Plasmid-mediated drug resistance in mycobacteria: the tip of the iceberg?

Macrolides, such as clarithromycin, are crucial in the treatment of nontuberculous mycobacteria (NTM). NTM are notoriously innately drug resistant, which has made the dependence on macrolides for their treatment even more important. Not surprisingly, resistance to macrolides has been documented in some NTM, including Mycobacterium avium and Mycobacterium abscessus, which are the two NTM species most often identified in clinical isolates. Resistance is mediated by point mutations in the 23S ribosomal RNA or by methylation of the rRNA by a methylase (encoded by an erm gene). Chromosomally encoded erm genes have been identified in many of the macrolide-resistant isolates, but not in Mycobacterium chelonae. Now, Brown-Elliott et al. (J Clin Microbiol 61:e00428-23, 2023, https://doi.org/10.1128/JCM.00428-23) describe the identification of a new erm variant, erm(55), which was found either on the chromosome or on a plasmid in highly macrolide-resistant clinical isolates of M. chelonae. The chromosomal erm(55) gene appears to be associated with mobile elements; one gene is within a putative transposon and the second is in a large (37 kb) insertion/deletion. The plasmid carrying erm(55) also encodes type IV and type VII secretion systems, which are often linked on large mycobacterial plasmids and are hypothesized to mediate plasmid transfer. While the conjugative transfer of the erm(55)-containing plasmid between NTM has yet to be demonstrated, the inferences are clear, as evidenced by the dissemination of plasmid-mediated drug resistance in other medically important bacteria. Here, we discuss the findings of Brown-Elliott et al., and the potential ramifications on treatment of NTM infections.

Increased whiB7 expression and antibiotic resistance in Mycobacterium chelonae carrying two prophages.

BACKGROUND: The global rise in the incidence of non-tuberculosis mycobacterial infections is of increasing concern due their high levels of intrinsic antibiotic resistance. Although integrated viral genomes, called prophage, are linked to increased antibiotic resistance in some bacterial species, we know little of their role in mycobacterial drug resistance. RESULTS: We present here for the first time, evidence of increased antibiotic resistance and expression of intrinsic antibiotic resistance genes in a strain of Mycobacterium chelonae carrying prophage. Strains carrying the prophage McProf demonstrated increased resistance to amikacin. Resistance in these strains was further enhanced by exposure to sub-inhibitory concentrations of the antibiotic, acivicin, or by the presence of a second prophage, BPs. Increased expression of the virulence gene, whiB7, was observed in strains carrying both prophages, BPs and McProf, relative to strains carrying a single prophage or no prophages. CONCLUSIONS: This study provides evidence that prophage alter expression of important mycobacterial intrinsic antibiotic resistance genes and additionally offers insight into the role prophage may play in mycobacterial adaptation to stress.

Skin and Soft Tissue Infections Caused by Mycobacterium chelonae: More Common Than Expected?

Mycobacterium chelonae is a rapidly growing non-tuberculous mycobacterium, which causes infections of the human skin and soft tissue. Despite an increasing incidence of such infections, patients are often misdiagnosed. We report here 5 patients with cutaneous and/or soft tissue infection due to M. chelonae who were diagnosed and treated at our centre. Two of the 5 patients were on immunosuppressive treatment. While clinical presentations differed in each patient, all had a long history of skin lesions. In addition to careful history-taking, tissue biopsies were obtained for mycobacterial culture and histopathological examination. Culture-directed antibiotic therapy was initiated, which resulted in a slow, but continuous, healing of the lesions. In summary, M. chelonae infections are still relatively rare, but should be considered in both immunocompromised and immunocompetent patients with prolonged skin lesions resistant to standard antibiotic treatment. For diagnosis, tissue analysis for mycobacterial culture and histopathological examination, and once diagnosed, adequate antibiotic treatment, is needed.

In Vitro Activities of Omadacycline against Rapidly Growing Mycobacteria.

The in vitro activity of omadacycline, a new tetracycline derivative, was evaluated against isolates of Mycobacterium abscessus, Mycobacterium chelonae, and Mycobacterium fortuitum using a broth microtiter dilution assay. Omadacycline had MIC90 values of 2 µg/ml, 0.25 µg/ml, and 0.5 µg/ml, respectively. The in vitro activity of omadacycline against rapidly growing mycobacteria indicates that it may have the potential to improve therapy for infections caused by these organisms.

Mycobacterium Chelonae Infection of the Buttocks Secondary to Lipofilling: A Case Report and Review of the Literature.

Mycobacterium chelonae is a nontuberculous mycobacterium, classified as a Runyon type IV mycobacterium. In relation to humans, it is most commonly associated with tissue trauma or pulmonary infections. The majority of medical reports describe finding M. chelonae in the surgical setting, attributing infection to inadequate sterilization of surgical equipment. Symptoms are often nonspecific and include pain, erythema, and draining subcutaneous nodules and skin lesions. Therefore, the diagnosis of M. chelonae is often difficult to establish without prior suspicion of the disease, but can be confirmed with culture. We will describe the case of a 40-year-old female who contracted M. chelonae infection of the buttocks after abdominal liposuction and gluteal fat injection. We will describe her symptomatology, diagnosis, and successful treatment with surgical excision and antibiotics. Level of Evidence V This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Disinfectant Susceptibility Profiling of Glutaraldehyde-Resistant Nontuberculous Mycobacteria.

OBJECTIVE Activated alkaline glutaraldehyde (GTA) remains one of the most widely used high-level disinfectants worldwide. However, several reports have highlighted the potential for nontuberculous mycobacteria to develop high-level resistance to this product. Because aldehyde resistance may lead to cross-resistance to other biocides, we investigated the susceptibility profile of GTA-resistant Mycobacterium chelonae and M. abscessus isolates to various disinfectant chemistries. METHODS High-level disinfectants commonly used in the reprocessing of endoscopes and other heat-sensitive, semicritical medical equipment, including different formulations of aldehyde-based products and oxidizing agents, were tested against 10 slow- and fast-growing, GTA-susceptible and GTA-resistant, Mycobacterium isolates in suspension tests and carrier tests at different temperatures. RESULTS While peracetic acid- and hydrogen peroxide-based disinfectants (S40, Resert XL, Reliance DG) efficiently killed all of the Mycobacterium isolates, GTA- and ortho-phthalaldehyde-based products (ie, Cidex, Aldahol, Cidex OPA) showed variable efficacy against GTA-resistant strains despite the ability of some formulations (Aldahol) to overcome the resistance of some of these isolates, especially when the temperature was increased from 20°C to 25°C. CONCLUSIONS Application permitting, oxidizing chemistries may provide a safe alternative to aldehyde-based products, particularly in GTA-resistant mycobacterial outbreaks. Infect Control Hosp Epidemiol 2017;38:784-791.

Antibiotic treatment of zebrafish mycobacteriosis: tolerance and efficacy of treatments with tigecycline and clarithromycin.

Zebrafish (Danio rerio) are a popular model organism used in a growing number of research fields. Maintaining healthy, disease-free laboratory fish is important for the integrity of many of these studies. Mycobacteriosis is a chronic bacterial infection caused by several Mycobacterium spp. and is the second most common disease found in laboratory zebrafish. Current mycobacteriosis control measures recommend the removal of infected fish and in severe outbreaks, depopulation. These measures can be effective, but less disruptive measures should be assessed for controlling mycobacteriosis, particularly when valuable and rare lines of fish are affected. Here, the in vivo efficacy of two drug candidates, tigecycline (1 µg g-1 ) and clarithromycin (4 µg g-1 ), was tested in adult zebrafish experimentally infected with Mycobacterium chelonae. We assessed both short (14 day)- and long-term (30 day) treatments and evaluated fecundity and pathological endpoints. Fecundity and histology results show that zebrafish tolerated antibiotics. Antibiotic treatments did not significantly impact the prevalence of acid-fast granulomas; however, the severity of infections (acid-fast granuloma intensity) was significantly decreased following treatments.

Zebrafish Embryo Disinfection with Povidone-Iodine: Evaluating an Alternative to Chlorine Bleach.

Mycobacteriosis is a common bacterial infection in laboratory zebrafish caused by several different species and strains of Mycobacterium, including both rapid and slow growers. One control measure used to prevent mycobacterial spread within and between facilities is surface disinfection of eggs. Recent studies have highlighted the effectiveness of povidone-iodine (PVPI) on preventing propagation of Mycobacterium spp. found in zebrafish colonies. We evaluated the effect of disinfection using 12.5-50 ppm PVPI (unbuffered and buffered) on zebrafish exposed at 6 or 24 h postfertilization (hpf) to determine if this treatment is suitable for use in research zebrafish. Our results show that 6 hpf embryos are less sensitive to treatment as fewer effects on mortality, developmental delay, and deformity were observed. We also found that buffered PVPI treatment results in a greater knockdown of Mycobacterium chelonae and Mycobacterium marinum, as well as results in decreased harmful effects on embryos. Treatments of shorter (2 min vs. 5 min) duration were also more effective at killing mycobacteria in addition to resulting in fewer effects on embryo health. In addition, we compared the efficacy of a rinsing regimen to rinsing and disinfecting. Based on the findings of this study, we recommend disinfecting embryos for 2 min with buffered PVPI at 12.5-25 ppm.

Epidemiology of Rapidly Growing Mycobacteria Bloodstream Infections.

BACKGROUND: Rapidly growing mycobacteria (RGM) bloodstream infections (BSI) are an emerging problem often associated with therapeutic challenges. We review the epidemiology, treatment and outcomes over a 5-year period of a heterogeneous group presenting to our institution with RGM BSI. MATERIALS AND METHODS: A retrospective cohort study of patients with primary RGM BSI from January 2006-December 2011 was conducted. Patient characteristics (age, race, sex and comorbidities), infection characteristics (catheter associated, hospital acquired, microbiology and antimicrobial susceptibilities), therapy and outcomes were recorded and compared by species. RESULTS: Among 32 patients, 33 RGM BSI occurred. Patients had an average of 3-4 comorbidities, most commonly malignancy (45.5%). Most isolates (30.3%) were Mycobacterium fortuitum or Mycobacterium mucogenicum (27.2%), followed by Mycobacterium abscessus/chelonae (18.2%) and Mycobacterium immunogenum (12.2%). In all, 85% were catheter associated and 27.3% were hospital acquired. Empiric therapy was started in 19 (57.6%) patients and among these, it was adequate (at least 2 active agents based on susceptibilities) in 12 (63.2%). Among 21 patients with outcome data, cure was assumed for 14 (66.7%). One death was attributable to RGM BSI. Cure rates were higher among those who received adequate empiric therapy compared to those who did not (83.3% versus 42.9%). In general, antibiotic susceptibility was favorable across species for clarithromycin, amikacin and imipenem. CONCLUSIONS: RGM BSI occurred in a population with multiple comorbidities, most commonly malignancy, and most were catheter associated. Higher cures were seen among those who received adequate empiric therapy and based on susceptibility data, a broad empiric regimen of clarithromycin, amikacin and imipenem would be expected to be adequate.

Induction therapy with linezolid/clarithromycin combination for Mycobacterium chelonae skin infections in immunocompromised hosts.

BACKGROUND: The optimal management of Mycobacterium chelonae disease in immunocompromised patients remains unclear. A combination of antimicrobial agents is recommended as monotherapy with clarithromycin has been associated with clinical failures due to acquired resistance. OBJECTIVES: We aim to report the efficacy and tolerability of linezolid in association with clarithromycin for the treatment of M. chelonae infections in immunocompromised patients. METHODS: We describe four immunocompromised patients treated by linezolid and clarithromycin for cutaneous M. chelonae disease. RESULTS: This combination was associated with rapid clinical efficacy in all patients with no relapse observed after a median follow-up of 2.25 years (1.4 years). However, this treatment was responsible for frequent adverse events including thrombocytopaenia, myalgia and mitochondrial toxicity. All adverse effects were reversible after linezolid discontinuation. CONCLUSIONS: We therefore suggest linezolid/clarithromycin combination as the initial therapeutic strategy for M. chelonae skin infections in immunocompromised patients.

Biofilms of Pathogenic Nontuberculous Mycobacteria Targeted by New Therapeutic Approaches.

Microbial infections of the cornea are potentially devastating and can result in permanent visual loss or require vision-rescuing surgery. In recent years, there has been an increasing number of reports on nontuberculous mycobacterial infections of the cornea. Challenges to the management of nontuberculous mycobacterial keratitis include delayed laboratory detection, low index of clinical suspicion, poor drug penetration, slow response to therapy, and prolonged use of antibiotic combinations. The ability of nontuberculous mycobacteria to evade the host immune response and the ability to adhere and to form biofilms on biological and synthetic substrates contribute to the issue. Therefore, there is an urgent need for new antimicrobial compounds that can overcome these problems. In this study, we evaluated the biofilm architectures for Mycobacterium chelonae and Mycobacterium fortuitum in dynamic flow cell chamber and 8-well chamber slide models. Our results showed that mycobacterial biofilms were quite resistant to conventional antibiotics. However, DNase treatment could be used to overcome biofilm resistance. Moreover, we successfully evaluated a new antimicrobial compound (AM-228) that was effective not only for planktonic mycobacterial cells but also for biofilm treatment and was compared favorably with the most successful "fourth-generation" fluoroquinolone, gatifloxacin. Finally, a new treatment strategy emerged: a combination of DNase with an antibiotic was more effective than an antibiotic alone.

Localized cutaneous infections in immunocompetent individuals due to rapidly growing mycobacteria.

Rapidly growing mycobacteria (RGM) cause skin infections that are refractory to standard antibiotic regimens. Although typically associated with disseminated cutaneous or other systemic infections in immunocompromised patients, RGM sometimes cause localized cutaneous infections in immunocompetent hosts. These infections are almost always associated with precedent skin trauma and inoculation, and therefore have been implicated in outbreaks involving contaminated tattoo ink and inadequately sterilized acupuncture needles. Histologic features often include suppurative granulomatous inflammation, and microorganisms are rarely visualized with stains for acid-fast bacilli. The differential diagnosis includes granulomatous fungal and non-RGM bacterial infections as well as noninfectious suppurative or sarcoidlike conditions. Because no pathognomonic histologic features exist for cutaneous RGM infections, clinical suspicion and appropriate workup are essential to reach an accurate and timely diagnosis. Most localized cutaneous RGM infections in immunocompetent individuals respond well to either clarithromycin or amikacin, in combination with surgical debridement.

Rapid molecular detection of inducible macrolide resistance in Mycobacterium chelonae and M. abscessus strains: a replacement for 14-day susceptibility testing?

The erm(41) gene causes inducible macrolide resistance in Mycobacterium abscessus but not Mycobacterium chelonae. erm(41) sequencing of 285 M. abscessus and 45 M. chelonae isolates was compared to 14-day susceptibility; agreement percentages were 98.9% and 100%, respectively. Extended incubation may not be necessary for M. chelonae, and the erm(41) genotype is a useful adjunct for M. abscessus.

[Drug sensitivity analysis of Mycobacterium chelonae and Mycobacterium abscessus and evaluation of Etest for susceptibility testing].

OBJECTIVE: To study the drug resistance profile of Mycobacterium(M.) chelonae and M.abscessus and to evaluate the clinical application of Etest(epsilometer test) for susceptibility testing. METHODS: Twenty clinical isolates of M.abscessus and 16 clinical isolates of M.chelonae from clinical specimens were collected.Strain identification was carried out by GenoType Mycobacterium CM assay(Hain Lifescience, Germany). The accuracy was evaluated by comparing Etest results to those obtained by broth microdilution. Thirty-six isolates were tested against amikacin, cefoxitin, ciprofloxacin, clarithromycin, doxycycline, imipenem, linezolid, sulfamethoxazole and tobramycin. The agreement among MICs and interpretive category was evaluated. Chi-squared test was used to compare observed frequency of each of the 2 examples. RESULTS: All of the isolates(36/36) were sensitive to amikacin and cefoxitin, and only 1 isolate(1/36) was resistant to clarithromycin, but more isolates(29/36) were resistant to ciprofloxacin, doxycycline, imipenem and sulfamethoxazole.For M.chelonae, only 2/16 were resistant to linezolid, and 7/16 resistant to tobramycin.For M.abscessus, more than 12/20 were resistant to linezolid and 16/20 resistant to tobramycin. The agreement between broth microdilution MICs and Etest MICs for 9 drugs was 149/324.With amikacin, clarithromycin, doxycycline and imipenem, the agreement for interpretive category was excellent(35/36), followed by sulfamethoxazole(34/36), which corresponded to rarely very major error of 2/36.With ciprofloxacin and tobramycin, agreement for interpretive category was 31/36 and 26/36.With cefoxitin and linezolid, the agreement of Etest MICs was the lowest(14/36), resulting in the resistant category. CONCLUSIONS: Isolates of M.chelonae and M.abscessus exhibit far more susceptibility to amikacin, cefoxitin and clarithromycin than any other antimicrobial agents.Linezolid and tobramycin showed sensitivity to some isolates of M.chelonae.It is suitable for the Etest method as a simple reliable method for the drug susceptibility of amikacin, ciprofloxacin, clarithromycin, doxycycline, imipenem, and tobramycin except to cefoxitin and linezolid. The Etest method of determining sulfamethoxazole susceptibility should be careful.