Epidemiology of Mycobacterium abscessus

ABP-Xplorer: A Machine Learning Approach for Prediction of Antibacterial Peptides Targeting Mycobacterium abscessus-tRNA-Methyltransferase (TrmD)

Mycobacterium abscessus (MAB) infections pose a significant treatment challenge due to their intrinsic resistance to antibiotics, requiring prolonged multidrug regimens with limited success and frequent relapses. tRNA (m1G37) methyltransferase (TrmD), an enzyme essential for maintaining the reading frame during protein synthesis in MAB and other mycobacteria, is a potential therapeutic target for identifying new inhibitors. This study introduces ABP-Xplorer, a machine learning-based (ML) model designed to predict the antibacterial potential of peptides targeting MAB-TrmD ribosomal sites. A systematic evaluation of 26 machine learning models identified the Random Forest (RF) classifier as the most effective, achieving 96% accuracy. To address data set imbalance and enhance predictive reliability, the Synthetic Minority Oversampling Technique (SMOTE) was applied, improving model generalization and reducing bias. After that, an ABP-Xplorer streamlit was developed to predict positive and negative antibacterial peptides (ABP), enabling easy sequence input and classification based on predictive scoring. For validation, 12 positive peptides with high predictive scores were selected for molecular docking by HADDOCK. Docking analysis of selected peptides confirmed strong binding to TrmD, with P1, P7, P8, and P9 as top candidates. Notably, P1 exhibited the best interaction with a HADDOCK score of -102.2, followed by P7 (-93.6) and P8 (-91.4), indicating their potential for further development as TrmD inhibitors.Moreover, Ramachandran plot analysis validated the structural reliability. Future research should focus on the experimental validation of these peptides and optimizing their stability and bioavailability for therapeutic applications.

Efficacy of carbonyl cyanide-3-chlorophenylhydrazone in combination with antibiotics against Mycobacterium abscessus

Given the intrinsic resistance of Mycobacterium abscessus to a wide range of conventional antibiotics, it is urgent to explore new therapeutic approaches to manage this infection effectively. Carbonyl cyanide 3-chlorophenylhydrazone (CCCP), a proton pump inhibitor, has shown good bacteriostatic activity against M. abscessus. This study aimed to determine its synergistic antimicrobial effects when combined with commonly used antibiotics. The M. abscessus reference strain and 39 clinical isolates were collected. The minimum inhibitory concentration and fractional inhibitory concentration index were determined for the combined treatment using CCCP with various antibiotics including clarithromycin, amikacin, linezolid, bedaquiline, and clofazimine. A time-killing assay was used to measure the effect of the combined drug regimens quantitatively. The simultaneous use of CCCP with traditional antibiotics shows a synergistic effect across a wide range, significantly boosting the ability to inhibit the growth of M. abscessus throughout its growth phases. When CCCP is used in combination with clarithromycin, amikacin, and linezolid, it produces a synergistic effect on both the standard strain and most clinical isolates. When CCCP is paired with bedaquiline and clofazimine, it exhibits additive effects. Moreover, high levels of CCCP in combination with other antibiotics were found to rapidly eradicate the bacteria. The use of CCCP as a potential treatment for M. abscessus infections shows promising results, especially when combined with other antibiotics to achieve a potent bactericidal effect.IMPORTANCEMycobacterium abscessus poses a significant public health threat due to its intrinsic resistance to a broad spectrum of conventional antibiotics. This resistance necessitates urgently exploring novel therapeutic strategies to effectively combat infections caused by this pathogen. Our previous research has identified carbonyl cyanide-3-chlorophenylhydrazone (CCCP) as a potent direct antimicrobial agent against M. abscessus and as an enhancer of clarithromycin activity. Our results demonstrate that the concurrent administration of CCCP with traditional antibiotics exhibits a synergistic effect across a wide range, which could be crucial for overcoming the challenges posed by M. abscessus infections. Furthermore, the use of high concentrations of CCCP in combination with other antibiotics was found to rapidly eliminate M. abscessus, suggesting a potential therapeutic advantage. These insights not only advance our understanding of antimicrobial synergy but also hold promise for the development of more effective treatment regimens against drug-resistant M. abscessus infections.

Durlobactam to boost the clinical utility of standard of care β-lactams against Mycobacterium abscessus lung disease

β-Lactams present several desirable pharmacodynamic features leading to the rapid eradication of many bacterial pathogens. Imipenem (IPM) and cefoxitin (FOX) are injectable β-lactams recommended during the intensive treatment phase of pulmonary infections caused by Mycobacterium abscessus (Mab). However, their potency against Mab is many-fold lower than against Gram-positive and Gram-negative pathogens for which they were optimized, putting into question their clinical utility. Here, we show that adding the recently approved durlobactam-sulbactam (DUR-SUL) pair to either IPM or FOX achieves growth inhibition, bactericidal, and cytolytic activity at concentrations that are within those achieved in patients and below the clinical breakpoints established for each agent. Synergies between DUR-SUL and IPM or FOX were confirmed across a large panel of clinical isolates. Through in vitro resistant mutant selection, we also show that adding DUR-SUL abrogates acquired resistance to IPM and FOX. Since the use of β-lactam injectables is firmly grounded in clinical practice during the intensive treatment phase of Mab pulmonary disease, their potentiation by FDA-approved DUR-SUL to bring minimum inhibitory concentration distributions within achievable concentration ranges could offer significant short-term benefits to patients, while novel β-lactam combinations are optimized specifically against Mab pulmonary infections, for which no reliable cure exists.

Identification of biomarkers associated with ferroptosis in macrophages infected with Mycobacterium abscessus using bioinformatic tools

Mycobacterium abscessus is a rapidly growing nontuberculous mycobacterium that causes severe pulmonary infections. Recent studies indicate that ferroptosis may play a critical role in the pathogenesis of M. abscessus pulmonary disease. We obtained gene expression microarray data from the Gene Expression Omnibus database, focusing on THP-1-derived macrophages infected with M. abscessus and uninfected controls. Differentially expressed genes related to ferroptosis were identified through weighted gene co-expression network analysis and the "limma" package, followed by gene set variation analysis and gene set enrichment analysis for enrichment assessment. To explore regulatory network relationships among hub genes, we constructed RBP-mRNA, ceRNA, and TF-mRNA networks. Additionally, a protein-protein interaction network was built, and functional enrichment analyses were conducted for the hub genes. The diagnostic value of these genes was assessed using receiver operating characteristic curves. Six differentially expressed genes associated with ferroptosis were identified in M. abscessus infection. The receiver operating characteristic curves demonstrated that these genes had excellent predictive value for the infection. Functional enrichment analysis showed that these genes were involved in immune responses, inflammation, cellular metabolism, cell death, and apoptosis. Pathway enrichment analysis revealed significant enrichment in pathways related to apoptosis, inflammation, and hypoxia. The RBP-mRNA network highlighted significant interactions between hub genes and key RNA-binding proteins, while the ceRNA network predicted that miRNAs and lncRNAs regulate ferroptosis-related genes NACC2 and ITPKB. Furthermore, interactions between the hub gene HSD3B7 and transcription factors LMNB1 and ASCL1 may promote ferroptosis in macrophages by influencing iron metabolism and reactive oxygen species production, contributing to the M. abscessus infection process. Our findings identified biomarkers linked to ferroptosis in M. abscessus infection, providing new insights into its pathogenic mechanisms and potential therapeutic strategies.

Evaluation of a Commercial Multiplex Real-Time PCR with Melting Curve Analysis for the Detection of Mycobacterium tuberculosis Complex and Five Nontuberculous Mycobacterial Species

BACKGROUND

Accurate and timely diagnosis of mycobacterial infections, including Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM), is crucial for effective disease management.

METHODS

This study evaluated the performance of the NeoPlex TB/NTM-5 Detection Kit (NeoPlex assay, Seongnam, Republic of Korea), a multiplex real-time PCR assay that incorporates melting curve analysis, compared with the line-probe assay (LPA). The NeoPlex assay could simultaneously detect and differentiate MTBC from five other NTM species: Mycobacterium intracellulare, Mycobacterium avium, Mycobacterium kansasii, Mycobacterium abscessus, and Mycobacterium massiliense. A total of 91 acid-fast bacillus culture-positive samples, comprising 36 MTBC and 55 NTM isolates, were collected from the Korea University Anam Hospital.

RESULTS

The NeoPlex assay successfully detected nucleic acids in 87 of the 91 isolates (95.6%). Notably, it identified additional mycobacterial nucleic acids not detected by the LPA in eight isolates. These findings were confirmed via DNA sequencing. The assay had 100% sensitivity and specificity for M. intracellulare, M. abscessus, M. massilense, NTM, and MTBC, whereas it had 100% specificity and sensitivity of 90.9% and 75.0% for M. avium and M. kansasii, respectively.

CONCLUSIONS

These results highlight the potential of the NeoPlex assay to enhance rapid and accurate diagnosis of mycobacterial infections, particularly in settings in which prompt treatment initiation is essential.

Port-a-Cath Infection of Mycobacterium senegalense: First Italian Case Report

Mycobacterium senegalense is a Non-Tuberculous Mycobacterium (NTM) belonging to the M. fortuitum group, often associated with veterinary diseases, such as bovine farcy. However, it can also cause human infections and appears to be involved in Catheter-Associated Infections in immunocompromised patients. Here, we report the first Italian isolation of a strain of M. senegalense from a 16-year-old oncological female patient being treated at Fondazione IRCCS Policlinico San Matteo Pavia (Italy). Following pain at the Port-a-Cath site, a pus culture was collected and the positivity for the M. fortuitum group revealed the NTM infection. Antimicrobial susceptibility tests were performed and interpreted according to the available CLSI breakpoints. This information allowed us to implement the correct antibiotic therapy that, together with the device removal, led to the patient's recovery. Finally, due to the increasing number of isolations, the possible presence of NTM infections in prosthetic devices should be among the primary diagnostic questions in a clinical setting.

Extrapulmonary Mycobacterium abscessus Infections, France, 2012-20201

Mycobacterium abscessus infection is challenging to treat. Extrapulmonary M. abscessus infections (EP-MAB) are less common than pulmonary M. abscessus infections. To evaluate treatment regimens, we retrospectively analyzed consecutive microbiologically confirmed EP-MAB cases diagnosed in France during 2012-2020. We studied 45 patients with EP-MAB, including 14 bone and joint infections, 10 skin and soft tissue infections, and 8 lymph node infections. Most (62%) patients had no reported immunodeficiency. In 27 patients, EP-MAB followed healthcare-associated (44%) or environmental (16%) injuries. Of the 45 isolates, 25 were subspecies abscessus, 10 bolletii, and 9 massiliense; 1 was unidentified. Cure was achieved for 36 (80%) patients who received a median antimicrobial regimen of 6 months; 22 (55%) also underwent surgery. Four patients died, and 5 were unavailable for follow-up. EP-MAB predominantly affects immunocompetent patients after an injury; outcomes are favorable. We propose a >6-month regimen of antimicrobial therapy with consideration for surgery and regular patient reassessment.

An alveolus lung-on-a-chip model of Mycobacterium fortuitum lung infection

Lung disease due to non-tuberculous mycobacteria (NTM) is rising in incidence. While both two dimensional cell culture and animal models exist for NTM infections, a major knowledge gap is the early responses of human alveolar and innate immune cells to NTM within the human alveolar microenvironment. Here we describe development of a humanized, three-dimensional, alveolus lung-on-a-chip (ALoC) model of Mycobacterium fortuitum lung infection that incorporates only primary human cells such as pulmonary vascular endothelial cells in a vascular channel, and type I and II alveolar cells and monocyte-derived macrophages in an alveolar channel along an air-liquid interface. M. fortuitum introduced into the alveolar channel primarily infected macrophages, with rare bacteria inside alveolar cells. Bulk-RNA sequencing of infected chips revealed marked upregulation of transcripts for cytokines, chemokines and secreted protease inhibitors (SERPINs). Our results demonstrate how a humanized ALoC system can identify critical early immune and epithelial responses to M. fortuitum infection. We envision potential application of the ALoC to other NTM and for studies of new antibiotics.

Combination of Imipenem-Cilastatin-Relebactam and Amoxicillin in the Antibiotic Regimen in Two Cases of Mycobacterium abscessus Lung Infection

Mycobacterium abscessus is a difficult-to-treat, multidrug-resistant human pathogen. Relebactam has been shown to inhibit M. abscessus β-lactamase (BLAMab) and increase the activity of imipenem and amoxicillin. We present two cases of lung infection due to M. abscessus, one caused by M. abscessussubsp. massiliense and the other by subsp. abscessus. Both strains showed moderate sensitivity to imipenem, and the second strain was also resistant to macrolides. A multidrug antibiotic regimen was administered in both cases, which included imipenem/cilastatin/relebactam adjusted to the estimated glomerular filtration rate (eGFR) and amoxicillin for three months. The regimen was well tolerated and both patients improved both clinically and radiologically after the first phase of treatment. The results of our patients indicate that the combination of imipenem/cilastatin/relebactam and amoxicillin could be used in the future in difficult infections by M. abscessus.

A laboratory perspective on Mycobacterium abscessus biofilm culture, characterization and drug activity testing

Mycobacterium abscessus is an emerging opportunistic pathogen causing severe pulmonary infections in patients with underlying lung disease and cystic fibrosis in particular. The rising prevalence of M. abscessus infections poses an alarming threat, as the success rates of available treatment options are limited. Central to this challenge is the absence of preclinical in vitro models that accurately mimic in vivo conditions and that can reliably predict treatment outcomes in patients. M. abscessus is notorious for its association with biofilm formation within the lung. Bacteria in biofilms are more recalcitrant to antibiotic treatment compared to planktonic bacteria, which likely contributes to the lack of correlation between preclinical drug activity testing (typically performed on planktonic bacteria) and treatment outcome. In recent years, there has been a growing interest in M. abscessus biofilm research. However, the absence of standardized methods for biofilm culture, biofilm characterization and drug activity testing has led to a wide spectrum of, sometimes inconsistent, findings across various studies. Factors such as strain selection, culture medium, and incubation time hugely impact biofilm development, phenotypical characteristics and antibiotic susceptibility. Additionally, a broad range of techniques are used to study M. abscessus biofilms, including quantification of colony-forming units, crystal violet staining and fluorescence microscopy. Yet, limitations of these techniques and the selected readouts for analysis affect study outcomes. Currently, research on the activity of conventional antibiotics, such as clarithromycin and amikacin, against M. abscessus biofilms yield ambiguous results, underscoring the substantial impact of experimental conditions on drug activity assessment. Beyond traditional drug activity testing, the exploration of novel anti-biofilm compounds and the improvement of in vitro biofilm models are ongoing. In this review, we outline the laboratory models, experimental variables and techniques that are used to study M. abscessus biofilms. We elaborate on the current insights of M. abscessus biofilm characteristics and describe the present understanding of the activity of traditional antibiotics, as well as potential novel compounds, against M. abscessus biofilms. Ultimately, this work contributes to the advancement of fundamental knowledge and practical applications of accurate preclinical M. abscessus models, thereby facilitating progress towards improved therapies for M. abscessus infections.

Structural basis for specific inhibition of salicylate synthase from Mycobacterium abscessus

Blocking iron uptake and metabolism has been emerging as a promising therapeutic strategy for the development of novel antimicrobial compounds. Like all mycobacteria, M. abscessus (Mab) has evolved several countermeasures to scavenge iron from host carrier proteins, including the production of siderophores, which play a crucial role in these processes. In this study, we solved, for the first time, the crystal structure of Mab-SaS, the first enzyme involved in the biosynthesis of siderophores. Moreover, we screened a small, focused library and identified a compound exhibiting a potent inhibitory effect against Mab-SaS (IC50 ≈ 2 μM). Its binding mode was investigated by means of Induced Fit Docking simulations, performed on the crystal structure presented herein. Furthermore, cytotoxicity data and pharmacokinetic predictions revealed the safety and drug-likeness of this class of compounds. Finally, the crystallographic data were used to optimize the model for future virtual screening campaigns. Taken together, the findings of our study pave the way for the identification of potent Mab-SaS inhibitors, based on both established and unexplored chemotypes.