Search

Introduction: Since its discovery in 1961, methicillin-resistant Staphylococcus aureus (MRSA) has been recognized as a significant healthcare-associated pathogen (HA-MRSA) and a notorious 'superbug'. Typing is crucial for surveillance, epidemiology analysis, infection control of MRSA and sequencing of the spa gene is one of the most common methods used for determining the origin of this bacterium in humans and animals. This research aimed to determine the antibiotic resistance and spa type of S. aureus strains collected from outpatients in two hospitals in the Wasit province of Iraq. Material & Methods: The study analyzed 200 outpatient MRSA isolates by collecting nasal and sputum samples from patients. Standard biochemical and molecular methods based on the nuc gene were used to identify S. aureus bacteria and amplify the mecA and spa genes. The Kirby-Bauer disc diffusion method was employed to determine the antibiotic sensitivity of the isolates using penicillin, cefoxitin, vancomycin, gentamicin, erythromycin, tetracycline, imipenem, clindamycin, chloramphenicol and rifampicin. Results: Methods. The prevalence of MRSA was more common in women than in men. Antibiogram results showed that most of the isolates were resistant to penicillin (94.2%) and sensitive to imipenem (100%), clindamycin (100%), and chloramphenicol (100%). Of these 35 isolates, 30 (87.5%) and 26 strains (74.3%) were positive for the mecA and spa genes. Typing based on spa gene sequencing revealed four different patterns: t386, t3579, U0002 and U0234. Conclusion: Variations in the spa gene among different S. aureus isolates may he of clinical importance when treating staphylococcal infections. In this study, spa typing revealed four different patterns in Iraq, representing diagnostic and therapeutic implications. [ABSTRACT FROM AUTHOR]

To search endophytic bacteria diversity and evaluate their antibacterial activity, healthy medicinal plant of Scrophularia striata was chosen in this study. One hundred endophytic bacteria were isolated from surface-sterilized tissues (root, stem and leaf) of S. striata. Using sequence analysis targeting 16S rRNA gene, eight genera, including Agrococcus, Arthrobacter, Bacillus, Chryseobacterium, Delftia, Kocuria, Pseudomonas and Sphingomonas were identified. Antibacterial activity of endophytic bacteria was examined against some test bacteria, employing agar well diffusion method. Out of 31 endophytic bacterial isolates, 24(77.42%) isolates showed significant antimicrobial activity against Bacillus cereus, 17(54.84%) isolates exhibited maximum activity against Staphylococcus aureus, 14(45.16%) isolates against Escherichia coli and 5(16.13%) isolates showed positive activity against Proteus mirabilis. The results obtained in this study suggested that the medicinal plant, S. striatais is a potent source of endophytic bacteria with antibacterial activity and offers promise for discovery of more impressive biological compounds. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The nucleotide sequences of partial 16S rRNA and bacterial RNA polymerase β-subunit (rpoB) genes for 57 mycobacterial strains were determined. Compared to the 16S rRNA gene sequences, variable regions were scattered along the whole fragment sequence, indicating that the rpoB gene is more polymorphic. Unlike 16S rRNA sequences, species variation was observed within M. fortuitum strains. The topology of the rpoB-based phylogenetic tree was almost the same as that of the 16S rRNA sequence analysis. These results suggest that the rpoB gene is a highly conserved gene, and taxonomical studies based on this gene may be comparable with similar studies based on the 16S rRNA gene. The overall mean distance for rpoB-gene-based sequences was 2.5 times greater than that of the 16S rRNA gene for all 57 mycobacterial strains examined. However, some slowly growing mycobacteria could not be differentiated based on rpoB gene sequences. Moreover, a bootstrap value above 70% was observed for 13 nodes, while this value was 14 nodes in the case of 16S rRNA sequences. To the best of our knowledge, this is the first investigation evaluating the use of 16S rRNA and rpoB sequence analyses for identification of aquatic mycobacteria obtained from diverse geographical locations. [ABSTRACT FROM AUTHOR]

Objective(s) In addition to several molecular methods and in particular 16S rDNA analysis, the application of a more discriminatory genetic marker, i.e., 16S-23S internal transcribed spacer gene sequence has had a great impact on identification and classification of mycobacteria. In the current study we aimed to apply this sequencing power to conclusive identification of some Iranian clinical strains of mycobacteria. Materials and Methods The test strains consisted of nineteen mycobacterial isolates which were initially identified by the use of conventional phenotypic techniques and molecular methods and subjected to further definitive identification using the 16S-23S internal transcribed spacer gene sequencing. Results Out of 19 studied strains, 7 isolates were found to be rapidly growing and 12 isolates as slowly growing mycobacteria. With the exception of one isolate, i.e., the isolate HNTM87, which yielded a distinct ITS sequence incomparable with all previously identified mycobacteria, the remaining isolates produced the sequences similar to the established mycobacteria and were clearly identified and differentiated from closely related taxa. A phylogenetic tree based on maximum parsimony analysis of 16S-23S internal transcribed spacer gene sequences constructed showing the relatedness of Iranian clinical isolates with the closely related type species of mycobacteria. Conclusion This study showed that the 16S-23S internal transcribed spacer gene of the genus Mycobacterium exhibits a high variation which is of value for discriminating closely related taxa and could be used independently or in combination with 16S rDNA sequencing to delineate the true identity of rare mycobacterial species. [ABSTRACT FROM AUTHOR]

The emergence of fluoroquinolone resistance among A. baumannii isolates is now of particular concern. Phenotypic and genotypic characteristics of resistance to ciprofloxacin among 50 Acinetobacter baumannii isolated from burn wound infections of Tehran were evaluated by E-test and broth microdilution in presence and absence of efflux pump inhibitor phenylalanine- arginine β-naphthylamide (PAβN) and PCR-sequencing methods. All isolates were then typed by REP-PCR fingerprinting to find the clonal relationship between resistant isolates. Our results indicated that resistance to ciprofloxacin among A. baumannii isolated from burn infections in Tehran are high with resistance rate of 100% and ciprofloxacin resistant isolates have a mutation of Serine 83 →Leucine in the quinolone resistance determining region (QRDR) of DNA gyrase subunit A (GyrA). 38% of the isolates showed MIC ranges of 64 to ≥512µg/ml and were considered as highly resistant. We could not detect Par C mutations and plasmid-mediated quinolone resistance A (qnrA) among ciprofloxacin resistant isolates. When we used the efflux pump inhibitor PAβN, MIC of ciprofloxacin was reduced two-to four folds. REP-type A (25/50; 50%), B (20/50; 30%) and C (10/50; 20%) were the most common REP-types among A. baumannii isolates. It seems that mutation in GyrA is the main mechanism of resistant to ciprofloxacin among A. baumannii isolates from burn infections and presence of efflux pumps is just secondary target for ciprofloxacin resistant among A. baumannii in Iran. Regarding with limitation of REP-types detected in this study, we found good correlation between resistance to ciprofloxacin and REP-types A-C. [ABSTRACT FROM AUTHOR]

Four slowly growing mycobacteria isolates were isolated from the respiratory tract and soft tissue biopsies collected in four unrelated patients in Iran. Conventional phenotypic tests indicated that these four isolates were identical to Mycobacterium lentiflavum while 16S rRNA gene sequencing yielded a unique sequence separated from that of M. lentiflavum. One representative strain AFP-003 T was characterized as comprising a 6,121,237-bp chromosome (66.24% guanosine-cytosine content) encoding for 5,758 protein-coding genes, 50 tRNA and one complete rRNA operon. A total of 2,876 proteins were found to be associated with the mobilome, including 195 phage proteins. A total of 1,235 proteins were found to be associated with virulence and 96 with toxin/antitoxin systems. The genome of AFP-003 T has the genetic potential to produce secondary metabolites, with 39 genes found to be associated with polyketide synthases and non-ribosomal peptide syntases and 11 genes encoding for bacteriocins. Two regions encoding putative prophages and three OriC regions separated by the dnaA gene were predicted. Strain AFP-003 T genome exhibits 86% average nucleotide identity with Mycobacterium genavense genome. Genetic and genomic data indicate that strain AFP-003 T is representative of a novel Mycobacterium species that we named Mycobacterium ahvazicum, the nineteenth species of the expanding Mycobacterium simiae complex.

The name 'Mycobacterium angelicum' dates back to 2003 when it was suggested for a slowly growing mycobacterium isolated from freshwater angelfish. This name is revived here and the novel species is proposed on the basis of the polyphasic characterization of four strains including the original one. The four strains presented 100 % 16S rRNA gene sequence similarity with Mycobacterium szulgai but clearly differed from M. szulgai for the milky white aspect of the colonies. The sequence similarity with the type strain of M. szulgai ranged, in eight additionally investigated genetic targets, from 78.9 to 94.3 %, an evident contrast with the close relatedness that emerged at the level of 16S rRNA gene. The average nucleotide identity between the genomes of M. szulgai DSM 44166T and strain 126/5/03T (type strain of the novel species) was 92.92 %, and supported the status of independent species. The confirmation of the name Mycobacterium angelicum sp. nov. is proposed, with strain 126/5/03T ( = CIP 109313T = DSM 45057T) as the type strain.

The emergence of fluoroquinolone resistance among A. baumannii isolates is now of particular concern. Phenotypic and genotypic characteristics of resistance to ciprofloxacin among 50 Acinetobacter baumannii isolated from burn wound infections of Tehran were evaluated by E-test and broth microdilution in presence and absence of efflux pump inhibitor phenylalanine- arginine β-naphthylamide (PAβN) and PCR-sequencing methods. All isolates were then typed by REP-PCR fingerprinting to find the clonal relationship between resistant isolates. Our results indicated that resistance to ciprofloxacin among A. baumannii isolated from burn infections in Tehran are high with resistance rate of 100% and ciprofloxacin resistant isolates have a mutation of Serine 83 →Leucine in the quinolone resistance determining region (QRDR) of DNA gyrase subunit A (GyrA). 38% of the isolates showed MIC ranges of 64 to ≥512μg/ml and were considered as highly resistant. We could not detect Par C mutations and plasmid-mediated quinolone resistance A (qnrA) among ciprofloxacin resistant isolates. When we used the efflux pump inhibitor PAbN, MIC of ciprofloxacin was reduced two-to four folds. REP-type A (25/50; 50%), B (20/50; 30%) and C (10/50; 20%) were the most common REP-types among A. baumannii isolates. It seems that mutation in GyrA is the main mechanism of resistant to ciprofloxacin among A. baumannii isolates from burn infections and presence of efflux pumps is just secondary target for ciprofloxacin resistant among A. baumannii in Iran. Regarding with limitation of REP-types detected in this study, we found good correlation between resistance to ciprofloxacin and REP-types A-C.

Objectives: In addition to several molecular methods and in particular 16S rDNA analysis, the application of a more discriminatory genetic marker, i.e., 16S-23S internal transcribed spacer gene sequence has had a great impact on identification and classification of mycobacteria. In the current study we aimed to apply this sequencing power to conclusive identification of some Iranian clinical strains of mycobacteria., Materials and Methods: The test strains consisted of nineteen mycobacterial isolates which were initially identified by the use of conventional phenotypic techniques and molecular methods and subjected to further definitive identification using the 16S-23S internal transcribed spacer gene sequencing., Results: Out of 19 studied strains, 7 isolates were found to be rapidly growing and 12 isolates as slowly growing mycobacteria. With the exception of one isolate, i.e., the isolate HNTM87, which yielded a distinct ITS sequence incomparable with all previously identified mycobacteria, the remaining isolates produced the sequences similar to the established mycobacteria and were clearly identified and differentiated from closely related taxa. A phylogenetic tree based on maximum parsimony analysis of 16S-23S internal transcribed spacer gene sequences constructed showing the relatedness of Iranian clinical isolates with the closely related type species of mycobacteria., Conclusion: This study showed that the 16S-23S internal transcribed spacer gene of the genus Mycobacterium exhibits a high variation which is of value for discriminating closely related taxa and could be used independently or in combination with 16S rDNA sequencing to delineate the true identity of rare mycobacterial species.

Herein, we report repeated isolation of Mycobacterium europaeum from the sputum samples of an Iranian human immunodeficiency virus-infected patient and a cystic fibrosis patient with chronic pulmonary disease. To our knowledge, this is the first isolation of M. europaeum from human clinical specimens in Asia to be reported.

Slowly growing, non-chromogenic mycobacteria were isolated from striped barombi mbo cichlids (Stomatepia mariae) maintained at the London Zoo Aquarium, UK. The isolates could be differentiated from other slowly growing, non-pigmented mycobacteria by a combination of phenotypic features including their inability to grow at 37 degrees C, positive tests for heat-stable catalase, tellurite reduction and arylsulfatase activity, and the absence of urease activity, Tween 80 hydrolysis, nitrate reductase, iron uptake and semiquantitative catalase. The almost full-length 16S rRNA gene sequence, together with partial sequences from the 65 kDa heat-shock protein (hsp65) and the beta-subunit of the bacterial RNA polymerase (rpoB) genes and the 16S-23S internal transcribed spacer 1 (ITS 1) region were identical for all three novel strains, but distinct from those of all known mycobacterial species. Phylogenetic analysis based on 16S rRNA gene sequences placed the novel isolates within the slowly growing mycobacteria group in close proximity to Mycobacterium florentinum. Based on genotypic and phenotypic findings, it is proposed that these isolates represent a novel species of the genus Mycobacterium, for which the name Mycobacterium stomatepiae sp. nov. is proposed with strain T11(T) (=DSM 45059(T)=CIP 109275(T)=NCIMB 14252(T)) as the type strain.

Mycobacterial infections in fish are usually attributed to strains of Mycobacterium marinum, Mycobacterium chelonae and Mycobacterium fortuitum. Bacteria identified as M. chelonae have been isolated numerous times from salmonid fishes. Recently, this bacterium has been associated with salmon mortalities in the aquaculture industry. An M. chelonae-like species from salmon, 'Mycobacterium salmoniphilum', was described in 1960. However, the species name lost standing in nomenclature when it was omitted from the 1980 Approved Lists of Bacterial Names because the species could not be distinguished with confidence from M. fortuitum. In the 1980s, mycobacteria isolated from salmon were characterized as a distinct subspecies, 'Mycobacterium chelonae subsp. piscarium'. Again, the uncertainty of the validity of the species resulted in the subsequent withdrawal of the name. Since then, most studies have considered isolates from salmon to be M. chelonae. Nucleotide sequence analysis of the small-subunit rRNA, hsp65 and rpoB genes was used to examine the taxonomic relatedness of type cultures and authentic isolates in our culture collection available from earlier studies. The M. chelonae-like strains from salmon were phylogenetically distinct from other Mycobacterium strains and members of the M. chelonae complex. Moreover, the cell-wall-bound mycolic acids were not representative of known mycolate patterns for M. chelonae-complex organisms. These results supported the status of the species as a separate taxon and effect the valid publication of the name 'M. salmoniphilum' as Mycobacterium salmoniphilum (ex Ross 1960) sp. nov., nom. rev., with the type strain SCT (=ATCC 13578T =DSM 43276T).