Species diversity and molecular characterization of nontuberculous mycobacteria in hospital water system of a developing country, Iran

Fifteen years of phenotypic and genotypic surveillance and antibiotic susceptibility pattern of Actinomycetes (Mycobacterium, Nocardia, Rhodococcus, etc.) in clinical and environmental samples of Iran

Actinomycetes, ubiquitous in the natural world, have been known to inflict infections upon both immunocompromised and healthy individuals. Interestingly enough, these species are oftentimes found residing within the microbiota of humans and animals alike. Unfortunately, these infections are frequently misdiagnosed as more sinister ailments such as malignancy or tuberculosis. Due to this issue, this review deals with 15 years of study on clinical and environmental samples to determine Actinomycetes' prevalence, isolation, identification, and antibiotic susceptibility pattern in Iran by Davood Azadi et al. According to the Davood Azadi framework, we searched the following databases: PubMed/MEDLINE, Embase, Scopus, Web of Science, SID, and Google Scholar in the period from 2007 to 2023. This review aimed to provide an overview of the most recent techniques for collecting environmental samples, cultivating them, and identifying the Actinomycetes group's members. The isolation of Actinomycetes from clinical and ecological sources is becoming more prevalent and should be a concern for health authorities in developing countries. Health centers should take action to increase awareness of diagnostic criteria and management guidelines for actinomycete diseases. Improvements in national and regional reference laboratories may also aid in accurately diagnosing these diseases.

Screening, molecular identification, population diversity, and antibiotic susceptibility pattern of Actinomycetes species isolated from meat and meat products of slaughterhouses, restaurants, and meat stores of a developing country, Iran

Introduction

Actinomycetes can colonize surfaces of tools and equipment and can be transferred to meat and meat products during manufacture, processing, handling, and storage. Moreover, washing the meat does not eliminate the microorganisms; it only spreads them. As a result, these opportunistic pathogens can enter the human body and cause various infections. Therefore, the aim of the current study was to screen, identify, and determine the antibiotic susceptibility of Actinomycetes species from meat and meat products in the Markazi province of Iran.

Methods

A total of 60 meat and meat product samples, including minced meat, mutton, beef, chicken, hamburgers, and sausages, were collected from slaughterhouses, butchers, and restaurants in the Markazi province of Iran. The samples were analyzed using standard microbiological protocols for the isolation and characterization of Actinomycetes. PCR amplification of hsp65 and 16SrRNA genes and sequence analysis of 16SrRNA were used for genus and species identification. The minimum inhibitory concentrations (MICs) of antimicrobial agents were determined by the broth microdilution method and interpreted according to the CLSI guidelines.

Results

A total of 21 (35%) Actinomycetes isolates from 5 genera and 12 species were isolated from 60 samples. The most prevalent Actinomycetes were from the genus Mycobacterium, with six (28.6%) isolates (M. avium complex, M. terrae, M. smegmatis, and M. novocastrense), followed by the genus Rhodococcus with five (23.8%) isolates (R. equi and R. erythropolis), the genus Actinomyces with four (19.1%) isolates (A. ruminicola and A. viscosus), the genus Nocardia with four (19.1%) isolates (N. asiatica, N. seriolae, and N. niigatensis), and the genus Streptomyces with two (9.5%) isolates (S. albus). Chicken and sausage samples had the highest and lowest levels of contamination, with six and one isolates. Respectively, the results of drug susceptibility testing (DST) showed that all isolates were susceptible to Ofloxacin, Amikacin, Ciprofloxacin, and Levofloxacin, whereas all of them were resistant to Doxycycline and Rifampicin.

Discussion

The findings suggest that meat and meat products play an important role as a reservoir for the transmission of Actinomycetes to humans, thus causing life-threatening foodborne diseases such as gastrointestinal and cutaneous disorders. Therefore, it is essential to incorporate basic hygiene measures into the cycle of meat production to ensure food safety.

Potential Use of Mycobacterium paragordonae for Antimycobacterial Drug Screening Systems

Our recent genome-based study indicated that Mycobacterium paragordonae (Mpg) has evolved to become more adapted to an intracellular lifestyle within free-living environmental amoeba and its enhanced intracellular survival within Acanthamoeba castellanii was also proved. Here, we sought to investigate potential use of Mpg for antimycobacterial drug screening systems. Our data showed that Mpg is more susceptible to various antibiotics compared to the close species M. marinum (Mmar) and M. gordonae, further supporting its intracellular lifestyle in environments, which would explain its protection from environmental insults. In addition, we developed two bacterial whole-cell-based drug screening systems using a recombinant Mpg stain harboring a luciferase reporter vector (rMpg-LuxG13): one for direct application to rMpg-LuxG13 and the other for drug screening via the interaction of rMpg-LuxG13 with A. castellanii. Direct application to rMpg-LuxG13 showed lower inhibitory concentration 50 (IC₅₀) values of rifampin, isoniazid, clarithromycin, and ciprofloxacin against Mpg compared to Mmar. Application of drug screening system via the interaction of rMpg-LuxG13 with A. castellanii also exhibited lower IC₅₀ values for rifampin against Mpg compared to Mmar. In conclusion, our data indicate that Mpg is more susceptible to various antibiotics than other strains. In addition, our data also demonstrate the feasibility of two whole cell-based drug screening systems using rMpg-LuxG13 strain for the discovery of novel anti-mycobacterial drugs.

Dual Infection of an Open Fracture Caused by Mycobacterium setense and Clostridium celerecrescens

Infections caused by Mycobacterium setense or Clostridium celerecrescens are extremely rare. In this report, for the first time a dual infection with these two pathogens is described. An 18-year-old female suffered multiple injuries, including an open comminuted fracture of the right humeral diaphysis after falling from a fifth-floor balcony in January 2019. Five months after the accident, a fistula appeared in the scar, reaching the bone tissue. M. setense and C. celerecrescens were cultured from sinus swabs and subsequently from perioperative samples. The patient was initially treated with a combination of intravenous antibiotics (ATBs): imipenem, amikacin, and ciprofloxacin. One month after the fracture fixation with a titanium nail, C. celerecrescens was again detected; therefore, metronidazole was added to the therapy. A triple combination of oral (PO) ATBs (trimethoprim–sulfamethoxazole, moxifloxacin, and metronidazole) followed, 8 weeks after the initial intravenous therapy. C. celerecrescens was cultured again two times, most recently in November 2019, when surgical debridement was supplemented by the topical administration of cancellous bone impregnated with vancomycin. Signs of bone healing were found at follow-ups and ATB treatment was finished in March 2020 after a total of 9 months of therapy. To this day, there have been no signs of reinfection. This case thus illustrates the need for a combination of systemic and individualized local therapy in the treatment of complicated cases of dual infections with rare pathogens.

Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth

Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces.

Mycobacterium paragordonae is an emerging pathogen in human pulmonary disease: clinical features, antimicrobial susceptibility testing and outcomes

Objectives: Mycobacterium paragordonae (MPG) is an emerging and less common type of Non-tuberculous mycobacteria (NTM) and we know little about its characteristics and prognosis, hence we constructed this retrospective cohort study. Methods: MPG was identified using MALD-TOF MS, multi-target combined gene sequencing and WGS. Clinical information was collected, antimicrobial susceptibility testing was measured using the SLOMYCO panel, and optimal growth temperature testing was measured using Lowenstein-Jensen medium. Results: Eight MPGs were isolated from 1730 NTMs (0.46%); the mean age of MPG pulmonary disease (MPG-PD) patients was 42.38 ± 9.92 years, 37.5% were male, and the average BMI was 18.4 ± 0.51 kg/m². All patients had the symptoms of cough and sputum and CT images mainly presented in patchy or streaky shadows, MPG grew at 25°C, 30°C and 37°C, and the optimal growth temperature is 37°C. MPGs were sensitive to clarithromycin, rifabutin, amikacin, linezolid, moxifloxacin, cotrimoxazole and ciprofloxacin, two isolates were resistant to rifampicin. Two patients had follow up information, their imaging remained stable during the follow-up. Conclusions: MPG-PD is a rare NTM disease and is more likely to develop in middle-aged, female, and low BMI patients. The patients present with no specific features within the symptoms as well as the CT imaging. The optimal growth temperature of MPG is at 37°C, MPG-PD has excellent sensitivity to drugs recommended by CLSI and presents with a stable disease.

An update on prevalence of slow-growing mycobacteria and rapid-growing mycobacteria retrieved from hospital water sources in Iran - a systematic review

Introduction

This study aimed to assess the prevalence of slow growing mycobacteria (SGM) and rapid-growing mycobacteria (RGM) retrieved from hospital water sources in Iran from 2016 to 2020.

Methods

The review was conducted to get eligible published studies from 1^st January 2016 to 25^th March 2020 based on PRISMA protocol. A combination of related words from the Medical Subject Heading Terms (MeSH), with (AND, OR) were used to search for published studies reporting the prevalence of nontuberculous mycobacteria (NTM) in Scopus, MEDLINE, Web of Sciences, Google Scholar, and Iranian databases. Then data from the studies were extracted and reported.

Results

Our study showed that different water sources of hospitals were contaminated with NTMs. The prevalence of RGM isolates in hospital water samples varied between 42.2%-67.5%, and the prevalence of SGM varied between 32.5%-57.7%, respectively. M. lentiflavum (84.7%), M. avium complex(2.8%-56.4%)and M. gordonae (2.8%-56.2%) were the most prevalent NTM species amongst SGM, whereas M. fortuitum (2.9%-44.2%), M. chelonae (8%-36.8%), M. mucogenicum (8%-25.6%) were the most leading NTM isolates among RGM.

Conclusions

A high prevalence of NTM was reported from hospital environments particularly hospital water sources which can colonize medical devices, solutions, and water used for patients and cause nosocomial infection. Therefore, the hospitals should check the microbiological quality of the water used.

Drug susceptibility testing of Mycobacterium simiae: An emerging pathogen in Iran

INTRODUCTION

Mycobacterium simiaeis an emerging pathogen in Iran and little is known about drug susceptibility patterns of this pathogen.

MATERIALS AND METHODS

Twenty-five clinical isolates of M. simiaefrom 80 patients with confirmed NTM pulmonary disease were included in this study. For drug susceptibility testing (DST), proportional and broth microdilution methods were used according to the clinical and laboratory standards institute (CLSI) guideline.

RESULTS

All clinical isolates of M. simiaewere resistant to isoniazid, rifampicin, ethambutol, streptomycin, amikacin, kanamycin, ciprofloxacin, and clarithromycin. They also were highly resistant to ofloxacin (80%). Susceptibility to ofloxacin was only noted in the 5 isolates.

CONCLUSIONS

Clinical isolates of M. simiae were multidrug-resistant, and had different drug susceptibility patterns than previously published studies. DST results can assist in selecting more appropriate treatment regimens. Newer drugs with proven clinical efficacy correlating with in vitrosusceptibility should be substituted with first-and second-line anti-TB drug testing.

Prevalence and molecular characterization of non-tuberculous mycobacteria in hospital soil and dust of a developing country, Iran

The presence and diversity of mycobacteria that are capable of survival in a harsh and adverse condition, such as hospital environments, have not been comprehensively studied. This study aimed to assess the frequency and diversity of mycobacteria in hospital soil and dust of a developing country using a combination of molecular and conventional methods. A total of 318 hospital dust and soil samples collected from 38 hospitals were analysed using standard protocols for characterization of mycobacteria. The conventional tests were used for preliminary identification and Runyon's classification, the PCR amplification of the hsp65 gene and sequence analyses of 16SrRNA were applied for genus and species identification. In total, 28 samples (8.8 %) were positive for mycobacteria. The isolates included 33 mycobacteria species including 19 rapidly growing and 14 slowly growing organisms. The most prevalent species were M. setense and M. lentiflavum, five isolates (15.1 %) each, M. fortuitum, four isolates (12.12 %) and M. kumamotonense and M. massiliense/abscessus complex three isolates (9.1 %) each, M. arupense and M. frederiksbergense, two isolates (6 %) each. The remaining isolates consisted the single strains of eight various mycobacterium species, the results of our study revealed that soil and dust in hospitals can be the reservoir of mycobacteria. This reaffirms the fact that these organisms due to intrinsic resistance can persist in hospitals and create a threat to patient's health, in particular to those who suffer from weakness of immunity.

Microbiological Air Quality and Drug Resistance in Airborne Bacteria Isolated from a Waste Sorting Plant Located in Poland-A Case Study

International interests in biological air pollutants have increased rapidly to broaden the pool of knowledge on their identification and health impacts (e.g., infectious, respiratory diseases and allergies). Antibiotic resistance and its wider implications present us with a growing healthcare crisis, and an increased understanding of antibiotic-resistant bacteria populations should enable better interpretation of bioaerosol exposure found in the air. Waste sorting plant (WSP) activities are a source of occupational bacterial exposures that are associated with many health disorders. The objectives of this study were (a) to assess bacterial air quality (BAQ) in two cabins of a WSP: preliminary manual sorting cabin (PSP) and purification manual sorting cabin (quality control) (QCSP), (b) determine the particle size distribution (PSD) of bacterial aerosol (BA) in PSP, QCSP, and in the outdoor air (OUT), and (c) determine the antibiotic resistance of isolated strains of bacteria. Bacterial strains were identified on a Biolog GEN III (Biolog, Hayward, CA, USA), and disc diffusion method for antimicrobial susceptibility testing was carried out according to the Kirby-Bauer Disk Diffusion Susceptibility Test Protocol. A large share of fecal bacteria, Enterococcus faecalis and Alcaligenes faecalis spp. feacalis, was found in the tested indoor air, which is a potential health hazard to the workers of the monitored WSP. Our results demonstrate the necessity to take into account fecal air pollution levels to avoid making erroneous assumptions regarding the environmental selection of antibiotic resistance. Total elimination of many anthropogenic sources is not possible, but important findings of this study can be used to develop realistic management policies methods to improve BAQ.

Insights From the Genome Sequence of Mycobacterium paragordonae, a Potential Novel Live Vaccine for Preventing Mycobacterial Infections: The Putative Role of Type VII Secretion Systems for an Intracellular Lifestyle Within Free-Living Environmental Predators

Mycobacterium paragordonae (Mpg) is a temperature-sensitive Mycobacterium species that can grow at permissive temperatures but fails to grow above 37°C. Due to this unique growth trait, Mpg has recently been proposed as a novel live vaccine candidate for the prevention of mycobacterial infections. Furthermore, the increasing frequency of the isolation of Mpg from water supply systems led us to hypothesize that the free-living amoeba system is the natural reservoir of Mpg. In this study, we report the complete 6.7-Mb genome sequence of Mpg and show that this genome comprises four different plasmids with lengths of 305 kb (pMpg-1), 144 kb (pMpg-2), 26 kb (pMpg-3), and 17 kb (pMpg-4). The first two plasmids, pMpg-1 and -2, encode distinct Type VII secretion systems (T7SS), ESX-P5 and ESX-2, respectively. Genome-based phylogeny indicated that Mpg is the closest relative to M. gordonae, which has a 7.7-Mb genome; phylogenetic analysis revealed an average of 86.68% nucleotide identity between these two species. The most important feature of Mpg genome is the acquisition of massive genes related to T7SS, which may have had effect on adaptation to their intracellular lifestyle within free-living environmental predators, such as amoeba. Comparisons of the resistance to bacterial killing within amoeba indicated that Mpg exhibited stronger resistance to amoeba killing compared to M. gordonae and M. marinum, further supporting our genome-based findings indicating the special adaptation of Mpg to free-living amoeba. We also determined that, among the strains studied, there were more shared CDS between M. tuberculosis and Mpg. In addition, the presence of diverse T7SSs in the Mpg genome, including an intact ESX-1, may suggest the feasibility of Mpg as a novel tuberculosis vaccine. Our data highlight a significant role of lateral gene transfer in the evolution of mycobacteria for niche diversification and for increasing the intracellular survival capacity.

Molecular characterization of nontuberculous mycobacteria in hospital waters: a two-year surveillance study in Tehran, Iran

Microbiological control of hospital waters as one of the main sources of nontuberculous mycobacteria (NTM) is important for the prevention of NTM-associated illness. This study aimed to investigate the prevalence of NTM in the hospital water systems of Tehran, Iran. A total of 218 samples from different hospital waters (i.e., tap water and medical devices such as humidifying cup of oxygen manometer, dialysis devices, nebulizers, and dental units) were included in this study. Phenotypic and molecular tests were used to identify the isolated organisms to species level. Of 218, 85 (39.0%) samples at 37 °C and 87 (40.0%) samples at 25 °C were identified as NTM. Using hsp65-sequencing method, Mycobacterium lentiflavum was the most frequently encountered, followed by M. gordonae and M. paragordonae. No significant difference was seen in frequency and species in mycobacteria isolated at 37 °C and 25 °C temperatures. Humidifying cup of oxygen manometer had the most contaminated water among the investigated water distribution systems in hospitals. Isolation of NTM from hospital water sources is a serious public health problem in Iran and merits further attention by health authorities. Establishment of microbiological monitoring systems for hospital waters and expanding the number of facilitated laboratories are strongly recommended.

Studies of antimicrobial resistance in rare mycobacteria from a nosocomial environment

BACKGROUND

Nontuberculous mycobacteria (NTM) are ubiquitous in nature and recognized agents of opportunistic infection, which is often aggravated by their intrinsic resistance to antimicrobials, poorly defined therapeutic strategies and by the lack of new drugs. However, evaluation of their prevalence in anthropogenic environments and the associated antimicrobial resistance profiles have been neglected. In this work, we sought to determine minimal inhibitory concentrations of 25 antimicrobials against 5 NTM isolates recovered from a tertiary-care hospital surfaces. Antimicrobial susceptibilities of 5 other Corynebacterineae isolated from the same hospital were also determined for their potential clinical relevance.

RESULTS

Our phylogenetic study with each of the NTM isolates confirm they belong to Mycobacterium obuense, Mycobacterium mucogenicum and Mycobacterium paragordonae species, the latter initially misidentified as strains of M. gordonae, a species frequently isolated from patients with NTM disease in Portugal. In contrast to other strains, the M. obuense and M. mucogenicum examined here were resistant to several of the CLSI-recommended drugs, suggestive of multidrug-resistant profiles. Surprisingly, M. obuense was susceptible to vancomycin. Their genomes were sequenced allowing detection of gene erm (erythromycin resistance methylase) in M. obuense, explaining its resistance to clarithromycin. Remarkably, and unlike other strains of the genus, the Corynebacterium isolates were highly resistant to penicillin, ciprofloxacin and linezolid.

CONCLUSIONS

This study highlights the importance of implementing effective measures to screen, accurately identify and control viable NTM and closely related bacteria in hospital settings. Our report on the occurrence of rare NTM species with antibiotic susceptibility profiles that are distinct from those of the corresponding Type strains, along with unexpected resistance mechanisms detected seem to suggest that resistance may be more common than previously thought and also a potential threat to frail and otherwise vulnerable inpatients.

Mycobacteriosis and Tuberculosis: Laboratory Diagnosis

Background

Tuberculosis is one of the most important infectious diseases that has claimed its victims throughout much of known human history. With Koch's discovery of the tubercle bacillus as the etiologic agent of the disease, his sanitary and hygienic measures, which were based on his discovery and the development of a vaccine against tuberculosis by Albert Calmette and Camille Guérin in 1921, an attenuated Mycobacterium bovis strain, bacilli Calmette-Guérin (BCG), and the discovery of the first antibiotic against tuberculosis, streptomycin by Selman Waksman in 1943, soon led to the opinion that appropriate control measures had become available for tuberculosis and it had been assumed that the disease could ultimately be eradicated.The emergence of resistant strains of this bacteria and widespread distribution of the disease in the world, and the emergence of the AIDS epidemic destroyed any possibility of global control of tuberculosis in the foreseeable future.

Objectives

The purpose of this review is to highlight the current scientific literature on mycobacterial infections and provide an overview on the laboratory diagnosis of tuberculosis and non-tuberculosis infections based on conventional phenotypic and modern molecular assays.

Method

In this study, a number of 65 papers comprising 20 reviews, 9 case reports, and 36 original research in association with mycobacteriosis and the laboratory diagnosis of mycobacterial infections, were reviewed.

Results

Based on our analysis on the published documents methods applied for the laboratory diagnosis of tuberculosis are continually assessed and developed in order to achieve more rapid, less expensive, and accurate results. Acid-fast staining and culture for mycobacteria remain at the core of any diagnostic algorithm with the sensitivity of 20-70% and specificity of 95-98% for AFB microscopy and the sensitivity of 95% and the specificity of 98% for culture based diagnosis. Following growth in culture, molecular tests such as nucleic acid hybridization probes and DNA sequencing may be used for definitive species identification. Nucleic acid amplification methods provide the means for direct detection of Mycobacterium tuberculosis in respiratory specimens without the prerequisite to isolate or culture the organism, leading to more rapid diagnosis and better patient care.

Conclusion

As the researchers in a developing country, we strongly believe that despite significant advances in laboratory capacity, in many countries reliable confirmation of suspected mycobacterial diseases is hindered by a lack of knowledge on proper standardized methods, sufficient funds, suitably trained staff and laboratory supplies.

Identification of nontuberculous mycobacteria isolated from hospital water by sequence analysis of the hsp65 and 16S rRNA genes

Nontuberculous mycobacteria (NTM) have emerged as an important cause of opportunistic nosocomial infections. NTM has frequently been isolated from hospital water distribution systems. The aim of this study was to survey the risk of NTM infections and determine the prevalence of NTM species in the hospital water distribution systems in Tabriz, Iran. One hundred and twenty samples of water from different sources of Tabriz hospitals were collected. The samples were filtered through 0.45-µm pore size membranes and decontaminated with 0.01% cetylpyridinium chloride. The sediment was inoculated onto Lowenstein-Jensen medium and incubated for 8 weeks. For identification to the species level, partial sequence analysis of the hsp65 and 16S rRNA genes were used. NTM were detected in 76 (63.3%) of 120 samples. Potentially pathogenic mycobacteria and saprophytic mycobacteria were isolated. Mycobacterium gordonae was the only single species that was present in all types of water. The prevalence of NTM in Tabriz hospitals' water compared with many investigations on hospital waters was high. This indicates that the immunocompromised patients and transplant recipients are at risk of contamination which necessitates considering decontamination of water sources to prevent such potential hazards.

Drug Susceptibility of 33 Reference Strains of Slowly Growing Mycobacteria to 19 Antimicrobial Agents

Objectives. Slowly growing mycobacteria (SGM) are prevalent worldwide and cause an extensive spectrum of diseases. Methods. In this study, the antimicrobial susceptibility of 33 reference strains of SGM to 19 antimicrobial agents was tested using a modified microdilution method. Results. Cefmetazole (32/33) and azithromycin (32/33) exhibited the highest antimicrobial activity, and dapsone (9/33) exhibited the lowest activity against the tested strains. Cefoxitin (30/33), cefoperazone (28/33), and cefepime (28/33) were effective against a high proportion of strains, and macrolides were also highly effective as well as offering the benefit of convenient oral administration to patients. Linezolid (27/33), meropenem (26/33), sulfamethoxazole (26/33), and tigecycline (25/33) showed the highest activity; clofazimine (20/33) and doxycycline (18/33) showed intermediate activity; and rifapentine (13/33), rifabutin (13/33), and minocycline (11/33) showed low antimicrobial activity, closely followed by thioacetazone (10/33) and pasiniazid (10/33), against the tested organisms. According to their susceptibility profiles, the slowly growing species Mycobacterium avium and Mycobacterium simiae were the least susceptible to the tested drugs, whereas Mycobacterium intracellulare, Mycobacterium asiaticum, Mycobacterium scrofulaceum, Mycobacterium szulgai, Mycobacterium branderi, and Mycobacterium holsaticum were the most susceptible. Conclusions. In summary, cephalosporins and macrolides, particularly cefmetazole, azithromycin, clarithromycin, and roxithromycin, showed good antimicrobial activity against the reference strains of SGM.

Molecular identification and distribution of non-tuberculous mycobacteria isolated from clinical specimens by PCR-sequencing method in West of Iran

BACKGROUND AND AIMS

Infections by non-tuberculous mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis.

METHODS

A cross-sectional study was conducted on 45 diverse isolates collected from sputum in 2 years 2014-2015 using standard decontamination procedure. All mycobacterial isolates were grown on LJ medium and also conventional tests for preliminary identification of mycobacteria rely on traits and then DNA extraction. PCR was performed, and sequencing of 16S rRNA and rpoB genes was applied for NTM strains identification.

RESULTS

A total of 45 isolates collected, 37 samples (83%) were evaluated as NTM. All NTM strains using molecular methods by sequencing 16S rRNA and rpoB gene were identified, by this way 12 different species have been identified which sequencing of rpoB was able to identify all species. The major species obtained were Mycobacterium simiae (22%), M. fortuitum (19%), and M. abscessus (13%).

CONCLUSIONS

The results of our study showed that the patients were infected by a wide range of atypical mycobacteria. It was concluded that 16S rRNA gene sequencing coupled with rpoB marker is a high discriminatory power in identification of NTM. The presence of various species in clinical samples in Iran emphasizes the use of molecular method like sequence analysis of genes is necessary for reliable identification.