Drug Susceptibility and Mutation Profiles in Mycobacterium tuberculosis Isolates from a Tertiary Care Hospital in Kerala, India.

The rising prevalence of drug-resistant Mycobacterium tuberculosis (MTB) strains poses a significant challenge to global tuberculosis (TB) control efforts. This study aimed to analyze drug resistance patterns and investigate the molecular characteristics of 193 MTB clinical isolates to shed light on the mechanisms of drug resistance. Of the 193 MTB clinical isolates, 28.5% (n = 53) exhibited mono-drug or multidrug resistance. Pyrazinamide mono-drug resistance (PZAr) was the most prevalent (17%, n = 33), followed by isoniazid mono-drug resistance (3.6%, n = 7). Rifampicin resistance was associated with mutations in the rpoB gene (D435Y, D435V, S450L, L452P). Isoniazid resistance mutations were found in the katG (S315T), inhA (C[-15] T), and ndh (R268H) genes, whereas ethambutol resistance mutations were observed in the embB gene (M306V, M306I, M306L, G406S, Q497R). Surprisingly, 94% of PZAr isolates (n = 31) showed no mutations in the pncA or rpsA genes. The presence of the R268H mutation in the ndh gene, not previously linked to PZAr, was detected in 15% of PZAr isolates (n = 5), suggesting its potential contribution to PZAr in specific cases but not as a predominant mechanism. The specific molecular mechanisms underlying PZAr in the majority of the isolates remain unknown, emphasizing the need for further research to uncover the contributing factors. These findings contribute to the understanding of drug resistance patterns and can guide future efforts in TB control and management.

Non-invasive molecular biomarkers for monitoring solid organ transplantation: A comprehensive overview.

Solid organ transplantation is a life-saving intervention for individuals with end-stage organ failure. Despite the effectiveness of immunosuppressive therapy, the risk of graft rejection persists in all viable transplants between individuals. The risk of rejection may vary depending on the degree of compatibility between the donor and recipient for both human leucocyte antigen (HLA) and non-HLA gene-encoded products. Monitoring the status of the allograft is a critical aspect of post-transplant management, with invasive biopsies being the standard of care for detecting rejection. Non-invasive biomarkers are increasingly being recognized as valuable tools for aiding in the detection of graft rejection, monitoring graft status and evaluating the efficacy of immunosuppressive therapy. Here, we focus on the importance of molecular biomarkers in solid organ transplantation and their potential role in clinical practice. Conventional molecular biomarkers used in transplantation include HLA typing, detection of anti-HLA antibodies, killer cell immunoglobulin-like receptor genotypes, and anti-MHC class 1-related chain A antibodies, which are important for assessing the compatibility of the donor and recipient. Emerging molecular biomarkers include the detection of donor-derived cell-free DNA, microRNAs (regulation of gene expression), exosomes (small vesicles secreted by cells), and kidney solid organ response test, in the recipient's blood for early signs of rejection. This review highlights the strengths and limitations of these molecular biomarkers and their potential role in improving transplant outcomes.

Efficacy of Lysostaphin functionalized silicon catheter for the prevention of Staphylococcus aureus biofilm.

Staphylococcus aureus readily forms biofilms on tissue and indwelling catheter surfaces. These biofilms are resistant to antibiotics. Consequently, effective prevention and treatment strategies against staphylococcal biofilms are actively being pursued over the past two decades. One of the proposed strategies involve the incorporation of antibiotics and antiseptics into catheters, however, a persistent concern regarding the possible emergence of antimicrobial resistance is associated with these medical devices. In this study, we developed two types of silicone catheters: one with Lysostaphin (Lst) adsorbed onto the surface, and the other with Lst functionalized on the surface. To confirm the presence of Lst protein on the catheter surface, we conducted FTIR-ATR and SEM-EDS analysis. Both catheters exhibited hemocompatibility, biocompatibility, and demonstrated antimicrobial and biofilm prevention activities against both methicillin-sensitive and resistant strains of S. aureus. Furthermore, the silicone catheters that were surface-functionalized with Lst showed substantially better and more persistent anti-biofilm effects when compared to the catheters where Lst was surface-adsorbed, both under in vitro static and flow conditions, as well as in vivo in BALB/c mice. These results indicate that surface-functionalized Lst catheters have the potential to serve as a promising new medical device for preventing S. aureus biofilm infections in humans.

Identification of a Staphylococcus aureus amidase catalytic domain inhibitor to prevent biofilm formation by sequential virtual screening, molecular dynamics simulation and biological evaluation.

Staphylococcus aureus (S. aureus) is one of the common causes of implant associated biofilm infections and their biofilms are resistant to antibiotics. S. aureus amidase (AM) protein, a cell wall hydrolase that cleaves the amide bond between N-acetylmuramic acid and L-alanine residue of the stem peptide, is several fold over-expressed under biofilm conditions. Previous studies demonstrated an autolysin mutant in S. aureus that lacks the AM protein, is highly impaired in biofilm development. We carried out a structure-based small molecule design using the crystal structure of AM protein catalytic domain to identify inhibitors that can block amidase activity and therefore inhibits S. aureus biofilm formation. Sequential virtual screening followed by pharmacokinetic analysis and bioassay studies filtered 25 small molecules from different databases. Two compounds from the SPECS database, SPECS-1 and SPECS-2, were selected based on the best docking score and minimum biofilm inhibitory concentration towards S. aureus biofilms. SPECS-1 and SPECS-2 were further tested for their structural/energetic stability in complex with the AM protein using molecular dynamics simulation and MM-GBSA techniques. In vitro, biofilm inhibition studies on different surfaces confirmed that treatment with SPECS-1 and SPECS-2 at a concentration of 250 µg/ml exhibited significant prevention and disruption of S. aureus biofilms. Finally, the in vitro anti-biofilm activities of these two compounds were validated against Methicillin-resistant S. aureus clinical isolates. We concluded that the discovered compounds SPECS-1 and SPECS-2 are safe and exhibit biofilm preventive and disruption activity for inhibiting the S. aureus biofilms and hence can be used to treat implant-associated biofilm infections.

Exploring alternative strategies for Staphylococcus aureus nasal decolonization: insights from preclinical studies.

Nasal decolonization of Staphylococcus aureus with the antibiotic mupirocin is a common clinical practice before complex surgical procedures, to prevent hospital acquired infections. However, widespread use of mupirocin has led to the development of resistant S. aureus strains and there is a limited scope for developing new antibiotics for S. aureus nasal decolonization. It is therefore necessary to develop alternative and nonantibiotic nasal decolonization methods. In this review, we broadly discussed the effectiveness of different nonantibiotic antimicrobial agents that are currently not in clinical practice, but are experimentally proved to be efficacious in promoting S. aureus nasal decolonization. These include lytic bacteriophages, bacteriolytic enzymes, tea tree oil, apple vinegar, and antimicrobial peptides. We have also discussed the possibility of using photodynamic therapy for S. aureus nasal decolonization. This article highlights the importance of further large scale clinical studies for selecting the most suitable and alternative nasal decolonizing agent.

Identification of a PD1/PD-L1 inhibitor by structure-based pharmacophore modelling, virtual screening, molecular docking and biological evaluation.

PD-1/PD-L1 is a critical druggable target for immunotherapy against sepsis. Chemoinformatics techniques involved the structure-based 3D pharmacophore model development followed by virtual screening of small molecule databases to identify the small molecules against PD-L1 pathway inhibition. Raltitrexed and Safinamide act as potent repurposed drugs, and three other Specs database compounds using in silico methods. These compounds were screened based on the pharmacophore fit score and binding affinity towards the active site of the PD-L1 protein. In silico pharmacokinetic profiling of these screened compounds was done to test their biological activity. Next, experimental validation of the best four virtually screened hits was done in vitro for its hemocompatibility and cytotoxicity. Among these, Raltitrexed, Safinamide and Specs compound (AK-968/40642641) effectively increased the proliferation of immune cells and IFN-γ production. These compounds can act as potent PDL-1 inhibitors for adjuvant therapy against sepsis.

An update on possible alternative therapeutics for future periodontal disease management.

Periodontitis is an inflammatory disease caused by microbial infections of the gum. At an advanced stage, periodontitis can even destroy the alveolar bone. Fusobacterium nucleatum, Prevotella intermedia, Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Capnocytophaga gingivalis, and Pr. nigrescens are the major pathogens in periodontitis. Scaling and root planning are used together with local or systemic antibiotics to treat periodontitis. The difficulty in complete eradication of periodontal pathogens frequently leads to the relapse of the disease. As not many new antibiotics are available in the market, many researchers are now focusing on developing alternative strategies against periodontal microbes. This review provides an overview of the possible use of bacteriophages, lysins, honey, plant extracts, metallic salts, nanoparticles, and vaccines as alternative therapeutic agents against periodontal infections. The information provided here could help in designing alternative therapeutics for the treatment of periodontal infections.

Inhibitory Potential of Chromene Derivatives on Structural and Non-Structural Proteins of Dengue Virus.

Dengue fever is a mosquito-borne viral disease that has become a serious health issue across the globe. It is caused by a virus of the Flaviviridae family, and it comprises five different serotypes (DENV-1 to DENV-5). As there is no specific medicine or effective vaccine for controlling dengue fever, there is an urgent need to develop potential inhibitors against it. Traditionally, various natural products have been used to manage dengue fever and its co-morbid conditions. A detailed analysis of these plants revealed the presence of various chromene derivatives as the major phytochemicals. Inspired by these observations, authors have critically analyzed the anti-dengue virus potential of various 4H chromene derivatives. Further, in silico, in vitro, and in vivo reports of these scaffolds against the dengue virus are detailed in the present manuscript. These analogues exerted their activity by interfering with various stages of viral entry, assembly, and replications. Moreover, these analogues mainly target envelope protein, NS2B-NS3 protease, and NS5 RNA-dependent RNA polymerase, etc. Overall, chromene-containing analogues exerted a potent activity against the dengue virus and the present review will be helpful for the further exploration of these scaffolds for the development of novel antiviral drug candidates.

Integration of C-band SAR and high-resolution optical images for delineating palaeo-channels in Nagaur and Barmer districts, western Rajasthan, India.

Identifying hitherto unknown palaeo-channels, especially in the arid regions of the Thar Desert, is crucial since these channels may form excellent aquifers, and are also associated with valuable ore deposits of many precious minerals. This study employed integrated C-band Synthetic Aperture Radar (SAR) of Sentinel-1A and high-resolution multispectral Sentinel-2A data of pre- and post-monsoon seasons (June and November) to delineate playas and palaeo-channels. This approach is the first of its kind for this area. The palaeo-channels were delineated through a detailed visual inspection of colour composite (CC) images of Sentinel-2A data, SAR backscatter (VH) images and fused SAR and optical images. Then, we studied the topographic profiles generated from the Shuttle Radar Topography Mission - Digital Elevation Model (SRTM-DEM) across the identified palaeo-channels, Normalized Difference Vegetation Index (NDVI) and Normalized Difference Water Index (NDWI) to further confirm the existence of a palaeo-channel's course and playas. As a result, several playas and palaeo-channels in the area were successfully identified, some of which were previously unmapped and undetected. The results indicate that the post-monsoon datasets are more useful for the precise delineation of palaeo-channels due to the presence of relatively higher moisture along the palaeo-channels' courses.

A new approach against Helicobacter pylori using plants and its constituents: A review study.

Helicobacter pylori is a Gram-negative, spiral-shaped bacillus that colonizes 50% of the world population and is considered a class 1 carcinogen by the World Health Organization. This pathogen is the most common cause of infection-related cancers. Apart from cancer, it also causes several gastric and extra gastric diseases. Eradication of H. pylori using antibiotics is a global challenge because of its drug resistance. Alternative treatment options are gaining more attention to tackle drug-resistant H. pylori infections. Several medicinal plants and their isolated compounds have been reported for their antimicrobial activity against H. pylori. The mechanism of action of many of these plant extracts and plant-derived compounds is different from that of conventional antibiotics. Therefore they are shown to be effective against drug-resistant strains of H. pylori. They act by inhibiting bacterial enzymes, adhesions with gastric mucosa, suppression of nuclear factor-κB and by inhibition of oxidative stress. Extracts from Pistacia lentiscus, Brassica oleracea, Glycyrrhiza glabra, Camellia sinensis, Cinnamomum cassia, Allium sativum and Nigella sativa plants and isolated phyto-compounds such as curcumin, resveratrol, quercetin, allicin and ellagic acid demonstrated antimicrobial activity against H. pylori under in vivo conditions. The plant extracts of Zingiber officinale, Glycyrrhiza glabra; and phytochemical allicin and berberine when combined with standard treatment, result in a dramatic increase in H. pylori eradication. In this review, we highlighted the therapeutic efficacy of different plant extracts and isolated phyto compounds against H. pylori infection and described their role in tackling H. pylori resistance to antibiotics.

Protective efficacy of Alum adjuvanted Amidase protein vaccine against Staphylococcus aureus infection in multiple mouse models.

AIMS: Staphylococcus aureus is an opportunistic pathogen of humans. No commercial vaccine is available to combat S. aureus infections. In this study, we have investigated the protective immune response generated by S. aureus non-covalently associated cell wall surface protein N-acetylmuramoyl-L-alanine amidase (AM) in combination with Alum (Al) and heat-killed S. aureus (hkSA) using murine models. METHODS AND RESULTS: BALB/c mice were immunized with increasing concentrations of AM antigen or hkSA to determine their optimum concentration for vaccination. Fifty micrograms of AM and hkSA each were found to generate maximum anti-AM IgG antibody production. BALB/c mice were immunized next with 50 µg of AM, 50 µg of hKSA and 1 mg Al vaccine formulation. Vaccine efficacy was validated by challenging immunized BALB/c mice with S. aureus Newman and three clinical methicillin-resistant S. aureus strains. AM-hkSA-Al-immunized mice generated high anti-AM IgG antibody response with IgG1 and IgG2b as the predominant immunoglobulin subtypes. Increased survival (60%-90%) with decreased clinical disease symptoms was observed in the vaccinated BALB/c mice group. A significantly lower bacterial load and decreased kidney abscess formation was observed following the challenge with S. aureus in the vaccinated BALB/c mice group. Furthermore, the efficacy of AM-hkSA-Al vaccine was also validated using C57 BL/6 and Swiss albino mice. CONCLUSIONS: Using murine infection models, we have demonstrated that AM-hkSA-Al vaccine would be effective in preventing S. aureus infections. SIGNIFICANCE AND IMPACT OF STUDY: AM-hkSA-Al vaccine elicited strong immune response and may be considered for future vaccine design against S. aureus infections.

Superhydrophilic multifunctional nanotextured titanium dental implants: in vivo short and long-term response in a porcine model.

Current clinical demand in dental implantology is for a multifunctional device with optimum mechanical properties, improved biocompatibility and bioactivity, and having differential interactions with cells and pathogenic agents. This would minimise bacterial infection, biofilm formation and modulate inflammation, leading to a fast and durable osseointegration. The present study intends to establish the multifunctional behaviour of surface modified titanium dental implants that are superhydrophilic, with unique micro-nano or nanoscale topographies, developed by a facile hydrothermal technique. Here, the short and long-term performances of these textured implants are tested in a split mouth design using a porcine model, in pre- and post-loaded states. Quantitative and qualitative analyses of the bone implant interphase are performed through µ-CT and histology. Parameters that evaluate bone mineral density, bone contact volume and bone implant contact reveal enhanced bone apposition with better long-term response for the nano and micro-nano textured surfaces, compared to the commercial microtextured implant. Concurrently, the nanoscale surface features on implants reduced bacterial attachment by nearly 90% in vivo, outperforming the commercial variant. This preclinical evaluation data thus reveal the superiority of nano/micro-nano textured designs for clinical application and substantiate their improved osseointegration and reduced bacterial adhesion, thus proposing a novel dental implant with multifunctional characteristics.

Epidemiology of Nontuberculous Mycobacterial Infection in Tuberculosis Suspects.

Nontuberculosis mycobacteria (NTM) are opportunistic pathogens that cause a wide range of illnesses. Here, the species distribution and prevalence of NTM infections in tuberculosis suspects was analyzed. A total of 7,073 specimens from pulmonary and extrapulmonary sites were analyzed, and 709 (10%) were found to be culture positive for mycobacteria. Of these, 85.2% were identified as Mycobacterium tuberculosis complex and 14.8% as NTM (65.7% rapid growers and 34.3% slow growers). Speciation of the NTM isolates (n = 69) identified 19 NTM species. M. abscessus (33.3%) and M. fortuitum (24.6%) were the most dominant NTM species isolated from the patients, followed by M. porcinum (5.8%) and M. parascrofulaceum (4.3%). We also report peritonitis caused by rapidly growing NTM among the patients undergoing continuous ambulatory peritoneal dialysis and a case of M. senegalense peritonitis. A low prevalence but high species diversity of NTM was detected in our study. The high species diversity of NTM necessitates the need to unequivocally identify mycobacterial isolates for appropriate treatment.

Candidatus Dirofilaria Hongkongensis Infections in Humans During 2005 to 2020, in Kerala, India.

We tried to determine the epidemiology and species of human dirofilariasis observed at two tertiary care hospitals in Kerala. We searched the hospital database to identify cases of dirofilariosis from January 2005 to March 2020. Along with human isolates, one dog Dirofilaria isolate was also subjected to PCR and sequencing of pan filarial primers cytochrome oxidase subunits 1 and 12S rDNA. We documented 78 cases of human dirofilariosis. The orbit, eyelid, and conjunctiva were the most commonly affected sites. Molecular characterization identified one dog and five human isolates as Candidatus Dirofilaria Hongkongensis. A rare case of subconjunctival infestation by B. malayi was also documented. Human dirofilariosis is a public health problem in the state of Kerala in India, and it is mostly caused by Candidatus Dirofilaria Hongkongensis. We propose that all diroifilaria isolates are subjected to sequencing for identification.

Prevalence of high-risk HPV and its genotypes-Implications in the choice of prophylactic HPV vaccine.

The prevalence of human papillomavirus (HPV) types varies geographically between various countries and different parts of the same country. The efficacy of the HPV vaccines is dependent on the prevalent HPV types. Here, we have studied the prevalence of high-risk HPV (hrHPV) and its genotypes in women in our population. Cervical samples of 2443 women were screened for the presence of hrHPV using the careHPV system. To determine the HPV genotypes, viral DNA was isolated from the hrHPV-positive samples, nested PCR was used to amplify the L1 hypervariable region, and was subjected to Sanger sequencing. The prevalence of hrHPV was found to be 2%. HPV16 (52%), HPV33 (40%), HPV18 (4%), HPV31 (2%), and HPV66 (2%) genotypes were found in this study. In Kerala, HPV16 and HPV33 genotypes were found to be significantly higher compared with the other HPV types detected. As the bivalent (Cervarix) and quadrivalent (Gardasil-4) vaccines offer limited cross-protection against HPV33, nonavalent (Gardasil 9) vaccine would be more effective in preventing cervical carcinoma in Kerala.

Comparison of Phenotypic MRSA Detection Methods with PCR for mecA Gene in the Background of Emergence of Oxacillin-Susceptible MRSA.

Background: Phenotypic methods for detection of methicillin resistance in Staphylococcus aureus (MRSA) can be inaccurate due to heterogeneous expression of resistance and due to environmental factors that influence the expression of resistance. This study aims to compare various phenotypic methods of detection of methicillin resistance with polymerase chain reaction (PCR) for mecA gene and to detect the presence of oxacillin-susceptible MRSA (OS-MRSA). Materials and Methods: A total of 150 S. aureus isolates were tested using cefoxitin disk diffusion, oxacillin salt agar (OSA), latex agglutination test for penicillin binding protein 2a antigen, chromogenic MRSA ID agar, and mecA PCR. Results: Using PCR as the gold standard, 91 (60.66%) of 150 clinical S. aureus strains were identified as MRSA. Three oxacillin-susceptible (minimum inhibitory concentration ≤2 µg/mL) mecA-positive isolates were classified as OS-MRSA. Among the different phenotypic MRSA detection methods studied, latex agglutination had the highest sensitivity and specificity (98.9% and 98.3%), followed by cefoxitin disk diffusion (95.6% and 98.3%), MRSA ID (97.8% and 83.05%), and OSA (86.81% and 94.92%). Conclusion: The sensitivity of cefoxitin disk diffusion method may be reduced in areas with a high prevalence of OS-MRSA where a combination of cefoxitin disk diffusion test with MRSA ID agar or latex agglutination is recommended.

Improving Diagnosis of Hepatitis C Virus Infection Using Hepatitis C Core Antigen Testing in a Resource-Poor Setting.

INTRODUCTION: We compared the hepatitis C virus (HCV) core antigen test with the HCV RNA assay to confirm anti-HCV results to determine whether the HCV core antigen test could be used as an alternative confirmatory test to the HCV RNA test. METHODS: Sera from 156 patients were analyzed for anti-HCV and HCV core antigen using a chemiluminescent microparticle immunoassay (Architect i2000SR) and for HCV RNA using the artus HCV RG RT-PCR Kit (QIAGEN) in a Rotor-Gene Q instrument. RESULTS: The diagnostic sensitivity, specificity, and positive and negative predictive values of the HCV core antigen assay compared to the HCV RNA test were 77.35%, 100%, 100%, and 89.38%, respectively. HCV core antigen levels showed a good correlation with those from HCV RNA quantification (r =0.872). However, 13 samples with a viral load of less than 4000 IU/mL were negative in the HCV core antigen assay. All gray-zone reactive samples were also RNA positive and were positive on repeat testing. CONCLUSIONS: The Architect HCV core antigen assay is highly specific and has an excellent positive predictive value. At the present level of sensitivity (77%), the study is still relevant in a low-income setting in which most of the HCV-positive patients would go undiagnosed, since HCV RNA testing is not available and/or not affordable. HCV core antigen testing can also help determine the true burden of infection in a population, considering the fact that almost 50% of the anti-HCV positive cases are negative for HCV RNA.

Interaction mechanism of Mycobacterium tuberculosis GroEL2 protein with macrophage Lectin-like, oxidized low-density lipoprotein receptor-1: An integrated computational and experimental study.

BACKGROUND: Bacterial surface proteins act as potential adhesins or invasins. The GroEL is a signal peptide-free surface expressed protein that aids adhesion in Escherichia coli by binding to LOX-1 receptor of the host cells. Mycobacterium tuberculosis (Mtb) expresses GroEL2 protein, having high level sequence identity with E. coli GroEL. This study investigates the interaction mechanism of GroEL2 protein of Mtb with LOX-1 of macrophages using integrated computational and experimental approach. METHODS: Mtb GroEL2 protein was purified as histidine tagged protein using Ni-NTA chromatography. Confocal and scanning electron microscopies were used to study the uptake of GroEL2 coated fluorescent latex beads through the LOX-1 receptor in RAW264.7 macrophage cell line. Docking studies were performed to understand the interaction between the GroEL2 and LOX-1 proteins. Polyinosinic acid (PIA) was used as a LOX-1 inhibitor in both in silico and in vitro experiments. RESULTS: GroEL2 protein coating enhances uptake of latex beads into macrophages through LOX-1 receptor. LOX-1 inhibitor PIA decreased the uptake of GroEL2 coated latex beads. GroEL2 interacts with the key ligand binding regions of the LOX-1 receptor, such as the basic spine and the saddle hydrophobic patch. PIA molecule destabilized the LOX-1-GroEL2 docked complex. CONCLUSION: Surface associated GroEL2 protein of Mtb is a potential ligand for macrophage LOX-1 receptor. Interaction between GroEL2 and LOX-1 receptor may be utilized by Mtb to gain its intracellular access. GENERAL SIGNIFICANCE: Surface associated GroEL2 of Mtb may bind to the macrophage LOX-1 receptor, enabling the internalization of the bacteria and progression of the infection.