Emergence of Rare Species of Nontuberculous Mycobacteria as Potential Pathogens in Saudi Arabian Clinical Setting

Phylogenetic Profile of Nonulcerans and Nontuberculous Environmental Mycobacteria Isolated in Côte d'Ivoire

BACKGROUND

Environmental mycobacteria are involved in several infections ranging from lung to skin infections. In Côte d'Ivoire, apart from Mycobacterium ulcerans and Mycobacterium tuberculosis, little information exists on other species. The culture of these species, a real challenge, especially in developing countries like Cote d'Ivoire, limits their identification. However, there are reports in literature of infections caused by these mycobacteria, and few species have never been described in human or animal infections. These are difficult cases to treat because of their resistance to most antituberculosis antibiotics. The aim of our work was to study the diversity of potentially pathogenic mycobacterial species in wastewater drainage channels in different townships and in two hospital effluents in the city of Abidjan.

METHODS

Wastewater samples were cultured, followed by conventional polymerase chain reaction (PCR) targeting mycobacterial 16S ribonucleic acid (16S RNA) using PA/MSHA primers. 16 S RNA identified were sequenced by Sanger techniques. Sequences obtained were analyzed, and a phylogenic tree was built.

RESULTS

Fast-growing mycobacteria, including Mycobacterium fortuitum, Mycobacterium phocaicum, Mycobacterium sp., and others presence, were confirmed both by culture and molecular techniques. M. fortuitum strain was the same in effluents of the Treichville University Hospital and in the wastewater of the township of Koumassi. New species never isolated in Côte d'Ivoire, such as M. phocaicum, have been identified in wastewater of the township of Yopougon.

CONCLUSION

This study showed that the sewer network in the city of Abidjan is colonized by both potentially pathogenic mycobacteria and saprophytic environmental mycobacteria.

Challenging diagnosis of Mycolicibacterium cosmeticum/canariasense infection: A case report and literature review

We present the case of an immunocompromised child with Mycolicibacterium cosmeticum/ canariasense infection. Our case highlights the difficulty in adequate speciation. Most isolates described in the literature were identified using 16 s-rRNA PCR, which if performed on our sample would at best be inconclusive. Misidentifications could have a real impact on the body of evidence collected on these isolates thus far.

Vertebral Osteomyelitis Caused by Mycobacterium arupense Mimicking Tuberculous Spondylitis: First Reported Case and Literature Review

Mycobacterium arupense is a slow-growing, nontuberculous mycobacterium widely found in the environment and is known to cause tenosynovitis and osteomyelitis, mainly in the hands and wrists. We present the first case of vertebral osteomyelitis caused by M arupense in a 78-year-old man with renal cell carcinoma. The patient had a history of tuberculous pleuritis in childhood. Although the nucleic acid amplification test of the vertebral tissue for Mycobacterium tuberculosis was negative, we initiated tuberculosis treatment based on the history and pathological findings of auramine-rhodamine-positive organisms and epithelioid cell granulomas. Subsequently, the isolated mycobacterium was identified as M arupense by genome sequencing. Accordingly, the treatment regimen was changed to a combination of clarithromycin, ethambutol, and rifabutin. Owing to a subsequent adverse event, rifabutin was switched to faropenem, and the patient was treated for a total of 1 year. In previous literature, we found 15 reported cases of bone and soft tissue infections caused by M arupense, but none of them had vertebral lesions. Physicians should be aware that M arupense can cause vertebral osteomyelitis mimicking tuberculous spondylitis. In addition, molecular testing of isolated mycobacteria is essential for diagnosis, even if tuberculous spondylitis is suspected.

Non-tuberculous mycobacteria immunopathogenesis: Closer than they appear. a prime of innate immunity trade-off and NTM ways into virulence

Introduction

The growing incidence of non‐tuberculous mycobacteria (NTM) and changes in epidemiological factors have indicated that immune dysregulation may be associated with the emergence of NTM. Minireview entails to acknowledge complex interaction and new ways NTM are evolving around diverse immune status.

Methods

In order to perform this review, we selected peer reviewed, NLM database articles under the terms NTM, mycobacterium complex ‘AND’ ‐Host‐ immune response, immunity regulation, Disease, Single Nucleotide Polymorphism (SNP´s), and ‐pathogen‐ followed by a snow ball rolling basis search on immune components and NTM related with diseases distribution.

Results

The universal exposure and diversity of NTM are well‐documented; however, hospitals seldom establish vigilant control of water quality or immunodeficiencies for patients with NTM infections. Depending on the chemical structures and immune mechanisms presented by various NTM varieties, they can trigger different effects in dendritic and natural killer cells, which release interleukin (IL)‐17, tumour necrosis factor‐α (TNF‐α), interferon‐γ (IFN‐γ) and rIL‐1B. The T helper (Th)2‐acquired immune response is responsible for autoimmune responses in patients with NTM infections, and, quite disturbingly, immunocompetent patients have been reported to suffer from NTM infections.

Conclusion

New technologies and a comprehensive view has taught us; to acknowledge metabolic/immune determinants and trade‐offs along transit through mutualism‐parasite continuous.

Pneumonia due to Mycobacterium cosmeticum in a renal transplant recipient

A 69-year-old man renal transplant recipient for 4 years, presented with 4-day history of cough and dyspnoea. He was diagnosed with community-acquired pneumonia and treated accordingly. He deteriorated requiring intensive care unit admission and intubation. Mycobacterial culture from bronchoalveolar lavage grew colonies within 7 days of incubation while Mycobacterium tuberculosis PCR was negative. The antibiotic regimen was adjusted to cover for rapidly growing mycobacteria with imipenem, amikacin and clarithromycin. The final culture reported Mycobacterium cosmeticum. He improved on the antibiotic regimen given which the organism turned to be sensitive to. We reported the second case with M. cosmeticum that fulfilled the diagnostic criteria for non-tuberculous mycobacterial lung infection. Improvement of patient’s lung infection on appropriate antibiotics points to a causal relationship.

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including Mycobacterium abscessus and Mycobacterium avium, many of the less common but clinically relevant NTM species, including M. kubicae, still lack complete genomes to serve as a comparative reference. Well-characterized representative genomes for each NTM species are important both for investigating the pathogenic potential of NTM, as well as for use in diagnostic methods, even for species that less frequently cause human disease. Here, we report the complete genomes of two M. kubicae strains, isolated from two unrelated patients. Hybrid short-read and long-read sequencing and assembly, using sequence reads from Illumina and Oxford Nanopore Technologies platforms, were utilized to resolve the chromosome and plasmid sequences of each isolate. The genome of NJH_MKUB1 had 5135 coding sequences (CDSs), a circular chromosome of length 5.3 Mb and two plasmids. The genome of NJH_MKUB2 had 5957 CDSs, a circular chromosome of 6.0 Mb and five plasmids. We compared our completed genomic assemblies to four recently released draft genomes of M. kubicae in order to better understand intraspecies genomic conservation and variability. We also identified genes implicated in drug resistance, virulence and persistence in the M. kubicae chromosome and plasmids. Virulence factors encoded in the genome and in the plasmids of M. kubicae provide a foundation for investigating how opportunistic environmental NTM may cause disease.

Isolation and Molecular Identification of Nontuberculous Mycobacterium from Different Species of Fish in Karbala Province, Iraq

This study was designed for isolation and molecular identification of Nontuberculous Mycobacterium (NTM) from fish during the period between October and December 2017 from Karbla province, Iraq. This study included 200 fresh fish samples from four different species including Spondyliosoma cantharus, Liza abu, Carassius carassius and Cyprinuscarpio. Three samples of each fish were taken including gills, muscles and all internal organs. The samples were processed by decontamination, concentration of 4% sodium hydroxide, and 0.1 ml of sediment was streaking on Löwenstein Johnson (LJ) media; then the bacterial cultures were incubated at 28-30 °C for 3days up to 4 weeks and suspected colonies were stained with acid fast stain to confirm the presence of Mycobacterium. Further identification, biochemical tests were carried out to confirm the diagnosis of isolates, PCR was done using 16s RNA gene for all isolates, hsp65 gene was used in unidentified NTM spp and to confirm the others. Results revealed that out of 200 fish samples, 19 isolates 9.5% were identified as NTM belonged to Rapid Growth Mycobacterium (RGM). of the total isolates, 18.26 % was investigated from Liza abu (Kishni, Abu khraiza). NTM (RGM) isolates on spp level identified six spp of these isolates. M. porcinum was 26.32% which was followed by M. fortuitum of 21.05%, others included M. neworleansense and M. mucogenicum 10.5% of each, M. cosmeticum and M. pallens 5.26% of each. The distribution of NTM spp in the fish organs, nine out of 19 (47.37%) NTM isolate were recovered from gills followed by muscles 36.84 %, while 15.79% from internal organs. These results were the first study concerning isolation of these spp of NTM from fish in Iraq, and some spp are not reported in other studies. This study concluded that the fish is an importance source or reservoir for NTM, especially the pathogenic spp.

Evaluation of the ASTA MicroIDSys matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures

OBJECTIVES

We evaluated the performance of the MicroIDSys Elite system, a newly developed matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures.

METHODS

Analytical specificity was evaluated with 63 reference strains grown in mycobacteria growth indicator tube media. Prospective performance evaluation was conducted with primary liquid cultures of sputum samples for identification of mycobacteria, and results were compared to multigenerational sequencing as the reference method. Liquid media subcultures were also analyzed.

RESULTS

The accuracy for the 63 reference strains was 98.4% (62/63). A total of 167 paired mycobacterial primary cultures and subcultures in liquid media, comprised of seven Mycobacterium tuberculosis isolates, 109 slowly growing nontuberculous mycobacterial isolates, and 51 rapidly growing nontuberculous mycobacterial isolates, was identified by the MicroIDSys Elite system. Using primary liquid cultures, the MicroIDSys Elite system correctly identified 143 (85.6%) isolates; 21 (12.6%) resulted in "no identification"; and three (1.8%) isolates were misidentified. Using liquid media subcultures with this system, 159 (95.2%) isolates were correctly identified; seven (4.2%) resulted in "no identification"; and one (0.6%) isolate was misidentified.

CONCLUSION

The MicroIDSys Elite system is a useful routine diagnostic tool for identification of mycobacterial species from liquid culture.

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation

Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN-FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.

The case report of Mycobacterium arupense wound infection in diabetes mellitus patients; the first report and literature review

Mycobacterium arupense is among the opportunist pathogens of atypical mycobacteria emergence (atypical mycobacteria) that is one of the isolated and reported environmental and clinical specimens. Numerous cases of osteo-articular infections of this bacterium are reported nowadays, while the pulmonary infection is rare. We identified Mycobacterium arupense in non-healing wound infection of an elderly woman with history of diabetes mellitus. She has negative tests for HIV, HBV and HCV, but was positive for HTLV-1. The patient was referred according to mild-fever, non-healing, destructive, and swelled lesion on her left foot. The mycobacterial wounds infection was suspected due to her non-conclusive previous treatment. The pathology, acid-fast staining, conventional and 16S rRNA sequencing confirmed the micro-organism to be M. arupense. Finally, the patient recovered following two-week consumption of clarithromycin, ethambutol and rifabutin. The results of this study provide evidence on the potential pathogenicity, clinical outcomes and treatment of infections caused by this bacterium.

Molecular epidemiology of mycobacteria among herds in Marajó Island, Brazil, reveals strains genetically related and potential zoonotic risk of clinical relevance

Mycobacterium bovis is the main causative agent of bovine tuberculosis (bTB) being among the animal-adapted Mycobacterium tuberculosis complex. Herds can also be infected with non-tuberculous mycobacteria (NTM) causing a negative effect on the economy and on animal and human health through zoonotic infections. Molecular tools are required for mycobacteria identification; thus, it is laborious to determine the epidemiological information of mycobacteria among herds. We aimed to describe the mycobacterial pathogens associated with cases of suspected bTB lesions in cattle/buffaloes slaughtered for consumption and to investigate bTB transmission. We evaluated 74 lesion samples from 48 animals (27 bovine/21 buffaloes) from 16 mapped farms. Positives samples from nested-PCR were cultured in Lowenstein-Jensen (LJ), 2% pyruvate (LJ + P), and 2% glycerol (LJ + G) media, followed by Ziehl-Neelsen (ZN) staining technique and partial gene sequencing (hsp65, rpoB, and 16S-rRNA). Spoligotyping and 24-MIRU-VNTR were performed. The LJ + P increased the chance of obtaining bacilli. The respiratory tract and the oral cavity were the most important infection route. In addition, the calcified part of the lesions suggested chronic bTB. Spoligotypes of M. bovis (SIT986/SB0885) differed from others found in South America, and the MIRU-VNTR 24 loci suggested that bTB was associated to highly related strains. The NTM species found are of clinical importance in humans.

Pulmonary Mycobacterium kyorinense disease: A case report and review of literature

We report here the first case of pulmonary infection due to Mycobacterium kyorinense in a 55-year-old hypertensive woman treated for pulmonary tuberculosis earlier on two occasions. She presented with productive cough, intermittent episode of left-sided chest pain, loss of appetite, low-grade fever, and breathlessness. Sputum cultures revealed non-tuberculous mycobacteria (NTM). She remained persistently symptomatic with sputum cultures positive for acid-fast bacilli even after 6 months of treatment. Hence, a 16SrRNA gene amplification and sequencing were done that revealed M. kyorinense. Based on the guidelines of the American Thoracic Society, she was started on weight-based dosing of clarithromycin, levofloxacin, ethambutol, isoniazid and injection amikacin daily. The patient improved symptomatically and became culture-negative after 3 months of therapy with the above regimen and continued to be culture negative for 12 months of treatment. She continues to remain symptom-free without evidence of any clinical or bacteriological relapse.

Burden of non-tuberculous mycobacterial diseases in Saudi Arabian children: The first nationwide experience

BACKGROUND

Non-tuberculous mycobacteria (NTM) causing pulmonary and extra-pulmonary diseases are increasing worldwide. A large paucity of data related to pediatric NTM diseases exists globally and particularly in Saudi Arabia.

METHODS

The first nationwide exploratory study on existence of NTM diseases among Saudi Arabian children (0-14 years old) has been carried out during 2016-2017. Suspected NTM isolates with clinical and demographical data were enrolled from regional reference laboratories. Species level identification of isolates was carried out by commercial line probe assays and gene sequencing.

RESULTS

In 12 months, 52 culture positive cases with 44(84.6%) confirmed disease incidences were identified. Demographically, Saudi nationals (86.5%) were dominated and 77.3% cases have different comorbid conditions. Lymphadenitis (40.4%) followed by 26.9% of pulmonary cases with 42.8% of confirmed clinical relevance were mainly reported. Species identification showed Mycobacterium simiae (31.8%), M. abscessus (23.1%) and nine other species including rarely encountering M. riyadhense. Ascites caused by M. monacense, pulmonary disease caused by M. riyadhense and M. monacense were rarest clinical events and reported for the first time globally in a pediatric cohort.

CONCLUSIONS

Diverse NTM diseases even in immunocompetent children are an upcoming challenge in Saudi Arabia. Lack of awareness on NTM disease must be addressed with immediate development of management plans.

Diversity of Nontuberculous Mycobacteria in Kuwait: Rapid Identification and Differentiation of Mycobacterium Species by Multiplex PCR, INNO-LiPA Mycobacteria v2 Assay and PCR Sequencing of rDNA

OBJECTIVE

Nontuberculous mycobacteria (NTM) often cause disease that is clinically indistinguishable from tuberculosis. Specific identification is important as treatment varies according to Mycobacterium species causing the infection. This study used multiplex PCR (mPCR) assay for rapid differentiation of mycobacterial growth indicator tube 960 system (MGIT) cultures as Mycobacterium tuberculosis (MTB) or NTM together with INNO LiPA Mycobacteria v2 assay (LiPA) and/or PCR sequencing of rDNA for species-specific identification of selected MTB and all NTM isolates in Kuwait.

MATERIALS AND METHODS

DNA was extracted from MGIT cultures (n = 1,033) grown from 664 pulmonary and 369 extrapulmonary specimens from 1,033 suspected tuberculosis patients. mPCR was performed to differentiate MTB from NTM. LiPA was performed and results were interpreted according to kit instructions. rDNA was amplified and sequenced by using panmycobacterial primers.

RESULTS

mPCR identified 979 isolates as MTB, 53 as NTM and 1 isolate as mixed culture. LiPA and/or PCR sequencing confirmed 112 of 979 selected isolates as MTB. Mixed culture contained M. tuberculosis and M. fortuitum. LiPA yielded 12 patterns and identified 10 species/species complexes among 47 NTM, M. kansasii + M. scrofulaceum in one culture and 5 isolates only at genus level. PCR sequencing yielded more specific identification for 22 isolates at the species/subspecies level.

CONCLUSIONS

mPCR rapidly differentiated MTB from NTM. LiPA identified 44 of 52 NTM isolates at the species/species complex level and 2 mixed cultures. PCR sequencing yielded more specific identification at the species/subspecies level. Rapid differentiation as MTB or NTM by mPCR, followed by species-specific NTM identification by LiPA/PCR sequencing is suitable for the proper management of mycobacterial infections in Kuwait.

The first Saudi Arabian national inventory study revealed the upcoming challenges of highly diverse non-tuberculous mycobacterial diseases

BACKGROUND

Incidences of nontuberculous mycobacteria (NTM) causing pulmonary and extrapulmonary diseases are reportedly increasing globally and the current epidemiologic situation in Saudi Arabia remains unclear. To study such trend, we carried out a nationwide systematic epidemiological study focusing on NTM diseases for the first time in the country.

METHODS/PRINCIPLE FINDINGS

A nationwide collection of NTM isolates with clinical and demographical data was conducted for a period of 24 months. Primary species identification was carried out by line probe assays followed by sequencing of 16S rRNA, 16S-23S ITS region, rpoB and hsp65 genes. The laboratory findings were comprehensively analysed against demographical and clinical data. A total of 527 isolates were enrolled with a higher proportion of Saudi citizens (76.5%), elderly (>60 years) patients (34.2%), and male gender (65.3%) respectively. Overall, 75.1% isolates were pulmonary origin with a proven clinical significance of 44.7%. In total, 34 NTM species including 17 rare species were identified, in addition to 8 'undefined' isolates. M.simiae (22.6%), M.fortuitum (18.1%) and M.abscessus (17.8%) were predominant species. Interestingly, 27 new cases of clinically relevant M.riyadhense were also noticed (Primary data on emergence of rare NTM species and M.riyadhense has been recently reported). Results showed, rare clinical events such as mycobacteremia, cecum abscess, peritonitis and ascites caused by M.wolinskyi, M.holsaticum, M.duvalii and M.monacence respectively. Diabetes mellitus (P value-0.04) and previous history of tuberculosis (P value- 0.001) were identified as independent risk factors associated with NTM diseases.

CONCLUSIONS/SIGNIFICANCE

NTM disease spectrum and pathogen diversity is an emerging challenge to any nation, including Saudi Arabia. Therefore, more priorities will be given to NTM's with an immediate initiative to develop diagnostic infrastructures and disease management plans.

Isolation of Mycobacterium arupense from pleural effusion: culprit or not?

BACKGROUND

Mycobacterium arupense, first identified in 2006, is a slow-growing nontuberculous mycobacterium (NTM) and an emerging cause of tenosynovitis, potentially associated with immunosuppression. However, unlike the diagnostic value of its isolation from osteoarticular specimens, the significance of detecting M. arupense in respiratory specimens is not yet clear.

CASE PRESENTATION

To our knowledge, we, for the first time, described the identification of M. arupense from the pleural effusion of an immunocompetent patient, who presented with fever and chylothorax. The symptoms resolved with doxycycline treatment for 45 days and a low-fat, high-protein diet. Follow-up at 14 months showed no relapse.

CONCLUSIONS

Because the patient fully recovered without combined anti-NTM treatment, we did not consider M. arupense the etiological cause in this case. This indicates that M. arupense detected in pleural effusion is not necessarily a causative agent and careful interpretation is needed in terms of its clinical relevance.