[Determination of Capsule Types, Antibiotic Resistance Profiles and Phylogenetic Relationships of Group B Streptococcus Isolates Isolated from Patients Followed in Various Clinics and Polyclinics]. / Çesitli Klinik ve Polikliniklerde Takip Edilen Hastalardan Izole Edilen Grup B Streptokok Izolatlarinin Kapsül Tiplerinin Belirlenmesi, Antibiyotik Direnç Profilleri ve Filogenetik Iliskilerinin Arastirilmasi.

Group B streptococci (GBS) are microorganisms that cause various systemic infections. In this study, it was aimed to investigate the capsule serotypes, antibiotic resistance and phylogenetic similarity relationship between GBS isolates. One hundred and ten GBS isolates isolated from female patients who admitted to Adana City Hospital with various complaints were included in the study. Kirby-Bauer disc diffusion method was used for the antibiotic resistance patterns and evaluated with CLSI criteria. The genes ermB, ermTR, mefA for erythromycin resistance and linB genes for clindamycin resistance were investigated by multiplex PCR method. Multiplex PCR method was used for GBS capsule serotyping. Similarity relationship between the isolates was analyzed by pulsed-field gel electrophoresis (PFGE) method. As a result of the study; all strains were found to be sensitive to penicillin and vancomycin. Erythromycin, clindamycin ofloxacin, and ceftriaxone resistance rates were observed as 60%, 11.8%, 6.4%, and 4.5%, respectively. The mefA gene was not found while 53% and 47% of the erythromycin-resistant isolates carried ermTR and ermB genes, respectively. The linB gene was not found in clindamycin-resistant GBS isolates. The capsule serotype distributions of GBSs were found as, Ib 42.7%, Ia 35.5%, III 10%, II 8.2%, and V 3.6%, respectively. In the analysis of the similarity relationships between GBS isolates with the PFGE method, no significant relationship was found. In conclusion, it was thought that more studies should be conducted to show the prevalence of GBS capsule serotypes and patterns of antibiotic resistance.

[The Mutations on embA, embB and embC Gene Region in Ethambutol-Resistant and Susceptible Clinical Mycobacterium tuberculosis Complex Isolates]. / Etambutole Dirençli ve Duyarli Mycobacterium tuberculosis Kompleksi Klinik Izolatlarinda embA, embB ve embC Gen Bölgesi Mutasyonlari.

Ethambutol (EMB) is one of the first-line drugs used in the standard combination therapy for tuberculosis (TB) caused by Mycobacterium tuberculosis complex (MTC), and resistance to drugs that play a key role in treatment is increasing worldwide. Mutations in the embCAB operon that have been confirmed to be associated with resistance are responsible for EMB resistance. In this study, it was aimed to determine the frequency and patterns of mutations in embA, embB and embC gene regions in clinical MTC isolates found to be phenotypically resistant and susceptible to EMB. A total of 64 MTC isolates, 44 of resistant to EMB and 20 of susceptible to EMB, isoniazid, rifampicin, and streptomycin by conventional phenotypic drug susceptibility test, were included in the study. Following the DNA isolation, embA, embB and embC gene regions associated with EMB resistance were amplified with specific primer sequences. The PCR products were cycle sequenced using the Bigdye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems, USA) and electrophoretically separated on the ABI PRISM 3130XL Genetic Analyzer (Applied Biosystems, USA). Mutated gene regions were identified by aligning sequence analysis data in multiple sequence analysis programs. In the study, genomic mutations in the embCAB operon were detected in 68.2% (30/44) of the EMB resistant isolates. Mutations in the embB gene region were detected in 66% (29/44) of the resistant isolates, 76% (22/29) of these mutations were at codon 306 and the most common mutation patterns in this codon were determined as ATG→GTG (M306V; 58.6%; 17/29), ATG→ATA, ATC or ATT (M306I; 17.2%; 5/29). Other mutations in the embB gene region were determined as Y334H (3.4%; 1/29), D354A (6.9%; 2/29), E378A (3.4%; 1/29), G406C (3.4%; 1/29), M423I (3.4%; 1/29) and E521A (3.4%; 1/29). Of the 44 EMB-resistant isolates, mutations were detected in one (2.3%) of the isolate in the embA gene region (L330L) and in two (4.5%) of the isolates in the embC gene region (T270I in one isolate and T270I and E305E in the other isolate). Of the phenotypically EMB susceptible isolates, mutation was detected in only one (5%) of the isolates in the embA gene region (E180G). In our study, it was determined that mutations frequently occur in codon 306 of the embB gene in EMB-resistant MTC isolates and this mutation has a potential role in the development of EMB resistance. However, it was concluded that the absence of mutations does not exclude phenotypic EMB resistance. Our results will shed light on the molecular epidemiology of embCAB operon mutations that cause EMB resistance in our country.

The Distribution of Cytotoxic Necrotizing Factors (CNF-1, CNF-2, CNF-3) and Cytolethal Distending Toxins (CDT-1, CDT-2, CDT-3, CDT-4) in Escherichia coli Isolates Isolated from Extraintestinal Infections and the Determination of their Phylogenetic Relationship by PFGE.

Backgrounds: Diagnostic markers of extraintestinal infection in Escherichia coli (E. coli) remain unclear in the literature. Extraintestinal pathogenic E. coli (ExPEC) is differentiated from other E. coli isolates in terms of virulence factors, such as host cell adhesion, invasion, cytotoxic necrotizing factor (CNF (cnf1-cnf3)) and cytolethal distending toxin (CDT (cdt1-cdt4) that are responsible for cell death. We aimed to investigate the frequency of CNF-CDT and the relationship between the clinical diagnosis and genotypes in E. coli isolates with different clinical origins. Methods: A total of 646 E. coli isolates (obtained from 645 patients) isolated from different infection sites other than the intestine were evaluated in aspects of the CNF, CDT virulence genes, phylogenetic grouping, and phylogenetic relationship by using PCR and PFGE. Results: At least one virulence gene was present in 156 (24%) of the 646 ExPEC isolates. We detected cnf1, cnf2, and cnf3, in 78, 12, and 20 ExPEC isolates, respectively. Also, cdt1, cdt2, cdt3, and cdt4 genes were present in 20, 4, 4, and 4 isolates, respectively. Some isolates harbored more than one gene, being cnf1-cnf3 (n = 6), cnf1-cdt1 (n = 4), and cdt1-cdt4 (n = 4). These 156 isolates were distributed into 106 large clusters by PFGE. Virulent ExPEC is primarily related to groups B2 (60%) and D (32%). Conclusion: To our knowledge, this study demonstrated the presence of cnf2, cnf3, cdt1, cdt2, cdt3, and cdt4 genes for the first time in the literature for Turkey. The widespread presence of the CNF gene in E. coli helps distinguish ExPEC from commensal isolates.

Distribution of emm, superantigen and other virulence genotypes and detection of phylogenetic relationships in group A streptococcal isolates.

Group A streptococci are important pathogens with various virulence factors, such as M protein, superantigens, hemolysins, deoxyribonuclease, and proteases. The aims of this study are to investigate the detection of emm genotypes and other virulence genes, such as SAgs, DNase, protease, antibiotic resistance, and phylogenetic relationships in GAS strains isolated from clinical samples.Test strains were obtained from Çukurova University Balcali Hospital and regional hospitals in Adana province. The M proteins were detected by sequence analysis of emm genes. SAgs and other virulence gene profiles were determined using the Multiplex-PCR method. The antibiotic susceptibility of the isolates was performed by the disc diffusion method and evaluated according to CLSI criteria. The PFGE method was used to determine the clonal relationship between the strains.The emm gene was positive in 86 isolates. The most common emm genotypes were emm28 (22%), emm1 (18.6%), emm12 (13.9%), and emm3 (11.6%). Also, the most common virulence genes were speG (58.1%), speC (56.9%), sdaB (53.4%), and mac (53.4%). The rates of resistance to erythromycin, clindamycin, levofloxacin, ciprofloxacin and telithromycin were 19.8%, 16.3%, 4.7%, 3.5%, and 3.5%, respectively.As a result, additional regional studies on the detection and prevalence of GAS virulence factors in Turkey are required. We believe that this study will provide valuable information for epidemiological studies on emm sequences, Sags, and other virulence factors of Streptococcus pyogenes in Turkey.

Investigation of the Relationship between Colistin Resistance and Capsule Serotypes in Carbapenem Resistant Klebsiella pneumoniae Strains.

Carbapenem-resistant Klebsiella pneumoniae is associated with high morbidity and mortality, and capsule serotypes make treatment difficult. The aim of this study is to investigate the relationship between colistin resistance and capsule types in carbapenem-resistant K. pneumoniae isolates. In 2018- 2020, we conducted our study with 115 carbapenem-resistant K. pneumoniae strains diagnosed by matrix-mediated laser desorption ionization time-of-flight mass spectrometry method (MALDI-TOF MS; Bruker Daltonics, Germany). Colistin sensitivities were determined by using DxM MicroScan WalkAway System (Beckman Coulter, ABD) automated system and were then verified by liquid microdilution (MIC). Capsule serotypes were investigated by conventional polymerase chain reaction (PCR) method. Among the carbapenem resistant K. pneumoniae isolates, 42% (48) were resistant to colistin and 58% (67) were susceptible to colistin. In the K. pneumoniae isolates with colistin resistance 33% (16) K5, 13% (6) K2, 8% (4) K20 4% (2) K1 and 2% (1) K54 and K57 capsule serotypes were found, while in the K. pneumoniae isolates with colistin susceptible 12% (8) K5, 4% (3) K2, 3% (2) K20, 1.5% (1) K1 and K54 capsule serotypes were found. Serotype K5 was very frequent in isolates collected from patients with urinary tract diseases. The resistance profile data obtained from the present study can serve as an information base to understand the infection pattern prevailing in the hospital.

Toxoplasma gondii seroprevalence among tuberculosis patients: A systematic review and meta-analysis.

Toxoplasma gondii and Mycobacterium tuberculosis are intracellular pathogens, both infecting a substantial proportion of human population. We conducted a systematic review and meta-analysis to estimate the pooled T. gondii seroprevalence in tuberculosis patients. Three international databases were systematically searched for literature on prevalence of T. gondii in tuberculosis patients. A total of 1389 documents were identified, and eight papers were eligible to be included in the systematic review and meta-analysis. Geographical data gaps were evident, as no studies were identified from many countries where both infections are important. The pooled seroprevalence of IgG, IgM, and both IgG and IgM antibodies against T. gondii in tuberculosis patients were estimated to be 35.9% (95% confidence interval [CI], 19.3-56.7%), 35.0% (95% CI, 3.0-90.3%), and 13.4% (95% CI, 2.4-49.0%), respectively. In the included case-control studies, the pooled T. gondii seroprevalence (proportion anti- T. gondii IgG antibody positive) was higher in tuberculosis patients than in their controls, with an odds ratio by random effects model of 1.63 (95% CI, 1.28-2.08). The results of our work suggest an association between T. gondii seropositivity and being a tuberculosis patient, which should however be interpreted with caution because the timeline of the infections and the disease process are not accounted for. Our work showed that T. gondii seropositivity, indicating chronic infection with the zoonotic parasite, was relatively common among tuberculosis patients.

Genetic evaluation of Mycobacteriumbovis isolates with MIRU-VNTR and spoligotyping

Background/aim: Determining the epidemiological characteristics of M. bovis strains isolated from human and animal tuberculosis cases will assist in taking more appropriate and effective control measures in controlling tuberculosis originating from animal Materials and methods: In this study, 32 M. bovis isolates of animal origin and 10 of human origin were isolated and identified in the Çukurova region between March 2011 and June 2012. The 12-locus MIRU-VNTR and spoligotyping methods were used. Results: Six different patterns were determined by spoligotyping and 10 by MIRU-VNTR. When both methods were used together, the number of patterns was found to be 28; MIRU4, MIRU26, MIRU31, and MIRU40 had the highest locus discrimination powers by MIRU-VNTR. The isolates concentrated in the SB0120 pattern at the rate of 42.85% in spoligotyping. By the same method, it was seen that 7 isolates were M bovis ssp. caprae pattern and 2 human isolates were M. bovis BCG pattern. Nevertheless, spoligotyping and MIRU-VNTR patterns showed that 5 M. bovis isolates of human origin were 100% compatible with isolates originating from cattle. Conclusion: In this study, we determined that the use of spoligotyping and MIRU-VNTR methods together was found to be more sensitive in the epidemiological analysis of M. bovis isolates.

[Detection and Molecular Analysis of Moxifloxacin MIC Values of Mycobacterium tuberculosis Strains Isolated from Clinical Specimens]. / Klinik Örneklerden Elde Edilen Mycobacterium tuberculosis Izolatlarinin Moksifloksasin MIK Degerlerinin Tespiti ve Moleküler Analizi.

Tuberculosis (TB) is a chronic, granulomatous and necrotizing disease caused by microorganisms belonging to the Mycobacterium tuberculosis complex group. In 2017, 6.4 million new TB cases have been reported according to the World Health Organization 2018 Global Tuberculosis Report. TB remains among the major health problems of our time due to the increasing drug resistance problem and the difficulties in definitive diagnosis in recent years. It is stated by clinicians that intensive use of quinolone group drugs with oral form in simple indications such as respiratory or urinary tract infections may lead to resistance and this may result in treatment failures. The aim of this study was to determine the moxifloxacin susceptibility of M.tuberculosis isolates obtained from clinical specimens by phenotypical methods, to determine the resistance rates of moxifloxacin and to investigate the relationship between phenotypical resistance and mutations in the gyrA gene. A hundred (n= 100) consecutive non-multidrug resistant and 37 non-consecutive multidrug resistant M.tuberculosis strains isolated from the clinical specimens of patients with pulmonary tuberculosis were included in the study. The moxifloxacin susceptibility of the isolates was determined by using Löwenstein-Jensen medium and their epidemiological properties were investigated and also mutations detected by gyrA region were compared with drug susceptibility rates. Of the 137 isolates tested for phenotypical susceptibility, 25 (18.2%) were found to be resistant to moxifloxacin. Resistance rate among non-multidrug resistant and multidrug resistant isolates were determined as 17% and 21.6%, respectively. According to the results of the sequencing analysis, of the gyrA regions of all the isolates included in the study, a single base mutation was found in a total of six samples. The location positions of the mutations were determined as D94Y, D94G, A90V, G88A and among two strains as D89N. Two of the isolates with mutations were found to be phenotypically susceptible to moxifloxacin. In our study, it was found that moxifloxacin resistance in M.tuberculosis isolates was higher than similar studies and it was found that different mechanisms may be responsible for the existing resistance other than the mutations in the gyrA gene. It was concluded that the data obtained from the study should be shared with all clinicians in the country due to the possibility of resistance development to this group of drugs in a short time and considering this drug will have an important role in the treatment of TB, it should be used more limited in non-specific indications. Further studies using larger case groups and isolates are needed for the continuation of the research.

Molecular characterization of methicillin-resistant Staphylococcus aureus strains by spa typing and pulsed field gel electrophoresis methods.

BACKGROUND: Rapid detection of sources and transmission routes by molecular methods provides key data for risk management of methicillin-resistant Staphylococcus aureus-induced infections acquired in both the community and hospitals. This study aimed to determine the clonal relationship of methicillin-resistant S. aureus strains isolated from our hospital by pulsed-field gel electrophoresis (PFGE) and Staphylococcal protein A (spa) typing methods and to identify the predominant clones in Cukurova Region, Turkey. RESULTS: All isolates analyzed by PFGE were distributed among 11 clusters. Clusters A (n = 19) and B (n = 27) were 84.1% similar and accounted for 61% of all samples. All isolates were distributed among 18 spa types, with the most common type being t030 with 31 isolates (41.3%), followed by t223 with nine isolates (12%) and t127 with seven isolates (9.3%). CONCLUSIONS: We found that t030 was the most common spa type in the area where the study was conducted, as also previously shown in studies undertaken in Turkey. However, the rate of t030 in our study was below the rates reported in the literature. We also detected some rare or sporadic spa types like t127, which has not been previously defined in our country. We consider that the spa typing and PFGE methods are useful for research on clonal relations in monitoring the changing prevalent clones in specific regions.

Antimicrobial peptides as an alternative to anti-tuberculosis drugs.

Tuberculosis (TB) presently accounts for high global mortality and morbidity rates, despite the introduction four decades ago of the affordable and efficient four-drugs (isoniazid, rifampicin, pyrazinamide and ethambutol). Thus, a strong need exists for new drugs with special structures and uncommon modes of action to effectively overcome M. tuberculosis. Within this scope, antimicrobial peptides (AMPs), which are small, cationic and amphipathic peptides that comprise a section of the innate immune system, are currently the leading potential agents for the treatment of TB. Many studies have recently illustrated the capability of anti-mycobacterial peptides to disrupt the normal mycobacterial cell wall function through various modes, thereby interacting with the intracellular targets, as well as encompassing nucleic acids, enzymes and organelles. This review presents a wide array of antimicrobial activities, alongside the associated properties of the AMPs that could be utilized as potential agents in therapeutic tactics for TB treatment.

Evaluation of MALDI-TOF MS for identification of nontuberculous mycobacteria isolated from clinical specimens in mycobacteria growth indicator tube medium.

Nowadays, there is a rising worldwide incidence of diseases caused by nontuberculous mycobacteria (NTM) species, especially in immunocompromised patients and those with underlying chronic pulmonary diseases. Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) became a method of choice for the identification of NTM species. The aim of this study was to evaluate MALDI-TOF MS for the identification of NTM isolates compared to the PCR-restriction enzyme analysis (PRA)-hsp65 method. In this study, a total of 152 NTM strains isolated from various clinical specimens were retrospectively analysed. MALDI-TOF MS successfully identified 148 (97.4%) of the 152 NTM isolates but failed to identify four (2.6%) of them. Bruker mycobacteria library gave spectral scores higher than 2.0 for 45 (29.6%) of NTM isolates, between 1.6 and 2.0 for 98 (64.5%) of NTM isolates, and lower than 1.6 for nine (5.9%) NTM isolates. The discordant results between MALDI-TOF MS and PRA-hsp65 analysis were confirmed by sequence analysis. In conclusion, MALDI-TOF MS is a technique capable of performing accurate, rapid, cost-effective, and easy identification of NTM isolates.

Are There Any Other Compounds Isolated From Dermacoccus spp at All?

Microbial-derived natural products have functional and structural diversity and complexity. For several decades, they have provided the basic foundation for most drugs available to modern medicine. Microbial-derived natural products have wide-ranging applications, especially as chemotherapeutics for various diseases and disorders. By exploring distinct microorganisms in different environments, small novel bioactive molecules with unique functionalities and biological or biomedical significance can be identified. Aquatic environments, such as oceans or seas, are considered to be sources of abundant novel bioactive compounds. Studies on marine microorganisms have revealed that several bioactive compounds extracted from marine algae and invertebrates are eventually generated by their associated bacteria. These findings have prompted intense research interest in discovering novel compounds from marine microorganisms. Natural products derived from Dermacoccus exhibit antibacterial, antitumor, antifungal, antioxidant, antiviral, antiparasitic, and eventually immunosuppressive bioactivities. In this review, we discussed the diversity of secondary metabolites generated by genus Dermacoccus with respect to their chemical structure, biological activity, and origin. This brief review highlights and showcases the pivotal importance of Dermacoccus-derived natural products and sheds light on the potential venues of discovery of new bioactive compounds from marine microorganisms.

Posttraumatic keratitis caused by Elizabethkingia meningosepticum.

OBJECTIVE: To present a case of bacterial keratitis caused by Elizabethkingia meningosepticum in an eye after trauma. METHOD: Case report. RESULT: A 45-year-old woman was referred to our cornea clinic for keratitis, which had developed following nonpenetrating eye trauma from a tree branch. Cultures from a corneal smear demonstrated heavy growth of E. meningosepticum. Treatment with a combination of topical moxifloxacin and topical trimethoprim/polymyxin B effectively controlled the corneal ulcer. Corneal infection resolved within 2 months, but a central corneal scar and vascularization remained. CONCLUSIONS: E. meningosepticum is an opportunistic bacterium and gives rise to severe systemic infections in immunocompromised patients. Ocular infections caused by this bacterium are extremely rare in the literature. To our knowledge, this is the first report of posttraumatic keratitis caused by E. meningosepticum.

Bacterial Pathogens: Potential Source For Antimicrobial Peptides.

As more antibiotics become ineffective due to drug-resistant bacteria, alternative therapies for infections must be prioritized. While pathogenic bacteria are a major threat, they also supply a massive reservoir of potential drugs for treating a wide range of illnesses. The concerning emergence of antimicrobial resistance and the rapidly dwindling therapeutic pipeline need the quick discovery and development of new antibiotics. Despite their great promise for natural product medicine development, pathogenic microorganisms have remained mostly unexplored and understudied. We review the antibacterial activity of specialized metabolites derived from pathogenic bacteria, emphasizing those presently in pre-clinical studies or with promise for medication development. Several atypical biosynthetic pathways are outlined, together with the crucial functions. We also discuss the mechanism of action and antibacterial activities of the antibiotics under consideration. Pathogenic bacteria as a rich source of antibiotics, along with recent advances in genomics and natural product research methods, may usher in a new golden age of antibiotic discovery.

Meropenem in combination with baicalein exhibits synergism against extensively drug resistant and pan-drug-resistant Acinetobacter baumannii clinical isolates in vitro.

Several studies have demonstrated that the effectiveness of carbapenems against drug-resistant Acinetobacter baumannii infections has been decreasing. Combination therapy with two or more drugs is currently under investigation to overcome the emerging resistance against carbapenems. In this study, we tested the possible synergistic interactions of a potent antibacterial flavonoid, baicalein, with meropenem to illustrate this duo's antibacterial and antibiofilm effects on 15 extensively drug resistant or pan-drug-resistant (XDR/PDR) A. baumannii clinical isolates in vitro. Isolates included in the study were identified with MALDI-TOF MS, and antibiotic resistance patterns were studied according to EUCAST protocols. Carbapenem resistance was confirmed with the modified Hodge test, and resistance genes were also analyzed with genotypical methods. Then, checkerboard and time-kill assays were performed to analyze antibacterial synergism. Additionally, a biofilm inhibition assay was performed for screening the antibiofilm activity. To provide structural and mechanistic insights into baicalein action, protein-ligand docking, and interaction profiling calculations were conducted. Our study shed light on the remarkable potential of the baicalein-meropenem combination, since either synergistic or additive antibacterial activity was observed against every XDR/PDR A. baumannii strain in question. Furthermore, the baicalein-meropenem combination displayed significantly better antibiofilm activity in contrast to standalone use. In silico studies predicted that these positive effects arose from inhibition by baicalein of A. baumannii beta-lactamases and/or penicillin-binding proteins. Overall, our findings highlight the prospective potential benefits of baicalein in combination with meropenem for the treatment of carbapenem-resistant A. baumannii infections.

Pseudomonas aeruginosa infections due to electronic faucets in a neonatal intensive care unit.

AIM: To evaluate the role of electronic faucets in a newborn intensive care unit during a Pseudomonas aeruginosa outbreak. METHODS: After three patients had P. aeruginosa bacteremia, environmental cultures including those from patient rooms, incubator, ventilators, total parenteral nutrition solutions, disinfection solutions, electronic and hand-operated faucet filters/water samples after removing filters and staff hands were taken. RESULTS: Only filters of electronic faucets and water samples after removing filters and one liquid hand soap showed P. aeruginosa (3-7 × 106 cfu/mL). We have removed the electronic faucets and new elbow-operated faucets were installed. Pulsed-field gel electrophoresis analysis of outbreak-blood culture isolates from two patients and isolates from electronic water faucets/one liquid hand soap indicated the presence of 90.7% genetically related subtype, probably from the same clone. Water cultures from new faucets were all clean after installation and after 7 months. CONCLUSION: We suggest that electronic faucets may be considered a potential risk for P. aeruginosa in hospitals, especially in high-risk units.

Evidence for antisense transcription associated with microRNA target mRNAs in Arabidopsis.

Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated "transitivity" (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 5' upstream and 3' downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways.

[Genotyping of Mycobacterium tuberculosis strains isolated from pulmonary tuberculosis patients in Cukurova Region, Turkey by spoligotyping and MIRU-VNTR methods]. / Çukurova Bölgesinde Akciger Tüberkülozlu Hastalardan Izole Edilen Mycobacterium tuberculosis Suslarinin Spoligotiplendirme ve MIRU-VNTR Yöntemiyle Tiplendirilmesi.

More rapid, and specific molecular diagnostic methods are required to understand the epidemiology of tuberculosis in the population and to establish effective control measures. Molecular epidemiologic studies about Mycobacterium tuberculosis are yet limited in Turkey. Cukurova (Eastern Mediterranean part of Turkey) region is of special importance in terms of tuberculosis epidemiology due to its neighbourhood countries and relatively high number of immigrants to that area. This study was aimed to determine the genotypic characteristics of M.tuberculosis strains isolated from pulmonary tuberculosis patients in Cukurova region, by spoligotyping and 12 loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Unit- Variable Number Tandem Repeats) methods. A total of 467 M.tuberculosis strains isolated from patients with pulmonary tuberculosis admitted to 20 hospital/dispansery in seven different provinces (Adana, Mersin, Osmaniye, Antakya, Gaziantep, Sanliurfa, Kahramanmaras) at Cukurova region between January 2007-June 2010, were included to the study. Genotypic identification was done by spoligotyping and 12 loci MIRU-VNTR methods. M.tuberculosis complex strains were isolated from different samples (sputum, bronchoalveolar lavage and biopsy material) by MGIT 960-TB (BD Diagnostics, USA) liquid culture method in Regional Tuberculosis Laboratory. Spoligotyping analysis revealed that 443 (94.9%) of the strains were clustered in 21 groups while 24 (5.1%) of the isolates were described as orphan strains according to SpolDB4 database. The most common families were T1 genotype seen in 239 (51.9%) strains and LAM7 TUR genotype seen in 54 (11.5%) strains. Six (1.3%) strains isolated from one province were multidrug resistant strains and belonged to Beijing family. Combination of spoligotyping with 12- locus MIRU-VNTR divided the T1 family into 7 clusters of which members ranged from 2-158. Twenty one isolates showed unique pattern. According to this study, T1 family is the most common genotype among M.tuberculosis strains in Cukurova, Turkey and the prevalence of M.tuberculosis Beijing strains was 1.3%, detected only in one province (Sanliurfa). Active surveillance studies are necessary to follow the regional dissemination of M.tuberculosis genotypes and establish effective precautions to prevent the spread of especially drug resistant strains.

Overexpression of Efflux Pumps AcrAB and OqxAB Contributes to Ciprofloxacin Resistance in Clinical Isolates of K. pneumonia.

BACKGROUND: Infection caused by multidrug-resistant K. pneumoniae is regarded as a severe public health concern worldwide, with most countries reporting an increase in fatality rates over time. Efflux pumps are significant determinants of acquired and/or intrinsic resistance in K. pneumoniae. OBJECTIVES: Our aim is to explore efflux-mediated resistance mechanisms in K. pneumoniae by using quantitative real-time PCR in order to evaluate the expression of efflux pump genes (acrA, acrB, oqxA, and oqxB) and pump regulators (marA, soxS, and rarA). METHODS: Efflux pump inhibitor CCCP reduced MIC values of ciprofloxacin by 2 to 64-fold in 43/46 (93%) of MDR-K. pneumoniae isolates. RESULTS: Compared to the control strain (untreated one), our results demonstrated that acrA, acrB, oqxA, oqxB, marA, soxS, and rarA were overexpressed in 29 (63%), 24 (52%), 29 (63%), 24 (52%), 17 (37%), 16 (35%), and 16 (35%) of K. pneumoniae isolates, respectively. Additionally, a positive correlation was established between the expressions of acrAB and marA (r = 0.50, r = 0.45, respectively) and oqxAB and rarA (r = 0.462912, r = 0.519354, respectively). CONCLUSION: Ciprofloxacin resistance was caused by overexpression of the efflux pump genes acrAB and oqxAB, as well as the transcriptional regulators marA, soxS, and rarA in clinical isolates of K. pneumonia.

Polysaccharides to Combat Viruses (COVID-19) and Microbes: New updates.

COVID-19, which is speedily distributed across the world and presents a significant challenge to public health, is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Following MERS coronavirus (MERS-CoV) and SARS, this is the third severe coronavirus outbreak in less than 20 years. To date, there are no exact agents and vaccines available for the treatment of COVID-19 that are clinically successful. Antimicrobial medications are effective in controlling infectious diseases. However, the extensive use of antibiotics makes microbes more resistant to drugs and demands novel bioactive agents' development. Polysaccharides are currently commonly used in the biomedical and pharmaceutical industries for their remarkable applications. Polysaccharides appear to have a wide range of anti-virus (anti-coronavirus) and antimicrobial applications. Polysaccharides are able to induce bacterial cell membrane disruption as they demonstrate potency in binding onto the surfaces of microbial cells. Here, the antiviral mechanisms of such polysaccharides and their success in the application of antiviral infections are reviewed. Additionally, this report provides a summary of current advancements of well-recognized polysaccharides as antimicrobial and anti-biofilm agents.