria, however, have developed multiple counter‐strategies to persist and survive inside host cells. By manipulating host effector mechanisms, including phagosome maturation, vacuolar escape, autophagy, antigen presentation, and metabolic pathways, pathogenic mycobacteria are able to establish long‐lasting infection. Counteracting these mycobacteria‐induced host modifying mechanisms can be accomplished by host‐directed therapeutic (HDT) strategies. HDTs offer several major advantages compared to conventional antibiotics: (a) HDTs can be effective against both drug‐resistant and drug‐susceptible bacteria, as well as potentially dormant mycobacteria; (b) HDTs are less likely to induce bacterial drug resistance; and (c) HDTs could synergize with, or shorten antibiotic treatment by targeting different pathways. In this review, we will explore host‐pathogen interactions that have been identified for Mtb for which potential HDTs impacting both innate and adaptive immunity are available, and outline those worthy of future research. We will also discuss possibilities to target NTM infection by HDT, although current knowledge regarding host‐pathogen interactions for NTM is limited compared to Mtb. Finally, we speculate that combinatorial HDT strategies can potentially synergize to achieve optimal mycobacterial host immune control.

Overexpression of the celA1 gene in BCG modifies surface pellicle, glucosamine content in biofilms, and affects in vivo replication

Biofilm formed in vitro by mycobacteria has been associated with increased antibiotic tolerance as compared with planktonic cells. Cellulose has been identified as a component of DTT-exposed biofilms formed by M. tuberculosis. The celA1 gene of M. tuberculosis encodes a cellulase, which could affect the formation of biofilm by slow-growing mycobacteria. In this work, the celA1 gene of M. tuberculosis was cloned into the integrative pMV361 plasmid and then transformed into M. bovis BCG Pasteur to produce BCG:celA1, to have celA1 expressed from the strong promoter hsp60. We compared planktonic and biofilm growth, possible presence of CelA1 in whole protein extracts, quantitated biofilm, presence of monosaccharides, and bacillary burden in lungs after aerosol infection in BALB/c mice. Differences in the appearance of the surface pellicle and of the biofilm attached to the substrate were observed. In biofilms, we observed a significant decrease of glucosamine in BCG:celA1 compared with BCG:pMV361. Finally, BCG:celA1 had lower viable bacteria than the BCG:pMV361 strain after 24 h and 3 weeks post-infection, but no difference was found at 9 weeks post-infection.