Current treatment of nontuberculous mycobacteriosis: an update

Exploring binding preferences: Cu(II), Ni(II), and Zn(II) complexes of mycobacterial GroEL1 His-rich and Glu/His-rich domains

Mycobacterial histidine-rich GroEL1 protein significantly differs from the well-known methionine-glycine-rich GroEL chaperonin and most preferably participates in Cu(II) homeostasis. Some GroEL1 proteins, however, do not possess six but only three histidine residues and more acidic residues that can function as binding sites for metal ions. To evaluate the importance of this difference, we examined and compared the properties of GroEL1 His-rich or Glu/His-rich C-terminal domains as ligands for Cu(II), Ni(II), and Zn(II) ions. We studied the stoichiometry, stability, and binding sites of Cu(II)/Ni(II)/Zn(II) complexes of two model peptides: XEN = Ac-DKPEEEEDGHGHAH (M. xenopi) and ABS = Ac-DKPAEEADHGHGHHGHAH (M. abscessus) in the pH range 2-11. In the case of Cu(II), Ni(II), and Zn(II) complexes of XEN and ABS, ABS always formed more stable complexes. For XEN, there seemed to be no preference for Ni(II) or Zn(II) ions. In contrast, for ABS, Zn(II) formed a complex that was slightly more stable than the one formed by Ni(II). This may be due to the 6 His residues, which preferentially interact with Zn(II) rather than Ni(II). The study identified that an equilibrium of complexes-known as polymorphism-may occur in ABS complexes. Therefore, distinct sets of histidine residues may be involved in metal binding.

Hierarchy and interconnected networks in the WhiB7 mediated transcriptional response to antibiotic stress in Mycobacterium abscessus

Mycobacterium abscessus is intrinsically resistant to antibiotics effective against other pathogenic mycobacteria largely due to the drug-induced expression of genes that confer resistance. WhiB7 is a major hub controlling the induction of resistance to ribosome-targeting antibiotics. It activates the expression of >100 genes, 7 of which are known determinants of drug resistance; the function of most genes within the regulon is however unknown, but some conceivably encode additional mechanisms of resistance. Furthermore, the hierarchy of gene expression within the regulon, if any, is poorly understood. In the present work we have identified 56 WhiB7 binding sites using chromatin immunoprecipitation sequencing (CHIP-Seq) which accounts for the WhiB7-dependent upregulation of 72 genes, and find that M. abscessus WhiB7 functions exclusively as a transcriptional activator at promoters recognized by σA/σB. We have investigated the role of 18 WhiB7 regulated genes in drug resistance. Our results suggest that while some genes within the regulon (eg. erm41, hflX, eis2 and the ABCFs) play a major role in resistance, others make smaller contributions (eg. MAB_4324c and MAB_1409c) and the observed hypersensitivity ΔMabwhiB7 is a cumulative effect of these individual contributions. Moreover, our CHIP-Seq data implicate additional roles of WhiB7 induced genes beyond antibiotic resistance. Finally, we identify a σH-dependent network in aminoglycoside and tigecycline resistance which is induced upon drug exposure and is further activated by WhiB7 demonstrating the existence of a crosstalk between components of the WhiB7-dependent and -independent circuits.

Clinical Evaluation of Nontuberculous Mycobacteria (NTM) Elite Agar, a New Medium for the Isolation of NTM: a Multicenter Study

Nontuberculous mycobacteria (NTM) are gaining interest with the increased number of infected patients. NTM Elite agar is designed specifically for the isolation of NTM without the decontamination step. We assessed the clinical performance of this medium combined with Vitek mass spectrometry (MS) matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) technology for the isolation and identification of NTM in a prospective multicenter study, including 15 laboratories (24 hospitals). A total of 2,567 samples from patients with suspected NTM infection were analyzed (1,782 sputa, 434 bronchial aspirates, 200 bronchoalveolar lavage samples, 34 bronchial lavage samples, and 117 other samples). A total of 220 samples (8.6%) were positive with existing laboratory methods against 330 with NTM Elite agar (12.8%). Using the combination of both methods, 437 isolates of NTM were detected in 400 positive samples (15.6% of samples). In total, 140 samples of the standard procedures (SP) and 98 of the NTM Elite agar were contaminated. NTM Elite agar showed a higher performance for rapidly growing mycobacteria (RGM) species than SP (7% versus 3%, P < 0.001). A trend has been noted for the Mycobacterium avium complex (4% with SP versus 3% with NTM Elite agar, P = 0.06). The time to positivity was similar (P = 0.13) between groups. However, the time to positivity was significantly shorter for the RGM in subgroup analysis (7 days with NTM and 6 days with SP, P = 0.01). NTM Elite agar has been shown to be useful for the recovery of NTM species, especially for the RGM. Using NTM Elite agar + Vitek MS system in combination with SP increases the number of NTM isolated from clinical samples.

Hierarchy and networks in the transcriptional response of Mycobacterium abscessus to antibiotics

Mycobacterium abscessus causes acute and chronic pulmonary infection in patients with chronic lung damage. It is intrinsically resistance to antibiotics effective against other pathogenic mycobacteria largely due to the drug-induced expression of genes that confer resistance. Induction of genes upon exposure to ribosome targeting antibiotics proceeds via WhiB7-dependent and -independent pathways. WhiB7 controls the expression of >100 genes, a few of which are known determinants of drug resistance. The function of the vast majority of genes within the regulon is unknown, but some conceivably encode additional mechanisms of resistance. Furthermore, the hierarchy of gene expression within the regulon, if any, is poorly understood. In the present work we have identified 56 WhiB7 binding sites using chromatin immunoprecipitation sequencing (CHIP-Seq) which accounts for the WhiB7-dependent upregulation of 70 genes, and find that M. abscessus WhiB7 functions exclusively as a transcriptional activator at promoters recognized by σ A /σ B We have investigated the role of 18 WhiB7 regulated genes in drug resistance and demonstrated the role of MAB_1409c and MAB_4324c in aminoglycoside resistance. Further, we identify a σ H -dependent pathway in aminoglycoside and tigecycline resistance which is induced upon drug exposure and is further activated by WhiB7 demonstrating the existence of a crosstalk between components of the WhiB7-dependent and -independent circuits.

Abstract Importance

The induction of multiple genes that confer resistance to structurally diverse ribosome-targeting antibiotics is funneled through the induction of a single transcriptional activator, WhiB7, by antibiotic-stalled ribosomes. This poses a severe restriction in M. abscessus therapy as treatment with one ribosome-targeting antibiotic confers resistance to all other ribosome-targeting antibiotics. Here we uncover the intricacies of the WhiB7 regulatory circuit, identify three previously unknown determinants of aminoglycoside resistance and unveil a communication between WhiB7 dependent and independent components. This not only expands our understanding of the antibiotic resistance potential of M. abscessus but can also inform the development of much needed therapeutic options.

Mycobacterium biofilms

The genus Mycobacterium includes some of the deadliest pathogens of History (Mycobacterium tuberculosis, Mycobacterium leprae), but most of the species within the genus are environmental microorganisms. Because some of these nontuberculous mycobacteria (NTM) species can be human pathogens, the study of these mycobacterial biofilms has increased during the last decades, and the interest in this issue increased as well as the growing number of patients with diseases caused by NTM. Different molecular mechanisms have been described, being especially well known the importance of glycopeptidolipids. Moreover, the knowledge of the extracellular matrix has shown important differences with other microorganisms, especially because of the presence of lipidic molecules as a key component of this structure. The clinical importance of mycobacterial biofilms has been described for many chronic diseases, especially lung diseases and implant-related ones, both in vitro and in vivo, and even in patients. Moreover, the biofilm-producing capacity has been proven also in M. tuberculosis, while its importance is not well understood. Biofilm studies have also shown the increasing resistance of mycobacteria in sessile form, and the importance of this resistance in the management of the patients is beyond doubt, being surgery necessary in some cases to cure the patients. Diagnosis of mycobacterial diseases is still based on culture-based techniques designed for the detection of M. tuberculosis. Molecular biology-based methods are also broadly used but again designed for tuberculosis diagnosis. Antimicrobial susceptibility testing is also well developed for tuberculosis, but only some species of NTM have standardized techniques for this purpose. New tools or approaches are necessary to treat these patients, whose importance is increasing, as the number of potential hosts is also increasing throughout the world.

Vinegar: A functional ingredient for human health

Vinegar is a well-known natural food product derived from alcoholic and subsequently acetous fermentation of carbohydrate-rich foods. Vinegar is widely used in the food industry; domestically for pickling vegetables and fruits, and as an ingredient in condiments like salad dressings, ketchups, and mayonnaise; and traditionally as a food seasoning and preservative. Historically, vinegar has been used for medicinal purposes such as a cure for stomach aches, wounds, burns, rashes, and oedema conditions. Different types of vinegar are found worldwide such as rice, black, balsamic, grain, and fruit vinegars. These are produced from different raw materials, and using different fermentation methods to give unique tastes and flavours. Vinegar, while enhancing physiological functions such as lipid metabolism, blood glucose level control, and body weight management, also possesses anticancer, antibacterial, antioxidant, and anti-infection properties. It is considered as a good source material for many bioactive compounds including organic acids, melanoidins, polyphenols, ligustrazine, and tryptophol. The pharmacological and metabolic benefits of vinegar are believed to be due to these bioactive compounds present in vinegar. Acetic acid (CH3COOH) is the essential component of vinegar; it is slightly volatile and has a strong and sour aroma and flavour. Regular consumption of vinegar-containing foods is considered important for keeping many life-style related diseases like diabetes, hypertension, hyperlipidaemia, cancers, and obesity in check. Therefore, the present review aims at highlighting the health benefits associated with vinegar consumption for the physiological well-being of an individual.

Mycobacterium abscessus HelR interacts with RNA polymerase to confer intrinsic rifamycin resistance

Rifampicin (RIF), the frontline drug against M. tuberculosis, is completely ineffective against M. abscessus, partially due to the presence of an ADP-ribosyltransferase (Arr) that inactivates RIF. Using RNA-seq, we show that exposure of M. abscessus to sublethal doses of RIF and Rifabutin (RBT), a close analog of RIF, results in an ∼25-fold upregulation of Mab_helR in laboratory and clinical isolates. An isogenic deletion in Mab_helR results in RIF/RBT hypersensitivity, and overexpression of Mab_helR confers RIF tolerance in M. tuberculosis. We demonstrate an increased HelR-RNAP association in RIF-exposed bacteria and a MabHelR-mediated dissociation of RNAP from stalled initiation complexes in vitro. Finally, we show that the tip of the PCh-loop of Mab_helR, present in proximity to RIF, is critical for conferring RIF resistance but dispensable for dissociation of stalled RNAP complexes, suggesting that HelR-mediated RIF resistance requires a step in addition to displacement of RIF-stalled RNAP.

Substantial Improvement in Nontuberculous Mycobacterial Identification Using ASTA MicroIDSys Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry with an Upgraded Database

Identifying Mycobacterium using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is challenging. We evaluated the performance of MALDI-TOF MS in identifying nontuberculous mycobacteria (NTM) using the ASTA MicroIDSys system (ASTA Inc., Suwon, Korea) with the MycoDB v1.95s and upgraded MycoDB v2.0-beta databases. We tested 124 NTM isolates collected from Ogawa medium at Severance Hospital, Seoul, Korea, between January and April 2019. MicroIDSys scores were categorized into three groups: ≥140, reliable identification; 130-139, ambiguous identification; and <130, invalid identification. To validate the results, we used the reverse blot hybridization assay (Molecutech REBA MycoID, YD Diagnostics Corp., Korea). Initial analysis using MycoDB v1.95s resulted in 26.6% (33/124) reliable, 43.5% (54/124) ambiguous, and 29.8% (37/124) invalid identifications. Re-analysis using the upgraded MycoDB v2.0-beta database resulted in 94.4% (117/124) reliable, 4.0% (5/124) ambiguous, and 1.6% invalid (2/124) identifications. The percentage of reliable identifications that matched with the reference increased from 26.6% (33/124) with MycoDB v1.95s to 93.5% (116/124) with MycoDB v2.0-beta. The upgraded databases enable substantially improved NTM identification through deep learning in the inference algorithm and by considering more axes in the correlation analysis. MALDI-TOF MS using the upgraded database unambiguously identified most NTM species. Our study lays a foundation for applying MALDI-TOF MS for the simple and rapid identification of NTM isolated from solid media.

Whole Genome Sequencing in the Management of Non-Tuberculous Mycobacterial Infections

Infections caused by non-tuberculous mycobacteria (NTM) have been a public health problem in recent decades and contribute significantly to the clinical and economic burden globally. The diagnosis of infections is difficult and time-consuming and, in addition, the conventional diagnostics tests do not have sufficient discrimination power in species identification due to cross-reactions and not fully specific probes. However, technological advances have been made and the whole genome sequencing (WGS) method has been shown to be an essential part of routine diagnostics in clinical mycobacteriology laboratories. The use of this technology has contributed to the characterization of new species of mycobacteria, as well as the identification of gene mutations encoding resistance and virulence factors. Sequencing data also allowed to track global outbreaks of nosocomial NTM infections caused by M. abscessus complex and M. chimaera. To highlight the utility of WGS, we summarize recent scientific studies on WGS as a tool suitable for the management of NTM-induced infections in clinical practice.

Ribosome Protection as a Mechanism of Lincosamide Resistance in Mycobacterium abscessus

Mycobacterium abscessus has emerged as a successful pathogen owing to its intrinsic drug resistance. Macrolide and lincosamide antibiotics share overlapping binding sites within the ribosome and common resistance pathways. Nevertheless, while M. abscessus is initially susceptible to macrolides, they are completely resistant to the lincosamide antibiotics. Here, we have used RNA sequencing to determine the changes in gene expression in M. abscessus upon exposure to the lincosamide, clindamycin (CLY). We show that Mab_1846, encoding a putative ARE-ABCF protein, was upregulated upon exposure to macrolides and lincosamides but conferred resistance to CLY alone. A Mycobacterium smegmatis homologue of Mab_1846, Ms_5102, was similarly found to be required for CLY resistance in M. smegmatis. We demonstrate that Ms5102 mediates CLY resistance by directly interacting with the ribosomes and protecting it from CLY inhibition. Additional biochemical characterization showed that ribosome binding is not nucleotide dependent, but ATP hydrolysis is required for dissociation of Ms5102 from the ribosome as well as for its ability to confer CLY resistance. Finally, we show that in comparison to the macrolides, CLY is a potent inducer of Mab_1846 and the whiB7 regulon, such that exposure of M. abscessus to very low antibiotic concentrations induces a heightened expression of erm41, hflX, and Mab_1846, which likely function together to result in a particularly antibiotic-resistant state.

Non-pigmented rapidly growing mycobacteria smooth and rough colony phenotypes pathogenicity evaluated using in vitro and experimental models

Non-pigmented rapidly growing mycobacteria (NPRGM) are widely distributed in water, soil and animals. It has been observed an increasing importance of NPRGM related-infections, particularly due to the high antimicrobial resistance. NPRGM have rough and smooth colony phenotypes, and several studies have showed that rough colony variants are more virulent than smooth ones. However, other studies have failed to validate this observation. In this study, we have performed two models, invitro and in vivo, in order to assess the different pathogenicity of these two phenotypes. We used collection and clinical strains of Mycobacteriumabscessus, Mycobacterium fortuitum and Mycobacteriumchelonae. On the invitro model (macrophages), phagocytosis was higher for M. abscessus and M. fortuitum rough colony variant strains when compared to smooth colony variants. However, we did not find differences with colonial variants of M. chelonae. Survival of Galleriamellonella larvae in the experimental model was lower for M. abscessus and M. fortuitum rough colony variants when compared with larvae infected with smooth colony variants. We did not find differences in larvae infected with M. chelonae.Results of our in vivo study correlated well with the experimental model. This fact could have implications on the interpretation of the clinical significance of the NPRGM isolate colonial variants.

State-of-the-art treatment strategies for nontuberculous mycobacteria infections

INTRODUCTION

Non-tuberculous Mycobacteria (NTM) are a group of organisms whose importance in medicine seems to be increasing in recent times. The increasing number of patients susceptible to these diseases make it necessary to expand our knowledge of therapeutic options and to explore future possibilities for the development of a therapeutic arsenal.

AREAS COVERED

In this review, the authors provide a brief introduction about the present importance of NTM and describe the present recommendations of the available guidelines for their treatment. They include a description of the future options for the management of these patients, especially focusing on new antibiotics. The authors also look at possibilities for future therapeutic options, such as antibiofilm strategies.

EXPERT OPINION

No actual changes have been made to the current recommendations for the management of most NTM infections (except perhaps the availability of nebulized amikacin). However, it is also true that we have increased the number of available antibiotic treatment options with good in vitro activity against NTM. The use of these drugs in selected cases could increase the therapeutic possibilities. However, some problems are still present, such as the knowledge of the actual meaning of a NTM isolate, and will probably be a key part of future research.

In vitro activity of bedaquiline against slow-growing nontuberculous mycobacteria

Bedaquiline (BDQ) is a recently approved antibiotic for the treatment of multidrug-resistant tuberculosis, but its potential against slow-growing mycobacteria (SGM) is still unknown. The objective of this study was to determine the in vitro activity of BDQ on SGM by assessing their MIC and minimal bactericidal concentration (MBC). The MIC of BDQ against 17 clinical isolates including Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium chimaera, Mycobacterium kansasii and Mycobacterium simiae species was determined by the resazurin microtitre assay and the MBC by the c.f.u. determination on 7H10 agar plates. BDQ has a bacteriostatic activity on all SGM tested with a MIC range from 0.03 to 0.007 µg ml^-1 and surprisingly a good bactericidal activity on the majority of the isolates tested with an MBC of 1-2 µg ml^-1 . Based on these preliminary results BDQ seems to be very promising for treatment of diseases caused by SGM.

Cutaneous nontuberculous mycobacteria infections: A retrospective case series of 78 patients from the Texas Gulf Coast region

BACKGROUND

The incidence of cutaneous nontuberculous mycobacteria (NTM) infections is increasing. These infections are a diagnostic and therapeutic challenge.

OBJECTIVE

We investigated the clinical features, diagnosis, and management of cutaneous NTM infections.

METHODS

A retrospective case series studied 78 patients from a Gulf Coast tertiary referral center diagnosed with cutaneous NTM infection by culture or stain of a skin biopsy specimen.

RESULTS

A history of trauma, procedure, or environmental exposure was common. The mean time between the initial evaluation and diagnosis was 12 weeks. Only 15% of acid-fast bacillus-positive cultures had a positive acid-fast bacillus smear, and only 43% of those accompanied by skin biopsy specimen had a positive Fite stain. Immunosuppressed patients were more likely to have a positive Fite stain. Treatment included surgery and multiple antibiotics. Immunosuppressed patients and Mycobacterium abscessus group infections were more likely to have persistent disease.

LIMITATIONS

M chelonae and M abscessus isolates were indistinguishable and therefore were reported together. Five cases were not confirmed by culture.

CONCLUSIONS

Even with clinical suspicion, the diagnosis of NTM infection can be difficult. Results of acid-fast bacillus smears and special stains are frequently negative. Antibiotic resistance is common. Multidrug treatment is often required, and surgical therapy may be needed.

Historical evolution of the diseases caused by non-pigmented rapidly growing mycobacteria in a University Hospital

OBJECTIVE

Non-pigmented rapidly growing mycobacteria (NPRGM) are a group of organisms of increasing interest due to the growing number of potential patients and the difficulties for a proper treatment in many of them. However, the evolution of these diseases in a long period of time and its evolutionary changes has been described only in a scanty number of reports.

METHODS

We performed a retrospective study between January 1st 2004 and December 31st 2017 in order to evaluate the clinical significance and types of diseases caused by NPRGM. Patients with isolates of NPRGM during this period were selected for the study, and clinical charts were reviewed using a predefined protocol.

RESULTS

During this period we identified 59 patients (76 clinical samples) with isolates of NPRGM, with 12 cases of clinical disease and one patient with doubtful significance (including 6 respiratory tract infections, 2 catheter infections, 1 skin and soft tissue infection, 1 disseminated infection, 1 conjunctivitis, 1 prosthetic joint infection and 1 mastitis). Fifty percent of M. chelonae isolates, 37.5% of M. abscessus isolates and 23.33% of M. fortuitum isolates were clinically significant. None of the isolates of other species were significant.

CONCLUSIONS

Most isolates in respiratory samples were contaminants/colonizations. M. abscessus was the main etiological agent in respiratory syndromes, whereas M. chelonae and M. fortuitum were more frequently associated with other infections, especially clinical devices and skin and soft tissue infections.

Evaluation of Two Protein Extraction Protocols Based on Freezing and Mechanical Disruption for Identifying Nontuberculous Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry from Liquid and Solid Cultures

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has proved to be a useful diagnostic method for identifying conventional bacteria. In the case of mycobacteria, a good protein extraction protocol is essential in order to obtain reliable identification results. To date, no such protocol has been definitively established. The aim of this study was to compare the manufacturer's recommended protein extraction protocol (protocol A) with two novel protocols (protocols B and C), which apply different freezing temperatures and mechanical disruption times using an automatic tissue homogenizer. A total of 302 clinical isolates, comprising 41 nontuberculous mycobacteria (NTM) species, were grown in parallel on solid and liquid media and analyzed: 174 isolates were slow-growing mycobacteria (SGM) and 128 isolates were rapid-growing mycobacteria (RGM). Overall, MALDI-TOF MS identified a higher number of NTM isolates from solid than from liquid media, especially with protocol C (83.4 and 68.2%, respectively; P < 0.05). From solid media, this protein extraction method identified 57.9 and 3.9% more isolates than protocols A (P < 0.001) and B (P < 0.05), respectively. In the case of liquid media, protocol C identified 49.7 and 6.3% more isolates than protocols A and B, respectively (P < 0.001). With regard to the growth rate, MALDI-TOF MS identified more RGM isolates than SGM isolates in all of the protocols studied. In conclusion, the application of freezing and automatic tissue homogenizer improved protein extraction of NTM and boosted identification rates. Consequently, MALDI-TOF MS, which is a cheap and simple method, could be a helpful tool for identifying NTM species in clinical laboratories.

Mycobacterium Biofilms

The genus Mycobacterium includes human pathogens (Mycobacterium tuberculosis and Mycobacterium leprae) and environmental organisms known as non-tuberculous mycobacteria (NTM) that, when associated with biomaterials and chronic disease, can cause human infections. A common pathogenic factor of mycobacteria is the formation of biofilms. Various molecules are involved in this process, including glycopeptidolipids, shorter-chain mycolic acids, and GroEL1 chaperone. Nutrients, ions, and carbon sources influence bacterial behavior and have a regulatory role in biofilm formation. The ultrastructure of mycobacterial biofilms can be studied by confocal laser scanning microscopy, a technique that reveals different phenotypic characteristics. Cording is associated with NTM pathogenicity, and is also considered an important property of M. tuberculosis strains. Mycobacterial biofilms are more resistant to environmental aggressions and disinfectants than the planktonic form. Biofilm-forming mycobacteria have been reported in many environmental studies, especially in water systems. NTM cause respiratory disease in patients with underlying diseases, such as old tuberculosis scars, bronchiectasis, and cystic fibrosis. Pathogens can be either slowly growing mycobacteria, such as Mycobacterium avium complex, or rapidly growing species, such as Mycobacterium abscessus. Another important biofilm-related group of infections are those associated with biomaterials, and in this setting the most frequently isolated organisms are rapidly growing mycobacteria. M. tuberculosis can develop a biofilm which plays a role in the process of casseous necrosis and cavity formation in lung tissue. M. tuberculosis also develops biofilms on clinical biomaterials. Biofilm development is an important factor for antimicrobial resistance, as it affords protection against antibiotics that are normally active against the same bacteria in the planktonic state. This antibiotic resistance of biofilm-forming microorganisms may result in treatment failure, and biofilms have to be physically eradicated to resolve the infection. New strategies with potential antibiofilm molecules that improve treatment efficacy have been developed. A novel antibiofilm approach focuses on Methylobacterium sp. An understanding of biofilm is essential for the appropriate management of patients with many NTM diseases, while the recent discovery of M. tuberculosis biofilms opens a new research field.

Treatment of infections caused by nontuberculous mycobacteria

Nontuberculous mycobacteria are a heterogeneous group of microorganisms that can often cause human infection, although they may also be considered to be contaminants or colonisers on occasions. The management of these infections must necessarily take into account the identification of isolated species and their in vitro susceptibility testing (although not for all of them), as well as the characteristics of the patient, because these treatments are usually prolonged and must be carried out by experts in the management of these infections. Classically divided into slowly growing mycobacteria and rapidly growing mycobacteria, the treatment regimens and the antibiotics used are different for both groups. In addition, in certain circumstances, this treatment must necessarily be linked to other measures (removal of foreign bodies, surgery) in order to maximise the likelihood of curing the patient.

Impact of updating the MALDI-TOF MS database on the identification of nontuberculous mycobacteria

Conventional identification of mycobacteria species is slow, laborious and has low discriminatory power. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved highly effective for identifying conventional bacteria, and it may also be useful for identifying mycobacteria. The aim of this study was to evaluate and compare MALDI-TOF MS with currently recommended molecular methods for the identification of nontuberculous mycobacteria (NTM), applying Mycobacteria Libraries v3.0 (ML3.0) and v2.0 (ML2.0). A total of 240 clinical isolates of 41 NTM species grown on solid media were analysed: 132 isolates of slow-growing mycobacteria and 108 of rapid-growing mycobacteria. MALDI-TOF MS, using ML3.0, identified 192 (80%) NTM isolates with a score ≥1.7, encompassing 35 (85.4%) different species, that is, 17 (7.1%; p = 0.0863) isolates and 15 (36.6%; p = 0.0339) species more than currently recommended molecular techniques (polymerase chain reaction reverse hybridization). All these isolates were correctly identified according to molecular identification methods. The application of ML3.0 also identified 15 (6.2%) NTM isolates more than ML2.0 (p < 0.01). The scores obtained with MALDI-TOF MS using ML3.0 (mean score: 1.960) were higher in 147 (61.2%) isolates than when using ML2.0 (mean score: 1.797; p < 0.01). Three of the species analysed were not included in either database, so they were not recognized by this system. In conclusion, MALDI-TOF MS identified more isolates and species than the recommended polymerase chain reaction reverse hybridization assays. Although the new ML3.0 is not the definitive database, it yielded better results than ML2.0. This shows that the updating of the MALDI-TOF MS database plays an essential role in mycobacterial identification. Copyright © 2017 John Wiley & Sons, Ltd.

In vitro activity of bedaquiline against rapidly growing nontuberculous mycobacteria

Bedaquiline (BDQ) has been proven to be effective in the treatment of multidrug-resistant tuberculosis. We hypothesized that BDQ could be a potential agent to treat nontuberculous mycobacterial (NTM) infection. The objective of this study was to evaluate the in vitro activity of BDQ against rapidly growing mycobacteria by assessing the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) against 18 NTM strains. For MIC determination we performed the resazurin microtitre assay broth dilution, and for the MBC the c.f.u. was determined. BDQ exhibited a strong inhibitory effect against most NTM tested; however, for some NTM strains the MBC was significantly higher than the MIC. A new finding is that Mycobacterium flavescens has a mutation in the gene atpE associated with natural resistance to BDQ. These preliminary promising results demonstrate that BDQ could be potentially useful for the treatment of NTM.

[Nontuberculous mycobacteria]

Dermatologically relevant nontuberculous mycobacteria (NTM) include Mycobacterium marinum and Mycobacterium ulcerans and different rapidly growing mycobacteria (RGM). RGM are widely present in the environment and are facultative pathogenic. Diagnostic detection of nontuberculous mycobacteria is frequently challenging. Immune-competent individuals mostly develop localized infections. Immune-suppressed patients may present with severe and disseminated disease. In these cases, rapid initiation of medical treatment is important. Moreover, infections with the more aggressive Mycobacterium ulcerans should be treated early. Due to the risk for the development of inducible antibiotic resistance, antibiotic regimes for NTM infections typically require at least two drugs. Surgical treatment should also be considered. This article discusses clinical presentation, diagnostic workup, and in particular antibiotic treatment options for dermatologically relevant infections caused by NTM.

Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China

Pulmonary diseases caused by nontuberculous mycobacteria (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the species using conventional and molecular methods, including multilocus PCR, rpoB and hsp65 PCR-PRA, hsp65, rpoB, and 16S-23S internal transcribed spacer region sequencing. The isolates were identified into 3 bacterium genera, including NTM, Gordonia bronchialis, and Nocardia farcinica, and, for the 488 NTM isolates, 27 species were identified. For all the 27 species of NTM which were found to cause pulmonary infections in humans, the most prevalent species was M. intracellulare, followed by M. avium and M. abscessus. And seven other species were for the first time identified in patients with TB in China. NTM species identification is very important for distinguishing between tuberculosis and NTM pulmonary diseases, and the species diversity drives the creation of diverse and integrated identification methods with higher accuracy and efficacy.

General Overview on Nontuberculous Mycobacteria, Biofilms, and Human Infection

Nontuberculous mycobacteria (NTM) are emergent pathogens whose importance in human health has been growing. After being regarded mainly as etiological agents of opportunist infections in HIV patients, they have also been recognized as etiological agents of several infections on immune-competent individuals and healthcare-associated infections. The environmental nature of NTM and their ability to assemble biofilms on different surfaces play a key role in their pathogenesis. Here, we review the clinical manifestations attributed to NTM giving particular importance to the role played by biofilm assembly.

Effect of Antibiotics and Antibiofilm Agents in the Ultrastructure and Development of Biofilms Developed by Nonpigmented Rapidly Growing Mycobacteria

We analyze the effect of amikacin, ciprofloxacin, and clarithromycin, alone and associated with N-acetylcysteine (NAC) and Tween 80, at different times and concentrations in nonpigmented rapidly growing mycobacteria (NPRGM) biofilms. For this purpose, confocal laser scanning microscopy and image analysis were used to study the development and behavior of intrinsic autofluorescence, covered area, thickness, and cell viability in NPRGM biofilms after adding antibiotics alone and associated with antibiofilm agents. In this study, ciprofloxacin is the most active antibiotic against this type of biofilm and thickness is the most affected parameter. NAC and Tween 80 combined with antibiotics exert a synergistic effect in increasing the percentage of dead bacteria and also reducing the percentage of covered surface and thickness of NPRGM biofilms. Tween 80 seems to be an antibiofilm agent more effective than NAC due to its higher reduction in the percentage of cover surface and thickness. In conclusion, the results obtained in this work show that phenotypic parameters (thickness, percentage of covered surface, autofluorescence, percentage of live/dead bacteria) are affected by combining antibiotics and antibiofilm agents, ciprofloxacin and Tween 80 being the most active agents against NPRGM biofilms.

Mycobacterium fortuitum skin infections after subcutaneous injections with Vietnamese traditional medicine: a case report

Background

Iatrogenic skin and soft tissue infections by rapidly growing mycobacteria are described with increasing frequency, especially among immunocompromised patients.

Case presentation

Here, we present an immunocompetent patient with extensive Mycobacterium fortuitum skin and soft tissue infections after subcutaneous injections to relieve joint pains by a Vietnamese traditional medicine practitioner. Moreover, we present dilemmas faced in less resourceful settings, influencing patient management.

Conclusion

This case illustrates the pathogenic potential of rapid growing mycobacteria in medical or non-medical skin penetrating procedures, their world-wide distribution and demonstrates the dilemmas faced in settings with fewer resources.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-014-0550-z) contains supplementary material, which is available to authorized users.

Mycobacterial skin and soft tissue infection

Mycobacterial skin and soft tissue infection (SSTI) includes nontuberculous mycobacterial (NTM) infections, tuberculosis (TB), and leprosy. Diagnosis of mycobacterial SSTI can be challenging due to diverse clinical presentation, low yield from cultured specimens, and nonspecific histopathology on tissue biopsy. In addition, immunosuppressed patients may present with atypical or disseminated disease. Despite aggressive medical treatment and often with surgical intervention, results may be suboptimal with poor outcomes. Regimens typically require multiple antibiotics for extended periods of time and are often complicated by medication side effects and drug-drug interactions. Biopsy with culture is the gold standard for diagnosis, but newer molecular diagnostics and proteomics such as matrix-assisted laser desorption ionization-time of flight mass spectrometry have improved diagnosis with increased identification of clinically significant mycobacteria species in clinically relevant time frames. We will review updates in diagnostic tests along with clinical presentation and treatment of mycobacterial SSTI for NTM, TB, and leprosy.

Skin and soft tissue infections caused by nontuberculous mycobacteria

PURPOSE OF REVIEW

Skin and soft tissues infections (SSTIs) caused by nontuberculous mycobacteria (NTM) are underrecognized and difficult to treat. Controversies exist for optimal medical management and the role of surgery. Defining the epidemiology in the environment, in animals and in healthcare aids disease prevention. This review focuses on recent advances in epidemiology, risk factors, diagnostics and therapy.

RECENT FINDINGS

The increasing consumer appetite for cosmetic and body-modifying procedures (e.g. tattooing, mesotherapy, liposuction) has been associated with rises in sporadic cases and outbreaks of NTM SSTIs. In mainstream healthcare, recent epidemiological studies have helped to quantify the increased risk of NTM infection related to anti-tumour necrosis factor-α monoclonal antibody therapy. Cervicofacial lymphadenitis in children poses management dilemmas, but recent studies and resultant algorithms have simplified decision-making. Molecular studies have led to a better understanding of the epidemiology, therapy and course of Mycobacterium ulcerans infection (Buruli ulcer) that remains prevalent in many areas including sub-Saharan Africa and southeastern Australia. Apart from molecular methods, the widespread adoption of matrix-assisted laser desorption ionization-time of flight mass spectrometry by routine laboratories has potential to simplify and expedite the laboratory identification of NTMs.

SUMMARY

An improved understanding of the epidemiology of NTM SSTIs indicates a need to apply effective infection control and ensure regulation of cosmetic and related procedures associated with nonsterile fluids. Broader access to newer diagnostic methods will continue to improve recognition of NTM disease. Along with a paucity of therapeutic agents, there is need for more reliable methods to assess susceptibility and selection of effective combination therapy.

Lack of adherence to evidence-based treatment guidelines for nontuberculous mycobacterial lung disease

RATIONALE

The 2007 American Thoracic Society (ATS) and Infectious Diseases Society of America (IDSA) recommend that patients with pulmonary nontuberculous mycobacterial (PNTM) disease caused by Mycobacterium avium complex (MAC) or M. abscessus be treated with a macrolide-based multidrug antibiotic regimen until sputum culture negative for 1 year. After 6 years, the degree of adherence to recommended guidelines among physicians remains unknown.

OBJECTIVE

To describe antibiotic treatment practices among physicians treating patients with PNTM in the United States.

METHODS

A nationally representative sample of 1,286 U.S. physicians was contacted in December 2011 through January 2012; 582 of the responding physicians were treating patients with PNTM and were eligible to participate. Physicians were asked to extract medical record data on the last four patients they treated in the past year with PNTM disease from either MAC or M. abscessus. Treatment patterns were assessed for all patients by NTM species and physician specialty, and compared with the 2007 recommended ATS/IDSA guidelines.

MAIN RESULTS

Questionnaires were completed by 349 physicians on 915 patients with PNTM, including 744 (81%) with MAC and 174 (19%) with M. abscessus; 3 patients were positive for both. Physicians treated 76 (44%) patients with M. abscessus and 411 (55%) patients with MAC. Only 13% of antibiotic regimens prescribed to patients with MAC met ATS/IDSA guidelines, 56% did not include a macrolide, and 16% were for macrolide monotherapy. Among patients with M. abscessus, 64% of regimens prescribed did not include a macrolide.

CONCLUSIONS

Adherence to the 2007 ATS/IDSA guidelines for treating PNTM disease is poor. Across all physician specialties evaluated, suboptimal or potentially harmful antibiotic regimens were commonly prescribed.

Acetic Acid, the active component of vinegar, is an effective tuberculocidal disinfectant

Effective and economical mycobactericidal disinfectants are needed to kill both Mycobacterium tuberculosis and non-M. tuberculosis mycobacteria. We found that acetic acid (vinegar) efficiently kills M. tuberculosis after 30 min of exposure to a 6% acetic acid solution. The activity is not due to pH alone, and propionic acid also appears to be bactericidal. M. bolletii and M. massiliense nontuberculous mycobacteria were more resistant, although a 30-min exposure to 10% acetic acid resulted in at least a 6-log10 reduction of viable bacteria. Acetic acid (vinegar) is an effective mycobactericidal disinfectant that should also be active against most other bacteria. These findings are consistent with and extend the results of studies performed in the early and mid-20th century on the disinfectant capacity of organic acids. IMPORTANCE Mycobacteria are best known for causing tuberculosis and leprosy, but infections with nontuberculous mycobacteria are an increasing problem after surgical or cosmetic procedures or in the lungs of cystic fibrosis and immunosuppressed patients. Killing mycobacteria is important because Mycobacterium tuberculosis strains can be multidrug resistant and therefore potentially fatal biohazards, and environmental mycobacteria must be thoroughly eliminated from surgical implements and respiratory equipment. Currently used mycobactericidal disinfectants can be toxic, unstable, and expensive. We fortuitously found that acetic acid kills mycobacteria and then showed that it is an effective mycobactericidal agent, even against the very resistant, clinically important Mycobacterium abscessus complex. Vinegar has been used for thousands of years as a common disinfectant, and if it can kill mycobacteria, the most disinfectant-resistant bacteria, it may prove to be a broadly effective, economical biocide with potential usefulness in health care settings and laboratories, especially in resource-poor countries.

History, biology and chemistry of Mycobacterium ulcerans infections (Buruli ulcer disease)

Mycobacterium ulcerans infections (Buruli ulcer disease) have a long history that can be traced back 150 years. The successive discoveries of the mycobacteria in 1948 and of mycolactone A/B in 1999, the toxin responsible for this dramatic necrotic skin disease, resulted in a paradigm shift concerning the disease itself and in a broader sense, delineated an entirely new role for bioactive polyketides as virulence factors. The fascinating history, biology and chemistry of M. ulcerans infections are discussed in this review.

Autofluorescence as a tool for structural analysis of biofilms formed by nonpigmented rapidly growing mycobacteria

The structure of biofilms formed by seven nonpigmented rapidly growing mycobacteria, including saprophytes and opportunistic species, was analyzed. Analysis included amount of covered surface, thickness, cell viability, and presence of intrinsic autofluorescence at different times using confocal laser scanning microscopy and image analysis. Autofluorescence was detected inside and outside cells of all mycobacteria.