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European Spine Journal : Official... Dec 2023The aim is to compare the pathogen detection performance of metagenomic next-generation sequencing (mNGS) and the culturing of percutaneous needle biopsy samples... (Review)
Review
PURPOSE
The aim is to compare the pathogen detection performance of metagenomic next-generation sequencing (mNGS) and the culturing of percutaneous needle biopsy samples obtained from an individual with a suspected spinal infection.
METHODS
A retrospective study of 141 individuals with a suspected spinal infection was conducted, and mNGS was performed. The microbial spectra and detection performance between mNGS and the culturing-based method were compared, and the effects of antibiotic intervention and biopsy on the detection performance were assessed.
RESULTS
The microorganisms isolated most commonly via the culturing-based method were Mycobacterium tuberculosis (n = 21), followed by Staphylococcus epidermidis (n = 13). The most common microorganisms detected via mNGS were Mycobacterium tuberculosis complex (MTBC) (n = 39), followed by Staphylococcus aureus (n = 15). The difference in the type of detected microorganisms between culturing and mNGS was observed only in Mycobacterium (P = 0.001). mNGS helped identify potential pathogens in 80.9% of cases, which was significantly higher than the positivity rate of 59.6% observed for the culturing-based method (P < 0.001). Moreover, mNGS had a sensitivity of 85.7% (95% CI, 78.4% to 91.3%), a specificity of 86.7% (95% CI, 59.5% to 98.3%), and sensitivity gains of 35% (85.7% vs. 50.8%; P < 0.001) during culturing, while no differences were observed in the specificity (86.7% vs. 93.3%; P = 0.543). In addition, antibiotic interventions significantly lowered the positivity rate of the culturing-based method (66.0% vs. 45.5%, P = 0.021) but had no effects on the results of mNGS (82.5% vs. 77.3%, P = 0.467).
CONCLUSION
The use of mNGS could result in a higher detection rate compared to that observed with the culturing-based method in an individual with spinal infection and is particularly valuable for evaluating the effects of a mycobacterial infection or previous antibiotic intervention.
Topics: Humans; Retrospective Studies; High-Throughput Nucleotide Sequencing; Anti-Bacterial Agents; Biopsy; Mycobacterium tuberculosis; Sensitivity and Specificity
PubMed: 37237239
DOI: 10.1007/s00586-023-07707-3 -
Methods in Molecular Biology (Clifton,... 2024Intracellular pathogens comprise a diverse group of pathogens that all share a required location in a host cell to infect, survive, and replicate. Intracellular location... (Review)
Review
Intracellular pathogens comprise a diverse group of pathogens that all share a required location in a host cell to infect, survive, and replicate. Intracellular location allows pathogens to hide from host immune responses, avoid competition with other pathogens, mediate host cellular functions, replicate safely, and cause infection that is difficult to target with therapeutics. All intracellular pathogens have varying routes of infiltration into host cells and different host cell preferences. For example, bacteria Mycobacterium tuberculosis chooses to invade antigen-presenting cells, which allows them to moderate host antigen presentation to memory cells, whereas rabies virus prefers to invade neurons because they have pre-existing innate immunity protection systems. Regardless of the pathway that each intracellular pathogen follows, all share the capacity to cause disease if they succeed in entering host cells. Here, we give an overview of selected intracellular pathogens and infections they cause, immune responses they induce, and intervention strategies used to treat and control them.
Topics: Humans; Animals; Host-Pathogen Interactions; Mycobacterium tuberculosis; Immunity, Innate; Rabies virus
PubMed: 38888767
DOI: 10.1007/978-1-0716-3890-3_1 -
Frontiers in Cellular and Infection... 2023Mycobacteriophages are viruses that infect members of genus . Because of the rise in antibiotic resistance in mycobacterial diseases such as tuberculosis,...
Mycobacteriophages are viruses that infect members of genus . Because of the rise in antibiotic resistance in mycobacterial diseases such as tuberculosis, mycobacteriophages have received renewed attention as alternative therapeutic agents. Mycobacteriophages are highly diverse, and, on the basis of their genome sequences, they are grouped into 30 clusters and 10 singletons. In this article, we have described the isolation and characterization of a novel mycobacteriophage Kashi-VT1 (KVT1) infecting mc 155 () and isolated from Varanasi, India. KVT1 is a cluster K1 temperate phage that belongs to family as visualized in transmission electron microscopy. The phage genome is 61,010 base pairs with 66.5% Guanine/Cytosine (GC) content, encoding 101 putative open reading frames. The KVT1 genome encodes an immunity repressor, a tyrosine integrase, and an excise protein, which are the characteristics of temperate phages. It also contains genes encoding holin, lysin A, and lysin B involved in host cell lysis. The one-step growth curve demonstrated that KVT1 has a latency time of 90 min and an average burst size of 101 phage particles per infected cell. It can withstand a temperature of up to 45°C and has a maximum viability between pH 8 and 9. Some mycobacteriophages from cluster K are known to infect the pathogenic (); hence, KVT1 holds potential for the phage therapy against tuberculosis, and it can also be engineered to convert into an exclusively lytic phage.
Topics: Humans; Mycobacteriophages; Genome, Viral; Mycobacterium tuberculosis; Mycobacterium smegmatis; Tuberculosis; Bacteriophages
PubMed: 37545854
DOI: 10.3389/fcimb.2023.1173894 -
Science Signaling Dec 2023A virulence factor promotes foam cell formation by inhibiting DNA repair.
A virulence factor promotes foam cell formation by inhibiting DNA repair.
Topics: Mycobacterium tuberculosis; DNA Repair
PubMed: 38113336
DOI: 10.1126/scisignal.adn5031 -
Tuberculosis (Edinburgh, Scotland) Dec 2023The advent of effective drug regimen and BCG vaccine has significantly decreased the rate of morbidity and mortality of TB. However, lengthy treatment and slower... (Review)
Review
The advent of effective drug regimen and BCG vaccine has significantly decreased the rate of morbidity and mortality of TB. However, lengthy treatment and slower recovery rate, as well as reactivation of the disease with the emergence of multi-drug, extensively-drug, and totally-drug resistance strains, pose a serious concern. The complexities associated are due to the highly evolved and complex nature of the bacterium itself. One of the unique features of Mycobacterium tuberculosis [M.tb] is that it has undergone reductive evolution while maintaining and amplified a few gene families. One of the critical gene family involved in the virulence and pathogenesis is the Toxin-Antitoxin system. These families are believed to harbor virulence signature and are strongly associated with various stress adaptations and pathogenesis. The M.tb TA systems are linked with growth regulation machinery during various environmental stresses. The genes of TA systems are differentially expressed in the host during an active infection, oxidative stress, low pH stress, and starvation, which essentially indicate their role beyond growth regulators. Here in this review, we have discussed different roles of TA gene families in various stresses and their prospective role at the host-pathogen interface, which could be exploited to understand the M.tb associated pathomechanisms better and further designing the new strategies against the pathogen.
Topics: Humans; Mycobacterium tuberculosis; Tuberculosis; Toxin-Antitoxin Systems; Stress, Physiological; Bacterial Proteins
PubMed: 37722233
DOI: 10.1016/j.tube.2023.102395 -
Microbiological Research Aug 2023Being among the top 10 causes of adult deaths, tuberculosis (TB) disease is considered a major global public health concern to address. The human tuberculosis pathogen,... (Review)
Review
Being among the top 10 causes of adult deaths, tuberculosis (TB) disease is considered a major global public health concern to address. The human tuberculosis pathogen, Mycobacterium tuberculosis (Mtb), is an extremely competent and well-versed pathogen that promotes pathogenesis by evading the host immune systems through numerous tactics. Investigations revealed that Mtb could evade the host defense mechanisms by reconfiguring the host gene transcription and causing epigenetic changes. Although results indicate the link between epigenetics and disease manifestation in other bacterial infections, little is known regarding the kinetics of the epigenetic alterations in mycobacterial infection. This literature review discusses the studies in Mtb-induced epigenetic alterations inside the host and its contribution in the host immune evasion strategies. It also discusses how the Mtb-induced alterations could be used as 'epibiomarkers' to diagnose TB. Additionally, this review also discusses therapeutic interventions to be enhanced through remodification by 'epidrugs'.
Topics: Humans; Mycobacterium tuberculosis; Tuberculosis; Immune Evasion; Epigenesis, Genetic; Host-Pathogen Interactions
PubMed: 37196490
DOI: 10.1016/j.micres.2023.127400 -
International Journal of Antimicrobial... Oct 2023Pretomanid (PA-824), a novel anti-tuberculosis (TB) nitroimidazoxazine, has been approved for multi-drug-resistant TB treatment for a few years. Pretomanid has been... (Review)
Review
Pretomanid (PA-824), a novel anti-tuberculosis (TB) nitroimidazoxazine, has been approved for multi-drug-resistant TB treatment for a few years. Pretomanid has been demonstrated to be highly active against Mycobacterium tuberculosis when combined with other anti-TB drugs. This review provides an update of the current knowledge on the modes of action, resistance mechanisms, emergence of drug resistance, and status of antimicrobial susceptibility testing for pretomanid and its relevance for clinical practice. Pretomanid resistance has been reported in in-vitro and animal models but not yet in clinical trials. Pretomanid-resistance-associated mutations have been reported in the fbiA, fbiB, fbiC, fbiD, ddn and fgd1 genes. However, understanding of in-vivo molecular resistance mechanisms remains limited, and complicates the development of accurate antimicrobial susceptibility testing methods for pretomanid. As such, no reference method for antimicrobial susceptibility testing of pretomanid has been established to guide clinical use. Further studies linking specific mutations, in-vitro susceptibility, drug exposure and resistance mechanisms to treatment failure with pretomanid should be prioritized.
Topics: Animals; Antitubercular Agents; Mycobacterium tuberculosis; Nitroimidazoles; Tuberculosis; Tuberculosis, Multidrug-Resistant
PubMed: 37595848
DOI: 10.1016/j.ijantimicag.2023.106953 -
International Journal of Molecular... Dec 2023Mycolic acids constitute pivotal constituents within the cell wall structure of . Due to their structural diversity, the composition of mycolic acids exhibits... (Review)
Review
Mycolic acids constitute pivotal constituents within the cell wall structure of . Due to their structural diversity, the composition of mycolic acids exhibits substantial variations among different strains, endowing them with the distinctive label of being the 'signature' feature of mycobacterial species. Within , the primary classes of mycolic acids include α-, keto-, and methoxy-mycolic acids. While these mycolic acids are predominantly esterified to the cell wall components (such as arabinogalactan, alginate, or glucose) of , a fraction of free mycolic acids are secreted during in vitro growth of the bacterium. Remarkably, different types of mycolic acids possess varying capabilities to induce foamy macro-phages and trigger immune responses. Additionally, mycolic acids play a regulatory role in the lipid metabolism of host cells, thereby exerting influence over the progression of tuberculosis. Consequently, the multifaceted properties of mycolic acids shape the immune evasion strategy employed by . A comprehensive understanding of mycolic acids is of paramount significance in the pursuit of developing tuberculosis therapeutics and unraveling the intricacies of its pathogenic mechanisms.
Topics: Humans; Lipid Metabolism; Mycolic Acids; Mycobacterium tuberculosis; Alginates; Tuberculosis
PubMed: 38203570
DOI: 10.3390/ijms25010396 -
Acta Tropica Oct 2023Mycobacterium tuberculosis is a pathogenic bacterium that is parasitic in macrophages and show high adaptation to the host's immune response. It can also trigger a...
Mycobacterium tuberculosis is a pathogenic bacterium that is parasitic in macrophages and show high adaptation to the host's immune response. It can also trigger a complex immune response in the host. This relies on proteins encoded by a series of M. tuberculosis-encoded virulence genes. We found that the M. tuberculosis Rv3435c gene is highly conserved among pathogenic mycobacteria, and might be a virulence gene. To explore the gene function of Rv3435c, we used Mycobacterium smegmatis to construct a recombinant mycobacterium expressing Rv3435c heterologously. The results that Rv3435c is a cell wall-related protein that changes bacterial and colony morphology, inhibits the growth rate of recombinant mycobacteria, and enhances their resistance to various stresses. We also found that the fatty acid levels of the recombinant strain changed. Simultaneously, Rv3435c can inhibit the expression and secretion of inflammatory factors and host cell apoptosis, and enhance the survival of recombinant bacteria in macrophages. Experimental data indicated that Rv3435c might play an important role in Mycobacterium tuberculosis infection.
Topics: Humans; Cytokines; Mycobacterium tuberculosis; Bacterial Proteins; Host-Pathogen Interactions; Tuberculosis; Immunologic Factors
PubMed: 37355194
DOI: 10.1016/j.actatropica.2023.106974 -
International Journal of... 2023Tuberculous meningitis (TBM) is caused by the dissemination of Mycobacterium tuberculosis (MTB) from the primary site of infection to the central nervous system....
BACKGROUND
Tuberculous meningitis (TBM) is caused by the dissemination of Mycobacterium tuberculosis (MTB) from the primary site of infection to the central nervous system. However, the bacterial factors associated with the pathogenesis of TBM remain unclear. This study employed transcriptomic and proteomic methods to comprehensively analyze the changes in genes and proteins and their associated pathways in MTB strains isolated from cerebrospinal fluid (CSF) of TBM and sputum of pulmonary TB (PTB) cases.
METHODOLOGY
Five MTB strains were subjected to OMICs (transcriptomic and proteomic) analysis. Among five MTB strains, two were isolated from CSF and sputum samples of the same patient with PTB and TBM infections, one from the sputum of a different PTB patient, and a strain obtained from the CSF of another TBM patient. H37Rv was used as a reference strain. The reliability of transcriptomic results was validated by real time polymerase chain reaction with selected genes from 100 MTB isolates (CSF, 50 and sputum, 50).
RESULTS
The transcriptomic study revealed that overlapping differentially expressed genes of MTB strains isolated from TBM patients showed featured enrichment in benzoate degradation, lysine degradation, tryptophan metabolism, fatty acid degradation, ATP binding cassette transporters, microbial metabolism in diverse environments, biosynthesis of antibiotics, and metabolic pathways. Eleven genes were upregulated, and four were downregulated in MTB strains isolated from TBM compared to PTB. From proteomic analysis, we identified three candidate proteins belonging to plasminogen binding proteins (PBP) (enolase, dnaK, and isocitrate lyase 1) that were significantly upregulated in MTB strains isolated from TBM.
CONCLUSION
Overall, the transcriptomic and proteomic analyses provided an important base for understanding the unique feature of TBM pathogenesis. To the best of our knowledge, this is the first report highlighting the importance of PBPs on TBM pathogenesis.
Topics: Humans; Mycobacterium tuberculosis; Tuberculosis, Meningeal; Proteomics; Reproducibility of Results; Tuberculosis, Pulmonary; Gene Expression Profiling
PubMed: 38149538
DOI: 10.4103/ijmy.ijmy_159_23