Nontuberculous mycobacterial infections

Drug susceptibility profiles of Mycobacterium abscessus isolated in the state of São Paulo, 2008-2024

Introduction. Infections caused by Mycobacterium abscessus, an environmentally prevalent, rapidly growing mycobacteria, are increasingly frequent in developed countries.Objective. To analyse the drug susceptibility profiles of M. abscessus isolated in the state of São Paulo from 2008 to 2024.Methods. Of the 2,402 M. abscessus isolates identified during those 17 years, 558 (23.2%) met the American Thoracic Society's microbiologic and clinical criteria for drug susceptibility testing (DST), which was performed for five agents - clarithromycin, amikacin, cefoxitin, ciprofloxacin, and doxycycline.Results. Clarithromycin showed a dramatic increase in resistance phenotype from ≤10% in the early period to 73-90% over the last 8 years. Over half those isolates demonstrated inducible resistance. Resistance to amikacin was found in fewer than 5% of isolates from 2016 to 2021. In 2022, that result increased to 13%, but for 2023 and 2024, it had fallen back to 2%. Over the past decade, cefoxitin DST has reported the majority of isolates as intermediate, a problematic result in M. abscessus group (MAG) infections, which typically require long-term treatment for successful outcomes. Since 2018, the annual susceptibility rate has been ≤18%, and in five of the 7 years, ≤7%. Ciprofloxacin was typically assessed as susceptible from 2009 to 2011, then decreased sharply to ≤20% over the next several years, and since 2018, the rate has been less than 5%. Through the entire study, doxycycline resistance has remained consistently high; in the years since 2018, ≤6% of isolates have been susceptible.Conclusion. This study demonstrates wide variation among MAG clinical isolates in the frequency of susceptibility, both across different agents and within individual agents over time. These results emphasize the importance of performing high-quality DST on MAG clinical isolates and suggest the need to consider revising the standard panel of drugs tested.

Alleviation of mycobacterial infection by impairing motility and biofilm formation via natural and synthetic molecules

Mycobacterium species show distinctive characteristics with significant medical implications. Mycobacteria, including Mycobacterium tuberculosis and non-tuberculous mycobacteria, can form biofilms that facilitate their survival in hostile environments and contribute to development of antibiotic resistance and responses by the host immune system. Mycobacterial biofilm development is a complex process involving multiple genetic determinants, notably mmpL genes, which regulate lipid transport and support cell wall integrity, and the groEL gene, which is essential for biofilm maturation. Sliding motility, a passive form of surface movement observed across various mycobacterial species, is closely associated with biofilm formation and colony morphology. The unique sliding motility and biofilm-forming capabilities of Mycobacterium spp. are pivotal for their pathogenicity and persistence in diverse environments. A comprehensive understanding of the regulatory mechanisms governing these processes is crucial for the development of novel therapeutic strategies against mycobacterial infections. This review provides a detailed examination of our current knowledge regarding mycobacterial biofilm formation and motility, with a focus on regulation of these processes, their impact on pathogenicity, and potential avenues for therapeutic intervention. To this end, the potential of natural and synthetic compounds, including nanomaterials, in combating mycobacterial biofilms and inhibiting sliding motility are discussed as well. These compounds offer new avenues for the treatment of drug-resistant mycobacterial infections.

Successful Treatment of Cutaneous Mycobacterium chelonae Infection in an Immunocompromised Patient Using Moxifloxacin and Clarithromycin

Mycobacterium chelonae is a ubiquitous organism classified as a nontuberculous mycobacterium that rarely causes indolent skin or soft-tissue infections, especially in immunocompromised patients. Given the rarity of M. chelonae infection, diagnosis can be difficult because cutaneous lesions may be considered a worsening of the underlying disease or a benign condition. Here, we report a case of a rapidly progressing cutaneous M. chelonae infection in a patient with nephrotic syndrome. The cutaneous lesion was initially stable for five months, mimicking noninfectious etiologies; however, due to rapid worsening, prompt skin biopsy revealed M. chelonae infection. Clinicians should be aware of this unusual presentation of M. chelonae infection and have a low threshold for performing biopsies for the early diagnosis and prevention of disease progression. The patient was successfully treated using a combination of moxifloxacin and clarithromycin. The choices of antibiotics and duration of treatment for nontuberculous mycobacterial infections are not clearly determined and depend on the clinician's experience. As treatment duration is prolonged, it sometimes carries the risk of developing drug resistance. We also evaluated the efficacy of moxifloxacin and clarithromycin for treating cutaneous M. chelonae infections in immunocompromised patients who require long-term antibiotic therapy.

Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification

Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.

Differential Immune Responses and Underlying Mechanisms of Metabolic Reprogramming in Smooth and Rough Variants of Mycobacterium peregrinum Infections

Mycobacterium peregrinum (Mpgm) is a rapidly growing mycobacteria that is classified as a nontuberculous mycobacterium (NTM) and is commonly found in environmental sources such as soil, water, and animals. Mpgm is considered an opportunistic pathogen that causes infection in immunocompromised individuals or those with underlying medical conditions. Although there have been clinical reports on Mpgm, reports of the immune response and metabolic reprogramming have not been published. Thus, we studied standard Mpgm-ATCC and two clinical strains (Mpgm-S and Mpgm-R) using macrophages and mouse bone marrow-derived cells. Mpgm has two types of colony morphologies: smooth and rough. We grew all strains on the 7H10 agar medium to visually validate the morphology. Cytokine levels were measured via ELISA and real-time PCR. The changes in mitochondrial function and glycolysis in Mpgm-infected macrophages were measured using an extracellular flux analyzer. Mpgm-S-infected macrophages showed elevated levels of inflammatory cytokines, including interleukin (IL)-6, IL-12p40, and tumor necrosis factor (TNF)-α, compared to Mpgm-ATCC- and Mpgm-R-infected macrophages. Additionally, our findings revealed metabolic changes in Mpgm-ATCC and two clinical strains (Mpgm-S and Mpgm-R) during infection; significant changes were observed in the mitochondrial respiration, extracellular acidification, and the oxygen consumption of BMDMs upon Mpgm-S infection. In summary, within the strains examined, Mpgm-S displayed greater virulence, triggered a heightened immune response, and induced more profound shifts in bioenergetic metabolism than Mpgm-ATCC and Mpgm-R. This study is the first to document distinct immune responses and metabolic reorganization following Mpgm infection. These findings lay a crucial foundation for further investigations into the pathogenesis of Mpgm.

A Rare Case of Nontuberculous Mycobacterial Abscess Mimicking Brain Tumor in an Immunocompetent Patient

Nontuberculous mycobacteria (NTM) is a type of bacteria that typically infects the pulmonary system, and NTM-central nervous system (CNS) infection, which occurs in the brain, is a very rare disease. A 64-year-old female patient presented with seizures as the main symptom and was found to have a mass of less than 1 cm in the right temporal lobe with accompanying edema. Although diseases such as tumor metastasis and parasitic cyst were suspected, the patient underwent a surgical resection, and NTM-CNS infection with abscess was diagnosed through biopsy. Antibiotic treatment was initiated after surgery, and the patient has been followed up without any significant symptoms. In this report, we review a rare case of NTM-CNS infection and discuss the understanding and treatment of this disease.

Morphologic Spectrum of Lymphadenopathy in Adult-onset Immunodeficiency (Anti-interferon-γ Autoantibodies)

Adult-onset immunodeficiency syndrome (AOIS) caused by anti-interferon-γ autoantibodies is an emerging disease. Affected patients present typically with systemic lymphadenopathy, fatigue, and fever. We studied 36 biopsy specimens, 31 lymph nodes, and 5 extranodal sites, of AOIS confirmed by serum autoantibody or QuantiFERON-TB Gold In-Tube assay. We describe the morphologic features and the results of ancillary studies, including special stains, immunohistochemistry, and molecular testing. The overall median age of these patients was 60.5 years (range, 41 to 83 y) with a male-to-female ratio of 20:16. All biopsy specimens showed nontuberculous mycobacterial infection, and most cases showed the following histologic features: capsular thickening with intranodal sclerosing fibrosis, irregularly distributed ill-formed granulomas or histiocytic aggregates with neutrophilic infiltration, interfollicular expansion by a polymorphic infiltrate with some Hodgkin-like cells that commonly effaces most of the nodal architecture and proliferation of high endothelial venules. In situ hybridization analysis for Epstein-Barr virus-encoded RNA showed scattered (<1%) to relatively more common (4% to 5%) positive cells in 29 of 30 (97%) tested specimens, reflecting immune dysregulation due to an interferon-γ defect. In the 31 lymph node specimens, 23 (74%) cases showed increased immunoglobulin G4-positive plasma cells (4 to 145/HPF; mean, 49.7/HPF) with focal areas of sclerosis reminiscent of immunoglobulin G4-related lymphadenopathy, 4 (13%) cases resembled, in part, nodular sclerosis Hodgkin lymphoma, and 9 (29%) cases mimicked T-cell lymphoma. Among 33 patients with available clinical follow-up, 20 (61%) showed persistent or refractory disease despite antimycobacterial therapy, and 1 patient died of the disease. We conclude that the presence of ill-defined granulomas, clusters of neutrophils adjacent to the histiocytic aggregates, and some Epstein-Barr virus-positive cells are features highly suggestive of AOIS. A high index of clinical suspicion and awareness of the morphologic features and differential diagnosis of AOIS are helpful for establishing the diagnosis.

Clinical course of peritoneal dialysis-related peritonitis due to non-tuberculosis mycobacterium - A single centre experience spanning 20 years

BACKGROUND

Peritoneal dialysis (PD)-related peritonitis caused by non-tuberculous mycobacteria (NTM) are difficult to diagnose, is associated with significant morbidity and mortality, and clinical course remains unclear. We determined the prevalence and clinical course of peritonitis caused by these organisms through our kidney registry over 20-year period.

METHOD

We reviewed all patients with NTM peritonitis identified in our tertiary centre between July 2000 and July 2020. The demographic characteristics, microbiological and clinical outcomes were examined.

RESULT

Among 27 patients identified, 20 patients presented with abdominal pain and all had cloudy peritoneal fluid. Twenty-one cases had concomitant exit site infection and 14 cases had prior antibiotic use. The majority of the cases are caused by Mycobacterium chelonae (37%) and Mycobacterium fortuitum (29.7%), with most being resistant to fluoroquinolones (59.3%) and cefoxitin (73.1%). They are all sensitive to amikacin otherwise. None of the cases achieve primary response at day 10 and 20 cases resulted in Tenckhoff catheter removal. Only two of them were able to resume PD. Eight patients died in our cohort. The presence of exit site infection, the use of prior antibiotics and topical disinfectants did not associate with a poorer outcome.

CONCLUSION

NTM peritonitis remains difficult to treat and often with a delay in diagnosis. Refractory peritonitis with negative culture and a poor response to standard antibiotics should raise a possibility of NTM infection and prompt catheter removal and an expert with experience treating NTM infections should be consulted.

Lymphadenopathy Associated With Neutralizing Anti-interferon-gamma Autoantibodies Could Have Monoclonal T-cell Proliferation Indistinguishable From Malignant Lymphoma and Treatable by Antibiotics: A Clinicopathologic Study

Early recognition of adult-onset immunodeficiency associated with neutralizing anti-interferon gamma autoantibodies (anti-IFNγ Abs) remains difficult, and misdiagnoses have been reported. Although febrile lymphadenopathy is among the most common initial manifestations of this disorder, no comprehensive clinicopathologic analysis of lymphadenopathy in patients with anti-IFNγ Abs has been reported. Here, we describe 26 lymph node biopsy specimens from 16 patients. All patients exhibited concurrent disseminated nontuberculous mycobacterial infections, and 31% received a tentative diagnosis of lymphoma at initial presentation. We found 3 distinct histomorphologic patterns: well-formed granuloma (46%), suppurative inflammation or loose histiocytic aggregates (31%), and lymphoproliferative disorder (LPD, 23%). The latter shared some of the features of malignant T-cell lymphoma, IgG4-related disease, and multicentric Castleman disease. Half of the specimens with LPD had monoclonal T cells, and 33.3% were indistinguishable from angioimmunoblastic T-cell lymphoma as per current diagnostic criteria. All lymphadenopathy with LPD features regressed with antibiotics without administration of cytotoxic chemotherapy or immunotherapy. The median follow-up time was 4.3 years. Our study highlights the substantial challenge of distinguishing between lymphoma and other benign lymphadenopathy in the setting of neutralizing anti-IFNγ Abs. Increased vigilance and multidisciplinary discussion among clinicians and pathologists are required to achieve the most appropriate diagnosis and management.

Phenotypic and genomic hallmarks of a novel, potentially pathogenic rapidly growing Mycobacterium species related to the Mycobacterium fortuitum complex

Previously, we have identified a putative novel rapidly growing Mycobacterium species, referred to as TNTM28, recovered from the sputum of an apparently immunocompetent young man with an underlying pulmonary disease. Here we provide a thorough characterization of TNTM28 genome sequence, which consists of one chromosome of 5,526,191 bp with a 67.3% G + C content, and a total of 5193 predicted coding sequences. Phylogenomic analyses revealed a deep-rooting relationship to the Mycobacterium fortuitum complex, thus suggesting a new taxonomic entity. TNTM28 was predicted to be a human pathogen with a probability of 0.804, reflecting the identification of several virulence factors, including export systems (Sec, Tat, and ESX), a nearly complete set of Mce proteins, toxin-antitoxins systems, and an extended range of other genes involved in intramacrophage replication and persistence (hspX, ahpC, sodA, sodC, katG, mgtC, ClpR, virS, etc.), some of which had likely been acquired through horizontal gene transfer. Such an arsenal of potential virulence factors, along with an almost intact ESX-1 locus, might have significantly contributed to TNTM28 pathogenicity, as witnessed by its ability to replicate efficiently in macrophages. Overall, the identification of this new species as a potential human pathogen will help to broaden our understanding of mycobacterial pathogenesis.

Difference in drug susceptibility distribution and clinical characteristics between Mycobacterium avium and Mycobacterium intracellulare lung diseases in Shanghai, China

Introduction. Mycobacterium avium complex (MAC) has been reported as the most common aetiology of lung disease involving nontuberculous mycobacteria.Hypothesis. Antimicrobial susceptibility and clinical characteristics may differ between Mycobacterium avium and Mycobacterium intracellulare.Aim. We aimed to evaluate the differences in antimicrobial susceptibility profiles between two major MAC species (Mycobacterium avium and Mycobacterium intracellulare) from patients with pulmonary infections and to provide epidemiologic data with minimum inhibitory concentration (MIC) distributions.Methodology. Between January 2019 and May 2020, 45 M. avium and 242 M. intracellulare isolates were obtained from Shanghai Pulmonary Hospital. The demographic and clinical characteristics of patients were obtained from their medical records. The MICs of 13 antimicrobials were determined for the MAC isolates using commercial Sensititre SLOWMYCO MIC plates and the broth microdilution method, as recommended by the Clinical and Laboratory Standards Institute (CLSI; Standards M24-A2). MIC₅₀ and MIC₉₀ values were derived from the MIC distributions.Results. M. intracellulare had higher resistance rates than M. avium for most tested antimicrobials except clarithromycin, ethambutol, and ciprofloxacin. Clarithromycin was the most effective antimicrobial against both the M. avium (88.89 %) and M. intracellulare (91.32 %) isolates, with no significant difference between the species (P=0.601). The MIC₉₀ of clarithromycin was higher for M. avium (32 µg ml^-1) than M. intracellulare (8 µg ml^-1). The MIC₅₀ of rifabutin was more than four times higher for M. intracellulare (1 µg ml^-1) than M. avium (≤0.25 µg ml^-1). The percentages of patients aged >60 years and patients with sputum, cough, and cavitary lesions were significantly higher than among patients with M. intracellulare infection than M. avium infections.Conclusions. The pulmonary disease caused by distinct MAC species had different antimicrobial susceptibility, symptoms, and radiographic findings.

Approach to the diagnosis and treatment of non-tuberculous mycobacterial disease

Non-tuberculous mycobacteria (NTM) is a collective name given to a group of more than 190 species of Mycobacterium. The clinical presentation for most NTM infections is non-specific, often resulting in delayed diagnosis. Further complicating matters is that NTM organisms can be difficult to isolate. Medications used to treat NTM infection can be difficult for patients to tolerate, and prolonged courses of anti-mycobacterial therapy are often required for adequate suppression or eradication. Herein, we review different NTM syndromes, appropriate diagnostic tests, and treatment regimens.

Retrospective Study of Bone-TB in Oman: 2002-2019

Objective: Little information is available about the etiology, pathophysiology, risk factors, and epidemiologic features of Bone Tuberculosis (Bone-TB). In this work, we present the epidemiological data about the Bone-TB in the Sultanate of Oman.

Methods: Retrospectively, we identified and assessed those patients who were diagnosed with Bone-TB between January 2002 and December 2019 at Khoula Hospital. The following data were collected: demographics, clinical presentation, anatomical location, diagnosis, and treatment of the Bone-TB.

Results: During the study period, 115 cases of Bone-TB were diagnosed. Males were affected more than females (57.4% and 42.6%, respectively). About 30% of Bone-TB cases were primary diagnosed in other organs particularly the lungs and then after disseminated to the bone. However, the Bone-TB was detected in hip, leg, hand, shoulder, and skull bones, the most detected Bone-TB was in spine (66% of cases). After vaccination the Bacillus Calmette–Guérin (BCG) strains were identified in the bones of eight babies. Tubercle bacilli were detected by Acid-Fast Stain (AFS) in 59% of cases, and the rest of cases were confirmed using polymerase chain reaction (PCR) tests. There are two used treatment regimens, with 12.4% relapse. The gastrointestinal tract (GIT) disturbances were the most related side effects. The resistance has been detected to pyrazinamide in six cases, rifampicin in three cases, and isoniazid, streptomycin and kanamycin were detected in one case.

Conclusion: The most predominant Bone-TB cases were spine-TB that were mainly disseminated from the lungs. AFS failed to detect tubercle bacilli in 40% of cases. There is no statistical significance in relapse between the used two regimens. The death was predominant among skull-TB cases.

Polymicrobial Extensor Tenosynovitis Including Mycobacterium chelonae Caused by a Dog Bite: A Case Report

CASE

A nonimmunocompromised 77-year-old man was bitten in the hand by his dog; redness, swelling, and exudate developed. Despite debridement and medications administered at another hospital, his symptoms did not improve. He was referred to us after 3 months. Debridement and negative-pressure wound therapy was performed. Cultures were positive for multiple bacterial organisms, including Mycobacterium chelonae. Polymicrobial extensor tenosynovitis including M. chelonae was diagnosed. Clarithromycin was given for 7 months based on drug sensitivity. His symptoms did not recur.

CONCLUSION

Mycobacterium chelonae infections after dog bites are rare; however, mycobacterial culture tests are important, especially if tissue shows granulomatous inflammation.

Clinical Performance of Mycobacterial Immunohistochemistry in Anatomic Pathology Specimens

OBJECTIVES

Diagnosis of mycobacterial infections poses significant challenges in anatomic pathology. We recently described the use of antimycobacteria immunohistochemistry (IHC) as a sensitive, efficient diagnostic tool and now report the clinical performance of this assay among general, noninfectious disease pathology-trained anatomic pathologists.

METHODS

Over a 2-year period, all cases were retrospectively identified in which mycobacterial IHC was performed during routine diagnostic workup.

RESULTS

From October 2017 to September 2019, mycobacterial IHC was evaluated for 267 cases, resulting in 58 (22%) positive stains. Compared with culture and molecular results, the sensitivity and specificity of IHC were 52% and 80%, respectively. IHC performed significantly better than acid-fast bacilli (AFB) staining (Ziehl-Neelsen) (P < .0001; sensitivity 21%, specificity 92%) but similarly to modified AFB staining (mAFB; Fite-Faraco) (P = .9; sensitivity 61%, specificity 84%). In cases with discordant IHC and mAFB staining, there were no differences in rates of culture or polymerase chain reaction-confirmed positivity.

CONCLUSIONS

Mycobacterial IHC was well adopted with superior clinical performance to AFB and comparable performance to mAFB. These results support the use of IHC as an adjunctive tool in the diagnosis of mycobacterial infections and suggests its potential role as a rapid screening test for molecular testing.

Evaluation of Various Diagnostic Techniques for the Diagnosis of Pulmonary and Extra Pulmonary Tuberculosis at a Tertiary Care Center in North India

INTRODUCTION

Tuberculosis (TB) is a one of the main causes of mortality and morbidity worldwide. Bactec MGIT (Mycobacteria Growth Indicator Tube) system is a rapid, reliable automated system for early diagnosis of pulmonary and extra pulmonary TB in setups where purchase of expensive instruments is not possible. The present study was thus carried out to evaluate AFB microscopy, culture on Lowenstein Jensen media and micro MGIT system for early and accurate diagnosis of Tuberculosis.

METHODS

A total of 280 samples were processed for direct AFB smear examination, and culture on micro MGIT and LJ media. The identification of Mycobacterium tuberculosis complex in positive cultures was done by MPT64 Ag card test (BD MGIT TBC Identification Test).

RESULTS

Out of the processed samples, (47.1%) 132/280 were positive for Mycobacterium spp by Micro MGIT, (35%) 98/280 on LJ medium and (25.7%) 72/280 by AFB smear. A total of (48.5%) 136 samples were positive by a combination of Micro MGIT and LJ medium. Among the total positive samples (136/280), Micro MGIT was found to be positive in 97% (132/136) of samples, LJ was positive in 72% (98/136), while 52.9% (72/136) were positive by AFB smear.

CONCLUSION

Manual MGIT System is a simple and efficient, safe to use the diagnostic system. It does not require any expensive/special instrumentation other than the UV lamp for the detection of fluorescence. In areas with limited resources where the purchase of expensive instruments such as the MGIT 960 is out of scope, the use of manual MGIT for rapid susceptibility testing for MDR-TB could be an option. We would recommend testing MGIT 960 using first and secondline drugs to determine DST.

Infectious Lung Disease

Infectious diseases are one of the main causes of morbidity and mortality worldwide. With new pathogens continuously emerging, known infectious diseases reemerging, increasing microbial resistance to antimicrobial agents, global environmental change, ease of world travel, and an increasing immunosuppressed population, recognition of infectious diseases plays an ever-important role in surgical pathology. This becomes particularly significant in cases where infectious disease is not suspected clinically and the initial diagnostic workup fails to include samples for culture. As such, it is not uncommon that a lung biopsy becomes the only material available in the diagnostic process of an infectious disease. Once the infectious nature of the pathological process is established, careful search for the causative agent is advised. This can often be achieved by examination of the hematoxylin and eosin-stained sections alone as many organisms or their cytopathic effects are visible on routine staining. However, ancillary studies such as histochemical stains, immunohistochemistry, in situ hybridization, or molecular techniques may be needed to identify the organism in tissue sections or for further characterization, such as speciation.

Effect of growth media and phase on Raman spectra and discrimination of mycobacteria

When developing a Raman spectral library to identify bacteria, differences between laboratory and real world conditions must be considered. For example, culturing bacteria in laboratory settings is performed under conditions for ideal bacteria growth. In contrast, culture conditions in the human body may differ and may not support optimized bacterial growth. To address these differences, researchers have studied the effect of conditions such as growth media and phase on Raman spectra. However, the majority of these studies focused on Gram-positive or Gram-negative bacteria. This article focuses on the influence of growth media and phase on Raman spectra and discrimination of mycobacteria, an acid-fast genus. Results showed that spectral differences from growth phase and media can be distinguished by spectral observation and multivariate analysis. Results were comparable to those found for other types of bacteria, such as Gram-positive and Gram-negative. In addition, the influence of growth phase and media had a significant impact on machine learning models and their resulting classification accuracy. This study highlights the need for machine learning models and their associated spectral libraries to account for various growth parameters and stages to further the transition of Raman spectral analysis of bacteria from laboratory to clinical settings.

Nontuberculous mycobacteria isolated from specimens of pulmonary tuberculosis suspects, Northern Tunisia: 2002-2016

Background

Reports on the worldwide ascending trend of pulmonary nontuberculous mycobacteria (NTM) isolation rates and their effective role in respiratory tract infections are compelling. However, as yet, there are no such data relating to Tunisia.

Methods

Here we carried out a retrospective review of mycobacterial cultures originating from Northern Tunisia, which have been processed in the laboratory of mycobacteria of the Institut Pasteur de Tunis, during the time period 2002–2016. All pulmonary NTM (PNTM) isolates available for culture were characterized phenotypically and their taxonomic status was further established based on polymorphisms in rpoB, 16S rRNA, hsp65, and sodA DNA gene sequences.

Results

Of the 10,466 specimens collected from HIV-negative Tunisian patients with presumptive clinical pulmonary TB, 60 (0.6%) yielded PNTM isolates. An overall annual PNTM isolation prevalence of 0.2/100,000 was estimated. As far as could be ascertained, this isolation rate accounts amongst the lowest reported hitherto throughout the world. Among the 30 NTM isolates that were available for culture, 27 (90.0%) have been identified to the species level. The most commonly encountered species was Mycobacterium kansasii (23.3%) subtype 1. Strikingly, all M. kansasii cases were male patients originating from Bizerte, an industrialized region particularly known for iron industry. The remaining NTM species were M. fortuitum (16.6%), M. novocastrense (16.6%), M. chelonae (10.0%), M. gordonae (6.6%), M. gadium (6.6%), M. peregrinum (3.3%), M. porcinum (3.3%), and M. flavescens (3.3%). There were no bacteria of the M. avium complex, the most frequently isolated NTM globally, and the main driver of the rise of NTM-lung diseases.

Conclusions

This study uncovered an exceptional low prevalence of PNTM isolation among HIV-negative TB suspects in Northern Tunisia, suggesting a very low burden of NTM pulmonary disease. However, the frequent isolation of M. kansasii subtype 1, the most pathogenic subtype, particularly from the industrialized region of Bizerte, strongly suggests its effective involvement in a typical pulmonary disease.

Supplementary information

Supplementary information accompanies this paper at 10.1186/s12879-019-4441-1.

Synovial Tissue Biopsy Collection by Rheumatologists: Ready for Clinical Implementation?

Synovial tissue from arthritis patients is increasingly used for both basic pathophysiological and clinical translational research. This development has been spurred by the development of biotechnological techniques for analysis of complex tissues and the validation of ultrasound guided biopsies for easier tissue sampling. This increasing use of synovial tissue raises questions on standardization of methodologies for tissue processing and cellular & molecular analyses. Furthermore, it raises the question if synovial tissue biopsy analysis may be more widely implemented in clinical practice, what are the methodological hurdles for implementation and what are the lessons that can be learned from previous experience. This will be the focus of this review.

Nontuberculous mycobacterial infections of the lower extremities: A 15-year experience

Objectives

Nontuberculous mycobacterial infection (NTMI), which is increasing in prevalence, is challenging to diagnose and manage despite the availability of capable laboratories because of subtle and nonspecific clinical findings and nonstandardized treatment guidelines. We aimed to present our experience with lower-extremity NTMI and to compare clinical characteristics and treatment outcomes between immunocompetent and immunocompromised patients.

Methods

To determine clinical presentations and outcomes, we reviewed electronic health records of all patients with lower-extremity NTMI treated and followed up at our institution from January 2002 through December 2017.

Results

Twenty-four patients were included in this study. Mean (SD) age was 58 (19) years. Eighteen patients (75%) were men; 13 (54%) were immunocompetent; and 9 (37%) had bone and joint involvement. No significant differences existed between immunocompetent and immunocompromised patients, except immunocompetent patients had significantly more infections at the hip, thigh, and toe. Bone and joint infection required significantly longer treatment time than skin and soft-tissue infection.

Conclusions

Regardless of immune status, patients with lower-extremity NTMI had similar characteristics, treatments, and outcomes. However, immunosuppression can be a major risk factor in the development of disseminated NTMI and associated complications. Acid-fast bacilli culture is strongly recommended for evaluation of delayed or nonhealing lesions. Aggressive medical and surgical management can be associated with good clinical outcomes.

Identification of Mycobacterium species and Rhodococcus equi in peccary lymph nodes

Mycobacterium species and the virulence-associated proteins (vapA, vapB, and vapN genes) of Rhodococcus equi isolated from 330 lymph nodes of collared peccaries (Tayassu tajacu) and white-lipped peccaries (Tayassu pecari) intended for human consumption were investigated. Thirty-six (10.9%) R. equi strains were isolated; 3.3% (n = 11/330) were from white-lipped peccary lymph nodes, and 7.6% (25/330) were from collared peccary lymph nodes. Among the 11 isolates of R. equi from the white-lipped peccaries, 90.9% (n = 10/11) were obtained from the mesenteric lymph nodes, and only 9.1% (n = 1/10) were obtained from the mediastinal lymph nodes. In the 25 isolates of R. equi obtained from the collared peccaries, 40.0% (n = 10/25) were recovered from the mesenteric lymph nodes, 36% (n = 9/25) from the submandibular lymph nodes, and 24.0% (n = 6/25) from the mediastinal lymph nodes. No vapA, vapB, or vapN genes (plasmidless) or three host-associated types (pVAPA, pVAPB, and pVAPN) were identified among the R. equi isolates. Mycobacterium species were isolated in 3.03% (n = 10/330) of all the lymph nodes analyzed. Among the 10 mycobacterial isolates, 60% (n = 6/10) were from the white-lipped peccary lymph nodes, and 40% (n = 4/10) were from the collared peccary lymph nodes. Ten Mycobacterium species were detected by PCR-PRA with a predominance of M. avium type 1. Sequencing of the hsp65 and rpob genes revealed mycobacteria that were saprophytic (M. sinense and M. kumamotonense) and potentially pathogenic (M. colombiense and M. intracellulare) to humans and animals. To our knowledge, this is the first description of R. equi and/or mycobacterial species identified in the lymph nodes of peccary specimens. R. equi (plasmidless) and the mycobacterial species described here have been reported as causes of pulmonary and extrapulmonary infections in both immunocompetent and immunocompromised humans.

Characterization of non-tuberculous mycobacterium from humans and water in an Agropastoral area in Zambia

Background

The non-tuberculous mycobacteria include those mycobacterium species that are not members of the Mycobacterium tuberculosis complex, the causative agent of pulmonary tuberculosis and Mycobacterium leprae. In Zambia, Non-tuberculous Mycobacteria are gaining recognition as pathogens of public health significance. However, there is scanty information on the isolation and speciation of these organisms for better patient management, consequently reducing the burden of these infections. Given the above information, the thrust of this study was to isolate and characterize NTM from humans and water in Namwala district of Zambia.

Method

This was a cross-sectional study were 153 individuals with suspected TB were sampled from four health facilities in Namwala district, sputum samples were also collected. Additionally, 149 water samples were collected from different water drinking sources such as Tap water, Borehole water, rivers, wells and streams. Standard TB culture methods were employed to isolate Non-tuberculous Mycobacteria and later 16S–23S internal transcribed spacer region Sequencing was employed to characterize NTM.

Results

Seven (7, 4.6%) NTM species were identified from humans with M. arupense (3, 42.9%) being the most common organism, while twenty three (23, 15.4%) NTM were identified from water with the common species being Mycobacterium gordonae (5, 21.7%). Mycobacterium avium and Mycobacterium fortuitum were both identified from human and water samples.

Conclusion

This study has shown the isolation of NTM species from humans and water. The isolation of NTM from drinking water sources could signify a public health risk to humans.

Delayed onset Mycobacterium intracellulare keratitis after laser in situ keratomileusis: A case report and literature review

RATIONALE

Infectious keratitis is a relatively uncommon but potentially sight-threatening complication of laser in situ keratomileusis (LASIK). Mycobacterial keratitis is usually regarded as late onset keratitis among post-LASIK keratitis. There has been no documented case of Mycobacterium intracellulare post-LASIK keratitis of a long-latent period.

PATIENT CONCERNS

A 36-year-old man was referred to our out-patient clinic, for persistent corneal epithelial defect with intrastromal infiltration. He had undergone uneventful bilateral LASIK procedure 4 years before. He complained decreased vision, accompanied by ocular pain, photophobia, and redness in his left eye for 7 months.

DIAGNOSIS

Lamellar keratectomy was taken using femtosecond laser. Bacterial culture with sequenced bacterial 16s ribosomal DNA confirmed the organism to be M intracellulare.

INTERVENTIONS

After 3 months of administration of topical clarithromycin, amikacin, and moxifloxacin, the corneal epithelial defect was resolved and the infiltration was much improved. However, newly developed diffuse haziness with surrounding granular infiltration in the central cornea was noted. Drug toxicity was suspected and topical moxifloxacin was discontinued, resulting in resolution of the diffuse haze with infiltration.

OUTCOME

The patient was followed up regularly without medication thereafter and recurrence was not found for 7 years.

LESSONS

This case presents the first case of M intracellulare keratitis after LASIK. LASIK surgeons should aware that post-LASIK keratitis can develop long after the operation and careful suspicion of infectious disease with meticulous diagnostic test is needed.

Pulmonary disease by non-tuberculous mycobacteria - clinical management, unmet needs and future perspectives

INTRODUCTION

The number of patients with pulmonary disease caused by non-tuberculous mycobacteria (NTM) is increasing globally. Poor resistance against infections, for example, due to pre-existing lung diseases, immune deficiency and immune-modulating treatment, predisposes the population to developing pulmonary NTM disease. The incidence of pre-existing lung diseases such as chronic obstructive pulmonary disease and bronchiectasis has also increased. NTM disease diagnosis is often delayed due to non-specific symptoms. The therapeutic arsenal is limited and adherence to treatment guidelines is often low since the treatment regimens are complex, lengthy and side effects are common. Thus, current disease management is far from satisfactory and needs to be improved. Areas covered: This review provides an overview of the current knowledge of NTM infections and includes pathogenesis, disease patterns, epidemiology, disease management, unmet needs and future perspectives. Expert commentary: NTM disease is becoming more prevalent, in part with our increased awareness and improved diagnostic methods. However, our understanding of the disease pathogenesis is limited and treatment decisions are challenging, with difficult to employ drug regimens. Optimal management requires collaboration between healthcare providers, patients and expert centers.

Peritoneal dialysis-associated catheter infection caused by Mycobacterium abscessus in an elderly patient who was successfully treated with catheter removal

An 89-year-old Japanese man on peritoneal dialysis (PD) was suspected of having a PD-associated catheter infection. He visited the hospital because of the discharge of pus from the exit site of his catheter. Gram staining of the pus showed Gram-positive bacilli, but these were acid-fast bacilli. The rapidly growing nontuberculous mycobacteria, Mycobacterium abscessus, was isolated. PD catheter removal and debridement were immediately performed. The patient received combination antibiotic therapy. His clinical course was good, but he required hemodialysis due to the discontinuation of PD. However, the patient and his family chose not to continue hemodialysis even when the symptoms of uremia appeared. Best supportive care was arranged by his primary care physician. M. abscessus is a rare causative organism for PD-associated catheter infections and is difficult to treat. In our case, a rapid and precise diagnosis was made using acid-fast staining and Mycobacterium culture. The risk of nontuberculous mycobacterial infections should be considered in patients on PD.

Microbiology and Biofilm Trends of Silicone Lacrimal Implants: Comparing Infected Versus Routinely Removed Stents

PURPOSE

To investigate the pathogens and biofilms responsible for clinically significant infection of silicone stents implanted within the lacrimal system.

METHODS

Retrospective review of culture results and patient demographics for all silicone lacrimal stents removed early for clinically significant infection and sent to the Bascom Palmer Microbiology Laboratory through the end of year 2010. As a control, routinely removed, clinically noninfected stents from the same institution were prospectively sent for culture over a 6-month period. Four clinically infected and 6 clinically noninfected stents showing mucus within the lumen at removal were sent for scanning electron microscopy. Images were randomized and graded by a microbiologist for the presence of organisms, matrix deposits, organisms within matrix, and overall impression of significant biofilm formation.

RESULTS

Nineteen stents were included in the study; 100% of clinically infected (n = 10) and noninfected (n = 9) stents were culture positive. Culture positivity for nontuberculous mycobacterium was found in 90% of infected stents and none of the noninfected stents (p < 0.001). Of infected stents, 50% grew Gram-positive organisms compared with 89% of noninfected stents (p = 0.07). Fifty percent of infected versus 67% of noninfected stents were culture positive for Gram-negative organisms (p = 0.46). Electron microscopy of stents revealed organisms consistent with culture results (size, shape) in planktonic and biofilm form. Masked observer image grading revealed a statistically significant higher amount of organism and biofilm on infected versus noninfected specimen.

CONCLUSION

Nontuberculous mycobacteria comprise the primary pathogens responsible for clinically significant infection of silicone stents in the lacrimal system in South Florida. Robust biofilm production by this organism likely plays a role in pathogenesis. Further research into biofilm-related lacrimal implant infection may aid in the development of useful prevention and treatment strategies.

Investigation of intra-herd spread of Mycobacterium caprae in cattle by generation and use of a whole-genome sequence

Single nucleotide polymorphisms (SNPs) calculated from whole genome sequencing (WGS) are ideally suited to study evolutionary relationships of pathogens and their epidemiology. Mycobacterium caprae infections have been documented frequently in cattle and red deer along the Bavarian and Austrian Alps during the last decade. However, little is still known about the transmission within cattle holdings and possible alterations of the genomes of M. caprae during such events. The aim of this study was to study the molecular epidemiology of bovine tuberculosis (bTB) in selected herds based on isolate-specific genome-wide SNPs and to perform a phylogenetic network analysis. In total, 61 M. caprae isolates were collected originating from eight cattle farms over a period of twelve years between 2004 and 2015. Analysis of their sequence data revealed that the M. caprae isolates of an affected farm differ at all in a few SNPs. In contrast, many more SNPs were found when comparing the M. caprae genomes originating from different herds. The results demonstrated that the spread of bTB in the affected farms occurred by direct transmission between the members of each herd rather than between herds and a M. caprae introduction in farms after contact events e. g. on summer pastures can readily be traced by WGS analysis. Furthermore, we assembled a nearly complete whole genome sequence of M. caprae derived from several cattle isolates originating from bTB cases in the Bavarian Alpine region.

Diagnostic yield of nontuberculous mycobacteria in patients booked for endoscopy at the University Teaching Hospital, Lusaka

BACKGROUND

The intestinal carriage of nontuberculous mycobacteria (NTM) is associated with disease, especially in severely immunocompromised individuals. These organisms, although often considered contaminants, have been known to cause various types of illnesses. We aimed to determine the prevalence of and associated factors for NTM among patients booked for colonoscopy at the University Teaching Hospital (UTH) in Lusaka.

METHODS

We randomly recruited 97 patients attending routine endoscopy procedures between November 2012 and October 2013 and after consent, administered a structured questionnaire. We collected stool and intestinal lavage samples, as well as biopsy samples from the descending colon and the caecal area during the endoscopy procedure. Samples were cultured using the mycobacteria growth indicator tube (MGIT) method followed by the GenoType Mycobacterium CM/AS assay for identification of NTM. Results were expressed as means and standard deviations; proportions were expressed as percentages with corresponding 95% confidence intervals. We used Fisher's exact Chi square test for cross-tabulations where appropriate. All statistical tests were two-sided, with a significance level set at p < 0.05.

RESULTS

Out of the 97 patients, 45 (46.4%) were female and 52 (53.6%) were males with mean ages 49.1 (±16.7, range 24-85) and 44.4 (±15.0, range 18-80) years respectively. The prevalence of NTM was 7.2% (95% CI 1.9-12.4), while that of Mycobacterium tuberculosis (MTB) was 6.2% (95% CI 2.3-13.0). Carriage of NTM was not significantly associated with age, sex or presenting symptoms such as diarrhoea, abdominal pain, weight loss as well as HIV status. There were no identifiable predictors of NTM carriage.

CONCLUSION

The results have shown that NTM and MTB are present in the intestines of the patients booked for colonoscopy at the University Teaching Hospital in Lusaka, but their presence is not related to presenting symptoms. Given that this may be an indicator of a bigger burden of NTM in this population, there is a need to explore this burden and the contribution it could have on abdominal disease in general as well as examine potential factors that might be important predictors.

Nontuberculous mycobacterial infection of the musculoskeletal system in immunocompetent hosts

BACKGROUND

Nontuberculous mycobacteria (NTM) were considered saprophytic organisms for many years but now are recognized as human pathogens. Although humans are routinely exposed to NTM, the rate of clinical infection is low. Such infections usually occur in the elderly and in patients who are immunocompromised. However, there has been an increasing incidence in recent years of infections in immunocompetent hosts. NTM infections in immunocompetent individuals are secondary to direct inoculation either contamination from surgical procedures or penetrating injuries rather than hematogenous dissemination. Clinically and on histopathology, musculoskeletal infections caused by NTM resemble those caused by Mycobacterium tuberculosis but are mostly resistant to routine antituberculosis medicines.

MATERIALS AND METHODS

Six cases of NTM infection in immunocompetent hosts presenting to the department from 2004 to 2015 were included in study. Of which two cases (one patella and one humerus) of infection were following an open wound due to trauma while two cases (one hip and one shoulder) of infection were by inoculation following an intraarticular injection for arthrogram of the joint, one case was infection following arthroscopy of knee joint and one case (calcaneum) was infection following local injection for the treatment of plantar fasciitis. All patients underwent inaging and tissue diagnosis with samples being sent for culture, staining, and histopathology.

RESULTS

Clinical suspicion of NTM inoculation led to the correct diagnosis (four cases with culture positive and two cases with histopathological diagnosis). There treatment protocol for extrapulmonary NTM infection was radical surgical debridement and medical management based on drug sensitivity testing in culture positive cases. At a mean follow up of 3 years (range1-9 years) all patients had total remission and excellent results.

CONCLUSIONS

Whenever a case of chronic granulomatous infection is encountered that does not respond to standard anti-tuberculous treatment, with a history of open trauma, surgical intervention, or injection as shown in this study, a possible NTM infection should be considered and managed appropriately.

Identification of Mycobacterium Species by MALDI-TOF Mass Spectrometry

Matrix-assisted laser desorption ionization - time-of-flight (MALDI-TOF) mass spectrometry enables to identify microorganisms by comparison of the protein content with reference spectra in the database. The aim of this study was to evaluate the efficacy of phenotypic identification of mycobacteria by MALDI-TOF mass spectrometry in laboratory practice. Seventy five isolates of mycobacteria were identified by molecular and phenotypic method, and the results were compared by MALDI-TOF. For MALDI-TOF, material was processed according to the Bruker Daltonics protocol and Mycobacterial Library database version 2.0, with 313 reference mycobacteria spectra. All except one of the 72 isolates agreed with regard to the species and genus by both methods. Forty three isolates were identified as the M. tuberculosis complex by MALDI-TOF. Thirty one isolates of nontuberculous mycobacteria were consistently identified by both methods to the species level. We conclude that MALDI-TOF mass spectrometry is an accurate method of bacterial identification. Simplicity, speed, and economic availability of the method makes it suitable for mycobacteria identification in a routine laboratory.

Pacemaker pocket infection due to environmental mycobacteria: Successful management of an outbreak and steps for prevention in future

Background

An outbreak of surgical site infection (SSI) due to environmental mycobacteria (EMB) occurred in a hospital in Eastern India.

Method

A quality improvement project (QIP) was undertaken to analyze the causes and prevent further outbreak. Step (1) Proof of the need: Four patients who had undergone pacemaker implantation consecutively during a 10-day period developed SSI. Step (2) Diagnostic journey: Since all patients developed SSI within 2 months of implantation, a common source of infection was likely. Atypical mycobacteria (AMB) were grown from surgical sites as well as from the surface of operation table, image intensifier, and lead aprons. It was a rapid growing variety that lacked pigment, a characteristic of EMB with pathogenic potential. The EMB was finally traced to its source, the overhead water tank. Step (3) Remedial journey: By thorough cleaning of the water tank and enriching its chlorine content, the EMB was eliminated from its source. Step (4) Holding the gains: Protocol for cleaning the water tank once in 3 months was made. A checklist was prepared to ensure compliance to asepsis protocol in the operation theater. In the ensuing 5 years, the infection did not recur.

Result

The bacteria that caused SSI were identified as EMB that grew in the water tank and contaminated the operation room. It could be eliminated by appropriate measures.

Interpretation

Water is a potential reservoir for EMB. Use of the term ‘environmental mycobacteria’ instead of ‘atypical mycobacteria’ will generate awareness about contamination as the cause of SSI.

Prevalence of nontuberculous mycobacteria among extrapulmonary tuberculosis cases in tertiary care centers in Northern India

The reports of nontuberculous mycobacteria (NTM) associated with extrapulmonary diseases are increasing in tertiary care hospitals. Despite a significant increase in knowledge about NTM infections, they still represent a diagnostic and therapeutic challenge. The aim of this study is to know the prevalence of NTN among extrapulmonary tuberculosis cases in tertiary care centers in Northern India. A total of 227 culture positive isolates from 756 cases were tested for niacin production and catalase assay. BIO-LINE SD Ag MPT64 TB test and final identification and differentiation between MTBC and different species of NTM were further confirmed by GenoType Mycobacterium CM/AS assay. 71 cases (9.3%) were positive for AFB by ZN staining and 227 cases (30.1%) were positive for mycobacteria by culture. Niacin production and catalase activity were negative in 62/227 (27.4%) strains and after using a panel of different biochemicals and final confirmation by GenoType Mycobacterium CM assay. Out of 227 cultures tested, 165 (72.6%) strains were confirmed as M. tuberculosis complex, and 62 (27.4%) were confirmed as NTM. The most common NTM species identified were M. fortuitum 17 (27.5%) and M. intracellulare 13 (20.9%). The rapid identification of NTM species may help in targeted therapy and management of the diseases.

Surgical site infections due to rapidly growing mycobacteria in puducherry, India

BACKGROUND

Rapidly growing Mycobacteria are increasingly recognized, nowadays as an important pathogen that can cause wide range of clinical syndromes in humans. We herein describe unrelated cases of surgical site infection caused by Rapidly growing Mycobacteria (RGM), seen during a period of 12 months.

MATERIALS AND METHODS

Nineteen patients underwent operations by different surgical teams located in diverse sections of Tamil Nadu, Pondicherry, Karnataka, India. All patients presented with painful, draining subcutaneous nodules at the infection sites. Purulent material specimens were sent to the microbiology laboratory. Gram stain and Ziehl-Neelsen staining methods were used for direct examination. Culture media included blood agar, chocolate agar, MacConkey agar, Sabourauds agar and Lowenstein-Jensen medium for Mycobacteria. Isolated microorganisms were identified and further tested for antimicrobial susceptibility by standard microbiologic procedures.

RESULTS

Mycobacterium fortuitum and M.chelonae were isolated from the purulent drainage obtained from wounds by routine microbiological techniques from all the specimens. All isolates analyzed for antimicrobial susceptibility pattern were sensitive to clarithromycin, linezolid and amikacin but were variable to ciprofloxacin, rifampicin and tobramycin.

CONCLUSION

Our case series highlights that a high level of clinical suspicion should be maintained for patients presenting with protracted soft tissue lesions with a history of trauma or surgery as these infections not only cause physical but also emotional distress that affects both the patients and the surgeon.

Performance of a real-time PCR assay for the rapid identification of Mycobacterium species

Mycobacteria cause a variety of illnesses that differ in severity and public health implications. The differentiation of Mycobacterium tuberculosis (MTB) from nontuberculous mycobacteria (NTM) is of primary importance for infection control and choice of antimicrobial therapy. The diagnosis of diseases caused by NTM is difficult because NTM species are prevalent in the environment and because they have fastidious properties. In the present study, we evaluated 279 clinical isolates grown in liquid culture provided by The Catholic University of Korea, St. Vincent's Hospital using real-time PCR based on mycobacterial rpoB gene sequences. The positive rate of real-time PCR assay accurately discriminated 100% (195/195) and 100% (84/84) between MTB and NTM species. Comparison of isolates identified using the MolecuTech REBA Myco-ID(®) and Real Myco-ID® were completely concordant except for two samples. Two cases that were identified as mixed infection (M. intracellulare-M. massiliense and M. avium-M. massiliense co-infection) by PCRREBA assay were only detected using M. abscessus-specific probes by Real Myco-ID(®). Among a total of 84 cases, the most frequently identified NTM species were M. intracellulare (n=38, 45.2%), M. avium (n=18, 23.7%), M. massiliense (n=10, 13.2%), M. fortuitum (n=5, 6%), M. abscessus (n=3, 3.9%), M. gordonae (n=3, 3.9%), M. kansasii (n=2, 2.4%), M. mucogenicum (n=2, 2.4%), and M. chelonae (n= 1, 1.2%). Real Myco-ID(®) is an efficient tool for the rapid detection of NTM species as well as MTB and sensitive and specific and comparable to conventional methods.

Increase in nontuberculous mycobacteria isolated in Shanghai, China: results from a population-based study

BACKGROUND

In China, the prevalence of nontuberculous mycobacteria (NTM) in isolates from mycobacterial culture-positive patients with pulmonary tuberculosis (TB) is largely unknown.

METHODS

We used conventional biochemical and 16S rRNA gene sequencing to identify species of mycobacteria in specimens from patients suspected of having TB. Drug-susceptibility testing was performed on NTM isolates using the proportion method. We also determined the independent risk factors associated with infection with NTM compared with infection with Mycobacterium tuberculosis.

RESULTS

The overall rate of NTM isolated from mycobacterial culture-positive patients was 5.9% in this population, with a significantly increasing trend from 3.0% in 2008 to 8.5% in 2012 (P for trend <0.001). The organism most frequently identified was M. kansasii (45.0%), followed by M. intracellulare (20.8%) and M. chelonae/abscessus (14.9%). The overall proportion of isolates resistant to the four first-line anti-TB agents were 64.6% for isoniazid, 77.6% for streptomycin, 63.3% for rifampicin and 75.1% for ethambutol. The risk factors most often associated with NTM infection were older age (P for trend <0.001), being a resident of Shanghai (adjusted odds ratio [aOR], 1.48; 95% CI, 1.10-2.00), having been treated for tuberculosis (aOR, 1.64; 95% CI, 1.18-2.29), having a cavity on chest X-ray (aOR, 1.51; 95% CI, 1.16-1.96), and being sputum smear-negative (aOR, 1.59; 95% CI, 1.16-2.18).

CONCLUSIONS

The prevalence of NTM isolated in Shanghai increased between 2008 and 2012, thus clinicians should consider NTM as a possible cause of TB-like disease. Accurate species identification is imperative so that proper treatment can be administered for diseases caused by the diversity of NTM species.

Antimicrobial susceptibility and molecular characterization of Mycobacterium intracellulare in China

Mycobacterium avium complex (MAC) is the most common non-tuberculosis mycobacterial pathogen isolated from respiratory samples, mainly including two species, Mycobacterium avium (M. avium) and Mycobacterium intracellulare (M. intracellulare). Although these two species belong to the same group, M. avium and M. intracellulare reveal significantly differences in pathogenicity and biology. Nevertheless, little is known regarding the drug resistant details profile of M. avium or M. intracellulare instead of MAC. Here, we examined the antimicrobial susceptibility profiles of 52 clinical M. intracellulare isolates against fourteen antimicrobial agents, which are widely selected for the treatment of nontuberculous mycobacteria (NTM) infection. The drug susceptibility test revealed that clarithromycin (47/52, 90.4%), rifampicin (41/52, 78.8%) and capreomycin (40/52, 76.9%) revealed highly antimicrobial activities against M. intracellulare isolates in vitro. Furthermore, all clarithromycin resistant isolates harbored mutations in the 23S rRNA gene, and the percentage of amikacin resistant ones with mutation in the rrs gene is 62.5% (10/16). The Hunter-Gaston Discriminatory Index (HGDI) value for the 16-loci Variable Number of Tandem Repeat (VNTR) typing of M. intracellulare isolates was 0.994, and M. intracellulare resistance to moxifloxacin was significantly more commonly found in clustered strains than in nonclustered strains (χ(2)=5.551, P=0.040). In conclusion, our data demonstrated that clarithromycin and capreomycin revealed highly antimicrobial activities against M. intracellulare isolates, and clarithromycin and amikacin resistance could be detected more readily and rapidly using molecular scanning of corresponding drug target than conventional drug susceptibility testing. We also found that infection by clustered strains was significantly associated with resistance to moxifloxacin.

Novel insights into transmission routes of Mycobacterium avium in pigs and possible implications for human health

Mycobacterium avium infection is a severe condition in humans, whereas pigs are often subclinically infected. Pig carcasses represent a possible source of human infection. Faecal excretion of M. avium was recently demonstrated in experimentally infected pigs, along with detection of M. avium in apparently normal lymph nodes. The present study investigates faecal excretion in naturally infected herds and the presence of live mycobacteria in lymph nodes. Two pig herds (A and B), with a history of sporadically suspected M. avium infection were sampled. Herd B used peat, as opposed to Herd A. Samples from peat, sawdust, drinking water, faeces and lymph nodes were collected. Identification of mycobacteria was performed by 16S rDNA sequencing and PCR. Mycobacterium avium isolates were analysed by Multi-Locus Variable Number of Tandem repeat Analysis (MLVA). Mycobacterium avium subsp. hominissuis was detected in samples of faeces, peat and lymph nodes from Herd B, often with identical MLVA profiles. Additionally, other non-tuberculous mycobacteria (NTM) were found in the same material. The absence of macroscopic lymph node lesions in the presence of M. avium subsp. hominissuis was frequently demonstrated. In Herd A, only one NTM isolate, which proved not to be M. avium, was found. Faeces might facilitate transmission of M. avium subsp. hominissuis between pigs and maintain the infection pressure in herds. The low incidence of macroscopic lesions together with the massive presence of M. avium subsp. hominissuis in lymph nodes from pigs kept on peat raises questions related to animal husbandry, food safety and human health.

Mycobacterium chelonae peritonitis in peritoneal dialysis. Literature review

Non-tuberculous mycobacteria are a rare but serious cause of peritoneal dialysis-related peritonitis. There are no clear guidelines for treating non-tuberculous mycobacteria peritoneal dialysis-associated infections. It has been recommended that at least two antibiotics be given for a prolonged period and peritoneal catheter should be removed. This paper describes the clinical course and treatment of a patient with M. chelonae peritoneal dialysis-related peritonitis and reviews the previously published cases.

Bacterial pathogens

Bacterial infections are frequent complications among patients treated for cancer. The type, severity, and treatment of bacterial infections vary and depend upon the specific malignancy, associated chemotherapies, and transplantation. This chapter discusses commonly encountered bacterial pathogens as well as Nocardia and mycobacteria in patients with cancer and addresses the clinical syndromes and management. Drug-resistant bacteria are becoming an increasingly recognized problem in patients with cancer. Antimicrobial resistance in select gram-positive and gram-negative bacteria are discussed along with the mechanisms of resistance and recommended therapies.

Histology of solid lateral cervical masses biopsied in children

INTRODUCTION

Solid cervical lateral neck masses in children may require surgical biopsy to confirm appropriate diagnostic and begin a directed therapeutic treatment. We aimed to describe the contribution of pathological results and compare them with the clinical diagnosis and the paraclinical tools.

METHODS

A retrospective review of surgical biopsies for solid lateral neck masses in children over a ten year period in a pediatric tertiary center was conducted. Demographic, imaging, laboratory analysis, surgical and pathological data were collected and analyzed using descriptive statistics with SPSS 17.0.

RESULTS

44 biopsies were done between 2002 and 2012. Inflammatory masses were found in 26/44 biopsies with half of them (13/26) being nontuberculous mycobacterial (NTM) lymphadenitis. Non-inflammatory/benign masses represented 9/44 biopsies and 5/44 masses were of malignant etiology. Malignant masses imaging had a sensitivity and specificity of 33% and 75%, respectively, for ultrasound, whereas Neck CT scan had 33% and 77%, respectively. The contribution of pathological results to the clinical management was questionable in 39% (17/44) of biopsies.

CONCLUSION

Inflammatory masses with NTM lymphadenitis were the most common diagnosis. Imaging was not helpful in establishing the diagnosis. Heterogeneity in the management of solid lateral neck masses between clinicians was important and indicates the need for guideline approach.

Probable hepatic tuberculosis masquerading as Klatskin tumour in an immunocompetent patient

A 55-year-old immunocompetent woman was presented with features of obstructive jaundice and a clinicoradiological picture suggestive of a hilar cholangiocarcinoma (Klatskin tumour). However, caseating granulomatous lesion associated with miliary nodules were revealed intraoperatively. The lesion responded to standard antituberculous therapy. This unusual presentation highlights the considerable diagnostic challenge in such case.

Molecular characterization of Mycobacterium avium subspecies hominissuis isolated from humans, cattle and pigs in the Uganda cattle corridor using VNTR analysis

BACKGROUND

Members of the Mycobacterium avium complex (MAC) cause disease in both human and animals. Their ubiquitous nature makes them both successful microbes and difficult to source track. The precise characterization of MAC species is a fundamental step in epidemiological studies and evaluating of possible reservoirs. This study aimed at identifying and characterizing Mycobacterium avium subsp. hominissuis isolated from human, slaughter cattle and pigs in various parts of the Uganda cattle corridor (UCC) at two temporal points using variable number of tandem repeat (VNTR) analysis.

METHODS

A total of 46 M. avium isolates; 31 from 997 pigs, 12 from 43 humans biopsies and three from 61 cattle lesions were identified to subspecies level using IS1245 and IS901 PCR, thereafter characterized using VNTR. Twelve loci from two previously described VNTR methods were used and molecular results were analyzed and interpreted using Bionumerics 6.1.

PRINCIPAL FINDINGS

37 of the isolates were identified as M. avium subsp. hominissuis and four as M. avium subsp. avium, while five could not be differentiated, possibly due to mixed infection. There was distinct clustering that coincides with the temporal and spatial differences of the isolates. The isolates from humans and cattle in the North Eastern parts of the UCC shared identical VNTR genotypes. The panel of loci gave an overall discriminatory power of 0.88. Some loci were absent in several isolates, probably reflecting differences in isolates from Uganda/Africa compared to isolates previously analyzed by these methods in Europe and Asia.

CONCLUSIONS

The findings indicate a molecular difference between M. avium subsp. hominissuis isolates from pigs in Mubende and cattle and human in the rest of the UCC. Although human and cattle shared VNTR genotypes in the North Eastern parts of the UCC, it is most likely a reflection of a shared environmental source.