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Here, we present the genome sequence of a novel Pseudomonas aeruginosa bacteriophage called UF_RH1. This lytic phage has a genome size of 42,567 bp and is classified as a member of the Siphoviridae family and the Septimatrevirus genus. UF_RH1 shares genetic similarities with Stenotrophomonas phage vB_SmaS-DLP_2.

PurposeAlpha-melanocyte stimulating hormone (α-MSH) is known to have anti-inflammatory effects. However, the anti-inflammatory properties of α-MSH on normal bronchial epithelial cells are largely unknown, especially in the context of in vitro sarcoidosis models.MethodsWe evaluated the anti-inflammatory effects of α-MSH on two different in vitro sarcoidosis models (lung-on-membrane model; LOMM and three-dimensional biochip pulmonary sarcoidosis model; 3D-BSGM) generated from NBECs and an in vivo sarcoidosis mouse model.ResultsTreatment with α-MSH decreased inflammatory cytokine levels and downregulated type I interferon pathway genes and related proteins in LOMM and 3D-BSGM models. Treatment with α-MSH also significantly decreased macrophages and cytotoxic T-cells counts in a sarcoidosis mice model.ConclusionOur results confirm the direct role of type I IFNs in the pathogenesis of sarcoid lung granulomas and highlight α-MSH as a potential novel therapeutic agent for treating pulmonary sarcoidosis.Graphical Abstract

Understanding the diversity of bacteria and E.coli levels at beaches is important for managing health risks. This study compared temporal changes of the bacterial communities of Belle Isle Beach (Detroit, MI) and Sand Point Beach (Windsor, ONT), both located near the Lake St. Clair origin of the Detroit River. Water samples collected 4 days/week for 12 weeks in summer, were subjected to 16S rRNA analysis of amplicon sequencing and E. coli enumeration. Bacterial communities changed over time, as determined by cluster dendrogram analysis, exhibiting different communities in July and August than in June and different communities at the two beaches. After June, alpha diversity decreased and relative abundance of Enterobacter (Gammaproteobacteria) increased at Sand Point; whereas, Belle Isle maintained its alpha diversity and dominance by Betaproteobacteria and Actinobacteria. Contamination at both beaches is dominated by birds (23% to 50% of samples), while only ∼10% had evidence of human-associated bacteria. High E. coli at both beaches was often associated with precipitation. Nearshore sampling counts were higher than waist-deep sampling counts. Despite the dynamic changes in bacterial communities between the two beaches, this analysis based on 16S rRNA amplicon sequencing is able to provide information about bacterial types associated with high E. coli levels and to use bacterial sequences to more precisely determine sources and health relevance of contaminants.

Background Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. Results We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. Conclusions As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health.

Objectives Growth hormone‐releasing hormone (GHRH) is a potent stimulator of growth hormone (GH) secretion from the pituitary gland. Although GHRH is essential for the growth of immune cells, the regulatory effects of its antagonist in granulomatous disease remain unknown. Methods Here, we report expression of GHRH receptor (R) in human tissue with sarcoidosis granuloma and demonstrate the anti‐inflammatory effects of MIA602 (a GHRH antagonist) in two in vitro human granuloma models and an in vivo granuloma model using different methods including ELISA, immunohistochemistry, RNA‐seq analysis and flow cytometry. Results MIA602 decreases the levels of IL‐2, IL‐2R, IL‐7, IL‐12, IL‐17A and TNF‐α in an in vitro granuloma model. Further, we show that the anti‐inflammatory effect of MIA602 appears to be mediated by a reduction in CD45+CD68+ cells in granulomatous tissue and upregulation in PD‐1 expression in macrophages. Analysis of the expression of proteins involved in the mitochondrial stage of apoptosis showed that MIA602 increases the levels of caspase‐3, BCL‐xL/BAK dimer and MCl‐1/Bak dimer in the granuloma. These findings indicate that MIA602 may not induce apoptosis. Conclusions Our findings further suggest that GHRH‐R is potentially a clinical target for the treatment of granulomatous disease and that MIA602 may be used as a novel therapeutic agent for sarcoidosis., GHRH‐R is potentially a target for treatment of granulomatous diseases such as sarcoidosis, which could be blocked by growth hormone‐releasing hormone‐R antagonists such as MIA602 as novel therapeutic agents for sarcoidosis.

IntroductionThe outbreak of pneumonia known as SARS-COV-2 and newly-emerging South African (B.1.351), the United Kingdom (B.1.1.7) and Brazil (P.1) variants have led to a more infectious virus and potentially more substantial loss of neutralizing activity by natural infection or vaccine-elicited antibodies.MethodsWe identified prevalent mutations using the spike receptor-binding domain (S-RBD) of SARS-CoV-2 deposited in the Nextstrain global database and comparing them to the Wuhan-Hu-1/2019 genomic sequence as a reference. Then we calculated the percentages of mutant genomes from the total regional subsample isolates from December 2019 to the end of January 2021. We developed two separate time series forecasting models for the SARS-CoV-2 B.1.1.7 variant. The computational model used the structure of the S-RBD to examine its interactions with the neutralizing antibody, named CV30 (isolated from a patient), and human angiotensin-converting enzyme 2 (hACE-2), based on a hybrid algorithm of template-based modeling to predict the affinity of S protein to the neutralizing antibodies and hACE-2 receptor.ResultsThe proportion of the B.1.1.7 strain in North America is growing fast. From these computations, it seems that the S-RBD and hACE-2 proteins are less favorable for the South African strain (K417N, E484K, and N501Y) as compared to the wild type structure and more favorable for B.1.1.7 and P.1 variants. In the present of crystallized CV30 neutralizing antibodies, docking scores suggest antibodies can be partially neutralize the B.1.1.7 variant, and, less efficiently, the B.1.351 and P.1 variants.ConclusionThe rapid evolution of SARS-CoV-2 has the potential to allow the newly-emerged B.1.351, and P.1 variants to escape from natural or vaccine-induced neutralizing immunity and viral spreading.

Bacteria play a key role in freshwater biogeochemical cycling as well as water safety, but short-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We sampled four public beaches in southern Ontario, Canada; in June, July, and August (2016) over a 24-h (diel) cycle at 2-h intervals. Using high-throughput sequencing of 16S rRNA gene, we found substantial bi-hourly and day/night variation in the bacterial communities with considerable fluctuation in the relative abundance of Actinobacteria and Proteobacteria phyla. Moreover, relative abundance of Enterobacteriaceae (associated with potential health risk) was significantly high at night in some dial cycles. Diversity was significantly high at night across most of the diel sampling events. qPCR assays showed a substantial bi-hourly variation of Escherichia coli levels with a significant high level of E. coli at night hours in comparison with day hours and the lowest levels at noon and during the afternoon hours. Taken together, these findings highlighted a considerable short-term temporal variation of bacterial communities which helps better understanding of freshwater bacterial dynamics and their ecology. E. coli monitoring showed that multiple samples in different hours will provide more accurate picture of freshwater safety and human health risk. Graphical abstract.

Background: Non-tuberculous mycobacteria (NTM) are defined as mycobacteria other than Mycobacterium tuberculosis (MTB), which do not cause tuberculosis or leprosy. Early and precise diagnosis of NTM is particularly important for the correct epidemiological control and specific treatments. The aim of this study was to identify the mycobacterium species isolated from patients referred to hospitals in Tehran using the high-performance liquid chromatography (HPLC) method. Materials and Methods: In this cross-sectional descriptive study, a collection of isolates (n=20) was obtained from clinical specimens submitted to the Masoud Laboratory in Tehran, Iran, during 2014-2015. The strains were isolated from sputum, urine, blood, and various sterile body fluid specimens. Chromatography was conducted at a flow rate with a curvilinear gradient of methanol and methylene chloride, beginning at 98% methanol containing 2% methylene chloride and ending at 35% methanol contained in 65% methylene chloride. Results: From a total of 20 clinical isolates, 8 isolates (40%) were identified as Mycobacterium abscessus, 6 isolates (30%) M. tuberculosis, 3 isolates (15%) M. intracellulare and 3 isolates (15%) M. fortuitum. Conclusion: For the proper treatment, rapid differentiation between MTB and NTM should be performed in persons who are diagnosed with or are suspected of having infectious TB disease. So, the HPLC method can be suggested as a cost-effective, specific and reliable method for rapid identification of MTB and differentiation of NTM strain from positive cultures isolated from clinical specimens.

The aquatic bacterial community (BC) plays a vital role in determining the nature and rate of ecosystem function. However, the biotic and abiotic factors influencing BC structure and function are largely unknown. Hence, the current study characterizes the impact of biotic and abiotic factors on aquatic bacterial biodiversity to determine whether the dominant effects are biotic or abiotic by partitioning their relative effects across temperate Canadian lakes. We collected water samples from sixty southern Ontario lakes and characterized their BC and microbial eukaryotic community (MEC) compositions using high throughput metabarcode sequencing of 16S and 18S rRNA gene fragments. The diversity and richness of aquatic BCs differed considerably among our study lakes, and those differences were explained by environmental, spatial, and biotic (MEC) factors (31%, 23%, and 23% of variance explained, respectively). The relatively large contribution from biotic and abiotic factors (54%), relative to spatial effects, shows deterministic processes prevail in shaping BC assembly in freshwater lakes. However, spatial effects also contributed significantly, highlighting the role of stochastic processes (ecological drift and coupled with limited dispersal) in shaping BC structure. Furthermore, our co-occurrence network analysis showed strong positive and negative interactions within and between the BCs and MECs, indicating mutualistic or antagonistic co-occurrence patterns relationships play important roles in driving the variation in BC composition among our sampled lakes. Considered together, our community analyses show that deterministic and stochastic processes combined contribute to determining the aquatic BC composition, and hence likely function as well, across a broad array of temperate freshwater lakes.

Tuberculosis (TB) is considered as one of the most important infectious diseases in the world, and recent rise and spread of multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains, have made the matter worsened. Due to the importance of TB prevalence in Iran, this study was designed to investigate the genetic diversity among MDR strains of MTB by MIRU-VNTR typing scheme. A total of 88 drug resistant M. tuberculosis isolates belong to pulmonary TB cases were collected from several TB reference centers of Iran. Drug susceptibility testing for Isoniazid and Rifampin was performed using the agar proportion method and MDR isolates were underwent genotyping by using 12-locus- based MIRU-VNTR typing. On performing proportion method, 22 isolates were identified as MDR. By typing of MDR isolates using 12-loci MIRU-VNTR technique, high diversity were demonstrated in MDR strains and these were classified into 20 distinct MIRU-VNTR genotypes. MIRU loci 10 and 26 were the most discriminatory loci with 8 and 7 alleles respectively; while MIRU loci 2, 20, 24 and 39 were found to be the least discriminatory with 1–2 alleles each. We noticed a mixed infection in isolate 53, as this isolate comprised simultaneous two alleles in MIRU loci 40, 10, 16 and 39. In conclusion, this result represents MIRU-VNTR typing as a useful tool for studying genetic diversity of MDR-MTB in regional settings, and will help the health sectors to construct a preventive program for MDR-TB. Additionally, it can detect mixed infection which can facilitate management of treatment.

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.

Introduction: Rodents are the primary source of several zoonotic infectious diseases. The upsurge of rodents’ population in Najaf Abad Village of Nishapur County, northeastern Iran in February 2014 raised the concerns about the outbreak of diseases such as plague and tularemia. This report discusses the lessons learned from the outburst of rodents’ population in that village and represent as well the investigations performed by a dispatched team from Pasteur Institute of Iran for detection of potentially pathogenic agents in the entrapped rodents. Methods: In this study, different areas of Najaf Abad village were explored. The animals were identified based on morphological features using identification keys. Sera from all rodents were tested for plague and tularemia using ELISA and agglutination tests, respectively. Results: Seven captured rodents belonged to the family Muridae Illiger, 1811, and the species, Mus musculus Linnaeus, 1758 (n=4), Meriones libycus Illiger, 1811 (n=2), and Nesokia indica Gray, 1830 (n=1) were identified. All the rodents were negative for plague and tularemia. Conclusion: The outburst rodents’ populations in this village that began in 2007 can be attributed to the old structure of the village, drought, and the disappearance of natural predators of rodents. Also, due to drought in the recent years, extensive agriculture was not possible, which might have led to the invasion of rodents to the human settlements. It is recommended that in such events, regular programs to be carried out under the supervision of an organization to achieve the best results in the shortest possible time.

A total of 237 natural water samples from ponds, rivers, lakes, springs and other surface waters from north western provinces of Iran (Kurdistan and Western Azerbaijan) were collected from September to November 2015. All samples were cultured forAmong the tested surface water samples, 40 (17.09%; 95% CI: 12.67-22.33%) and 12 (5.13%; 95%CI: 2.81-8.56%) samples were positive forThe prevalence of

The characterization of microbial community dynamics using genomic methods is rapidly expanding, impacting many fields including medical, ecological, and environmental research and applications. One of the biggest challenges for such studies is the isolation of environmental DNA (eDNA) from a variety of samples, diverse microbes, and widely variable community compositions. The current study developed environmentally friendly, user safe, economical, and high throughput eDNA extraction methods for mixed aquatic microbial communities and tested them using 16 s rRNA gene meta-barcoding. Five different lysis buffers including (1) cetyltrimethylammonium bromide (CTAB), (2) digestion buffer (DB), (3) guanidinium isothiocyanate (GITC), (4) sucrose lysis (SL), and (5) SL-CTAB, coupled with four different purification methods: (1) phenol-chloroform-isoamyl alcohol (PCI), (2) magnetic Bead-Robotic, (3) magnetic Bead-Manual, and (4) membrane-filtration were tested for their efficacy in extracting eDNA from recreational freshwater samples. Results indicated that the CTAB-PCI and SL-Bead-Robotic methods yielded the highest genomic eDNA concentrations and succeeded in detecting the core microbial community including the rare microbes. However, our study recommends the SL-Bead-Robotic eDNA extraction protocol because this method is safe, environmentally friendly, rapid, high-throughput and inexpensive.

BackgroundQ fever is a zoonotic disease of great public health importance in Iran. This disease is presented with high phase I antibody development in chronic and high phase II antibody in the acute form of illness. This study was conducted to evaluate the seroprevalence of Q fever among high-risk occupations in the Ilam province in Western Iran.Methods and findingsIn this cross-sectional study, 367 sera samples were collected from five groups comprised of animal husbandry workers, farmers, butchers, slaughterhouse workers, and park rangers. The collected sera were tested for IgG antibodies against Coxiella burnetii using ELISA. The seroprevalence of antibodies against C. burnetii in phase I and II was 24.38% and 26.37%, respectively (i.e., 32.42% overall). Low educational level, living in rural areas, keeping sheep/goats, ages older than 50 years, and a history of arthropod bites positively correlated with increased risk of Q fever infection. Animal husbandry workers (45.13%) were at higher risk of contracting Q fever compared with other occupations in the study (17.11%).ConclusionsHigh seroprevalence of C. burnetii among high-risk occupations is a serious challenge in the Ilam province. In addition, the high seroprevalence of endemic Q fever in rural and nomadic areas and a higher concentration of occupations who are directly engaged with livestock demonstrate the critical need for preventive medicine education and training in regards to mitigating risk for disease contraction in susceptible groups.

Members of Mycobacterium abscessus complex are known for causing severe, chronic infections. Members of M. abscessus are a new “antibiotic nightmare” as one of the most resistant organisms to chemotherapeutic agents. Treatment of these infections is challenging due to the either intrinsic or acquired resistance of the M. abscessus complex to the available antibiotics. Recently, successful phage therapy with a cocktail of three phages (one natural lytic phage and two engineered phages) every 12 h for at least 32 weeks has been reported against a severe case of the disseminated M. abscessus subsp. massiliense infection, which underlines the high value of phages against drug-resistant superbugs. This report also highlighted the limitations of phage therapy, such as the absence of lytic phages with a broad host-range against all strains and subspecies of the M. abscessus complex and also the risk of phage resistant bacteria over treatment. Cutting-edge genomic technologies have facilitated the development of engineered phages for therapeutic purposes by introducing new desirable properties, changing host-range and arming the phages with additional killing genes. Here, we review the available literature and suggest new potential solutions based on the progress in phage engineering that can help to overcome the present limitations of M. abscessus treatment.

Leptospirosis is a zoonosis and a major public health problem. Blood sampling was done in the province of Kurdistan from 250 members of different groups, including hunters and their families, butchers and slaughterhouse workers, healthcare workers (HCWs) and those referred to medical diagnostic laboratories for routine testing. Sera were tested using an ELISA method to detect specific Leptsopira IgG antibodies. We found 20.80% (95% confidence interval, 16.23–26.25%) to be positive. The highest and lowest seroprevalence were in hunters (26%) and HCWs (18%). There was significant positive correlation between age and seropositivity ( P = 0.01). Hunting and eating the meat of the hare and exposure to dead or dying wild animals were found to be the main risk factors ( P

Background Acinetobacter baumannii has become one of the most serious causative agents of nosocomial infections due to its significant ability to survive on hospital surfaces. It is mainly an emerging opportunistic pathogen infecting patients in intensive care units. This study was aimed to identify the clinical isolates of A. baumannii and to investigate their heterogeneity using polymerase chain reaction (PCR)-based typing methods. Methods A total of 197 nonduplicate isolates recovered from a wide range of clinical samples were subjected to conventional cultural and biochemical tests. For those isolates that were preliminary identified as A. baumannii, rpoB -based PCR with subsequent restriction fragment length polymorphism (RFLP) using two restriction enzymes ( Tag I and Hae III) was performed to investigate the genetic diversity of the strains and their presumptive relationships with different clinical presentation of the disease caused by this pathogen. Results In total, 50 isolates (25.4%) were identified as A. baumannii using conventional phenotypic methods with subsequent confirmation by rpoB sequencing. RFLP analysis demonstrated five different restriction enzyme patterns, designated as A–E clusters. Most A. baumannii isolates were categorized under Cluster A (32%). We found no significant relationship between clinical presentation and the clustering of the isolates. Conclusion This study showed that the rpoB region possesses high discriminatory power to identify the isolates to the species level. This marker showed high interspecies variability that might be useful for strain typing. The results also suggest the possibility of the existence of a predominant clone of A. baumannii among infected patients in Iran.

Background Nocardia species are nocardiosis agents particularly in immune disorder patients with the clinical manifestations including fatigue, malaise, weight loss, cough, and dyspnoea. Due to time - consuming bacterial culture and insufficient phenotypic tests alone, rapid molecular assays for the diagnosis of Nocardia are essential. The primary objective of this study was the analysis of the polymerase chain reaction - restriction fragment length polymorphism (PCR - RFLP) and PCR sequencing of 16S rRNA gene for the identification and differentiation of Nocardia species.Methods 32 Nocardia isolates were identified by single digestion of 441 - nt fragments of the 65 - heat - shock protein gene with endonucleases BstEII, MspI, and HinfI and sequencing of 16S rRNA gene. These isolates were collected from the soil of various geographical regions of Iran by paraffin baiting technique in our previous study.Results Some of the isolates had new patterns that were not identified by PCR - RFLP of hsp65 gene in literature; therefore, they were identified by sequence analysis of 16S rRNA gene. Six strains of Nocardia with new DNA banding patterns in PCR - RFLP of hsp65 (A and B) could not be identified by their hsp65 restriction - endonucleases fragment patterns. Strain En49 after analysis of sequencing data was recognized as Nocardia coubleae , which its PCR - RFLP profile of hsp65 has not been reported in the literature so far.ConclusionsThe PCR - RFLP - hsp65 is faster than other sequencing-based techniques, but species accurate identification in strains with new PCR - RFLP profiles is not possible. The 16S rRNA gene sequencing is a suitable method to determine the percent similarity and phylogenetic relationships of Nocardia species.

Absence of mutations within the genes encoding drug targets in some phenotypically drug resistant strains of Mycobacterium tuberculosis suggests possible involvement of alternative mechanisms such as over-expression of efflux pumps. We investigated the expression level of Rv1410c, Rv2459, Rv1218c and Rv1273c efflux pumps gene by real-time quantitative reverse transcription PCR (qRT-PCR) in 31 clinical isolates of M. tuberculosis. Susceptibility to first-line drugs was performed using the proportion method. Twenty one isolates were characterized with drug resistance (DR), and among them 12 showed a significantly elevated level of expression (>4 fold) for at least one of the studied genes encoding for efflux pumps. Point mutations in the katG (codons 315 or 335) and rpoB (codons 456 and 441) genes were found in 42.85% and 66.6% of drug resistant isolates, respectively. Only one isolate showed mutation at position -15 of the inhA promoter region. Among the 7 isolates (33.33%) which had no mutation in the studied regions of drug target genes, 5 isolates showed over-expression for efflux pumps. Our results demonstrated that over-expression of efflux pumps can contribute to drug resistance in M. tuberculosis.

Background Lack of knowledge toward tuberculosis (TB) among health care workers (HCWs) increases the risk of developing TB. The aim of this study was to assess the level of knowledge, attitude, and practice of HCWs in Iran. Methods We conducted a cross-sectional study in 50 universities of medical sciences throughout Iran. A questionnaire was developed to assess the knowledge, attitude, and practice of participants. The values of Cronbach α coefficients for the knowledge and attitude questions were .76 and .75, respectively. Results The mean scores of knowledge, attitude, and practice among TB laboratory staff regarding TB was 82.6 (95% confidence interval [CI], 82.0-83.7), 87.6 (95% CI, 87.1-88.0), and 57.9 (95% CI, 56.9-58.9), respectively. The mean scores of knowledge, attitude, and practice among non-TB laboratory staff regarding TB was 69.5 (95% CI, 67.9-71.1), 50.7 (95% CI, 50.1-51.4), and 40.82 (95% CI, 38.2-43.4), respectively. Conclusion TB laboratory staff scored relatively well in knowledge and attitude of TB, but they scored lower in practice regarding TB. Non-TB laboratory staff had lower scores than TB laboratory staff in knowledge, attitude, and practice. There is a major gap between knowledge and attitude and practice in both groups. It is therefore essential to plan for the continuing in-service training of HCWs and public training of the general population regarding TB.

Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0 % 16S rRNA gene sequence similarity, and 91.5–96.5 % similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9 %. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207T ( = DSM 46765T = JCM 18439T).

Traditionally Nocardia asteroids was considered the predominant species of causing no-cardiosis. The improved identification of isolates using molecular techniques have shown that the genus exhibits considerable taxonomic complexity and phenotypic base identification can be ambiguous. The aim of this study was to assess the species distribution of Nocardia strains mostly recovered from patients suspected of having tuberculosis, during three years period (2009-2012). The clinical isolates were identified to species level using conventional tests and genotypic methods using single and multi locus sequence analysis (MLSA) of 16S rRNA, gyrB and secA1 genes. Nocardiosis was diagnosed in 46 patients. The most frequent underlying condition were organ transplantation (6 patients; 13%), cancer (6 patients; 13%), human immunodeficiency virus (HIV) (6 patients; 13%), non-infectious chronic lung disease (5 patients; 10.8%) and tuberculosis (4 patients; 8.7%). Nocardia species was recovered from 46 different clinical specimens, the most common of which was bronchoalveolar lavage (BAL) (43.5%). Eleven different Nocardia species were identified: N. asteroides (n = 12), N. cyriacigeorgica (n = 9), N. farcinica (n = 7), N. wallacei (n = 6), N. carnea (n = 3), N. otitidiscaviarum (n = 3), N. abscessus (n = 1), N. arthritidis (n = 1), N. kruczakiae (n = 1), N. nova (n = 2) and N. veterana (n = 1). In conclusion, infection caused by Nocardia species appears to be more common than generally appreciated. The current study provides further evidence that Nocardia species are capable of causing a wide range of human diseases in healthy and immunocompromised patients. MLSA is a reliable method for accurate species identification of Nocardia isolates and would be more feasible for routine use in clinical laboratories.

Four strains isolated in Iran from pulmonary specimens of unrelated patients are proposed as representative of a novel Mycobacterium species. Similarity, at the phenotypic level, with Mycobacterium kansasii is remarkable with the photochromogenic yellow pigmentation of the colonies being the salient feature. They differ, however, genotypically from this species and present unique sequences in 16S rRNA, hsp65 and rpoB genes. The average nucleotide identity and the genome-to-genome distance fully support the status of an independent species. The name proposed for this species is Mycobacterium persicum sp. nov. with AFPC-000227T (=DSM 104278T=CIP 111197T) as the type strain.

The characterization of five Iranian isolates, four from hospital haemodialysis water and one from the sputum of a patient, led to the detection of a novel mycobacterium species. The strains were characterized by mucoid colonies developing in 3–5 days at temperatures ranging from 25 to 37 °C. The biochemical test pattern was unremarkable while the HPLC profile of mycolic acids resembled that of Mycobacterium fortuitum . The sequences of three major housekeeping genes (16S rRNA, hsp65 and rpoB) were unique and differed from those of any other mycobacterium. Mycobacterium brisbanense , which is the species that shared the highest 16S rRNA gene sequence similarity (99.03 %), was distinct, as shown by the average nucleotide identity and by the genome to genome distance values (91.05 and 43.10 %, respectively). The strains are thus considered to represent a novel species of the genus Mycobacterium, for which the name Mycobacterium aquaticum sp. nov. is proposed. The type strain is RW6T (=DSM 104277T=CIP111198T).

The Middle East Dust storms have greatly affected the south and west parts of Iran during the last decade. The main purpose of this study was to examine and compare culturable airborne bacteria concentration in particulate matter (PM) during normal, semi-dust, and dust event days in different places and seasons in Ahvaz from November 2011 to May 2012. Sampling was performed every 6 days and on dust event days at different sampling stations. The overall mean concentrations of PM10, PM2.5, and PM1 for the entire study period were 598.92, 114.8, and 34.5 μg/m3, respectively. The PM concentrations during the dust event days were much higher than normal and semi-dust event days. The highest mean PM concentrations were observed in March 2011. The low PM2.5/PM10 ratios indicate that these PM are mostly originating from natural sources such as dust storms. The overall mean concentration of total bacteria during the study period was 620.6 CFU/m3. The greatest bacterial concentrations were observed during dust event days and at areas with high traffic and more human activities compared with normal days and greener areas. The percentage of gram-positive bacteria was significantly higher than that during the study period (89 vs 11 %). During this study, 26 genera of culturable bacteria were identified from all the sampling stations. The most dominant genera in all sampling stations were Streptomyces, Bacillus, Kocuria, Corynebacterium, and Paenibacillus. The results also showed that there were positive correlations between PM and bacterial concentrations during the study period (p

The improved identification of isolates using molecular techniques have shown that the genus exhibits considerable taxonomic complexity and phenotypic base identification can be ambiguous. The aim of this study was to assess the species distribution of Nocardia strains mostly recovered from patients suspected of having tuberculosis. The clinical isolates were identified to species level using conventional tests and genotypic methods using single and multi locus sequence analysis (MLSA) of 16S rRNA and gyrB genes. Nocardiosis was diagnosed in 46 patients. The most frequent underlying condition were organ transplantation (6 patients; 13%), cancer (6 patients; 13%), human immunodeficiency virus (HIV) (6 patients; 13%), non-infectious chronic lung disease (5 patients; 10.8%) and tuberculosis (4 patients; 8.7%). Nocardia species was recovered from 46 different clinical specimens, the most common of which was bronchoalveolar lavage (BAL) (43.5%). In conclusion, infection caused by Nocardia species appears to be more common than is generally appreciated. The current study provides further evidence that Nocardia species are capable of causing a wide range of human diseases in healthy and immunocompromised patients. MLSA is a reliable method for accurate species identification of Nocardia isolates and would be more feasible for routine use in clinical laboratories.