The role of the major viral pathogens in a respiratory disease outbreak of broiler flocks in Eastern Iran.

Background: Infectious bronchitis virus (IBV), Newcastle disease virus (NDV), and avian influenza virus (AIV) H9N2 are major viral pathogens in broiler respiratory disease. Aims: Following a respiratory disease outbreak and economic losses in eastern Iran 2020-2021, we investigated the role of major viral pathogens and the implemented vaccination programs. Methods: Thirty-six respiratory disease affected broiler flocks in South Khorasan province were sampled, molecularly tested, and coinfections were investigated. The vaccination programs were obtained and the detected IBV were genotyped. Results: IBV, virulent NDV, and AIV H9N2 were detected in twenty-five, seven, and seven flocks, respectively. IBV+AIV, IBV+NDV, and NDV+AIV coinfections were respectively detected in six, five, and one flocks. Most IBV infected flocks (84%) had been immunized with a live IBV-Mass vaccine. All NDV infected flocks and 14.2% of AIV infected flocks had been vaccinated. IBV genotyping showed a high prevalence of variant 2 (83.3%), followed by Mass-type (12.5%), and Q1-type (4.2%). Variant 2 IB viruses were widely distributed in the province and half of them were mostly similar to the ones that had been detected in northern neighboring province, Khorasan Razavi. Conclusion: Single infection with variant 2 IBV was a major cause of the respiratory disease outbreak in which use of the Mass vaccine was probably not effective. The high coverage and multiple doses of vaccination against Newcastle disease possibly had reduced the prevalence of NDV. Considering the regional origin of IBV strains, strong biosecurity measures should be implemented and vaccination programs using appropriate vaccine strains should be used.

Bifidobacteriaceae Family Diversity in Gut Microbiota of Patients with Renal Failure.

Bifidobacteriaceae family are gut microbiota that exhibit probiotic or health promoting effects on the host. Several studies have suggested that gut microbiota are quantitatively and qualitatively altered in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD). The present study aimed to assess the members of Bifidobacteriaceae family in fecal samples of patients with CKD and ESRD and compare them with non-CKD/ESRD patients to find any changes in their counts and diversions in these patients. Twenty fresh fecal samples from patients with CKD/ESRD and twenty from non-CKD/ESRD patients were examined. Whole DNA was extracted from fecal samples and the gut microbiota composition was analyzed by next generation sequencing (NGS). A total of 651 strains were identified from 40 fecal samples, 8 (1.23%) strains of which were identified as family Bifidobacteriaceae. The most abundant species in both control and disease groups were Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum, and the least abundant species in the disease group was Bifidobacterium animalis subsp. lactis. There was no significant difference in the abundance of various species between the disease and control groups (p < 0.05). This study confirms that the members of the Bifidobacteriaceae family are not altered in patients with CKD/ESRD.

Genotyping of Mycobacterium tuberculosis isolates from northwest Iran for determination on the mechanism of transmission.

Planning to control tuberculosis requires identification of dominant strains in the region, transmission patterns and risk factors that are possible by using molecular genotyping techniques. The aim of this study is to determine the transmission of tuberculosis in the northwest of Iran in order to better understand the spread of disease in northwest of Iran. In this study, 194 positive mycobacterium cultivars in northwest of Iran were investigated using exact tandem repeat-variable number tandem repeats (ETR-VNTR) method. The ETR-VNTR method was identified 55 different patterns in 194 isolates, which contained 25 clusters and 30 unique patterns, and the largest cluster had 33 isolates, and discriminatory power of ETRVNTR method was determined 0.9322 in the examined samples. There are strains of Mycobacterium tuberculosis located in the northwest of Iran that infect people, and ETRVNTR method can be used as a first-line method to examine the dynamics of tuberculosis transmission.

Genotyping of Mycobacterium tuberculosis isolates from northwest Iran for determination on the mechanism of transmission

@#Planning to control tuberculosis requires identification of dominant strains in the region, transmission patterns and risk factors that are possible by using molecular genotyping techniques. The aim of this study is to determine the transmission of tuberculosis in the northwest of Iran in order to better understand the spread of disease in northwest of Iran. In this study, 194 positive mycobacterium cultivars in northwest of Iran were investigated using exact tandem repeat-variable number tandem repeats (ETR-VNTR) method. The ETR-VNTR method was identified 55 different patterns in 194 isolates, which contained 25 clusters and 30 unique patterns, and the largest cluster had 33 isolates, and discriminatory power of ETRVNTR method was determined 0.9322 in the examined samples. There are strains of Mycobacterium tuberculosis located in the northwest of Iran that infect people, and ETRVNTR method can be used as a first-line method to examine the dynamics of tuberculosis transmission.

Thymol and carvacrol strongly inhibit biofilm formation and growth of carbapenemase-producing Gram negative bacilli.

Discovery of novel drugs with new mechanisms of action and without cross-reaction with current therapeutic agents is crucial in the management of infections caused by multi-drug resistant (MDR) bacteria. The aim of the present study was to investigate effects of carvacrol and thymol on biofilm formation and antimicrobial activity against different carbapenemase-producing Gram negative bacilli. The antimicrobial and antibiofilm effect of thymol and carvacrol was investigated against strains harboring different genes related to carbapenemase resistance. Antimicrobial resistance was examined by an agar dilution method and antibiofilm effect was evaluated by microtiter plate assay and staining by crystal violet. Thymol and carvacrol had antibacterial effects ranging from 200-1600 µg/mL and 62-250 µg/mL respectively, and antibiofilm effect from 125-500 and 400-1600 µg/mL respectively. Seoul imipenemase- (SIM) producing isolates had the highest sensitivity, and NDM (New Delhi metallo-beta-lactamase) producing isolates had the lowest sensitivity to these components. Findings of the present study indicated a potential role of carvacrol and thymol in controlling carbapenemase-producing gram negative bacterial infections. These findings helped to develop herbal drugs for replacing antibiotics. In addition, their antibiofilm effects showed that carvacrol and thymol inhibit biofilm formation of carbapenemase-producing strains.

Suppressing the CRISPR/Cas adaptive immune system in bacterial infections.

Clustered regularly interspaced short palindromic repeats (CRISPR) coupled with CRISPR-associated (Cas) proteins (CRISPR/Cas) are the adaptive immune system of eubacteria and archaebacteria. This system provides protection of bacteria against invading foreign DNA, such as transposons, bacteriophages and plasmids. Three-stage processes in this system for immunity against foreign DNAs are defined as adaptation, expression and interference. Recent studies suggested a correlation between the interfering of the CRISPR/Cas locus, acquisition of antibiotic resistance and pathogenicity island. In this review article, we demonstrate and discuss the CRISPR/Cas system's roles in interference with acquisition of antibiotic resistance and pathogenicity island in some eubacteria. Totally, these systems function as the adaptive immune system of bacteria against invading foreign DNA, blocking the acquisition of antibiotic resistance and virulence factor, detecting serotypes, indirect effects of CRISPR self-targeting, associating with physiological functions, associating with infections in humans at the transmission stage, interfering with natural transformation, a tool for genome editing in genome engineering, monitoring foodborne pathogens etc. These results showed that the CRISPR/Cas system might prevent the emergence of virulence both in vitro and in vivo. Moreover, this system was shown to be a strong selective pressure for the acquisition of antibiotic resistance and virulence factor in bacterial pathogens.

Strain differentiation of Mycobacterium tuberculosis for epidemiology in northwest of Iran.

Tuberculosis is a major health problem throughout the world and there are still a great number of people with the disease. Planning for controlling tuberculosis is required to identify the sources of infection and screening for the disease. The aim of this study is the differentiation of Mycobacterium tuberculosis strains for better understands the spread of the disease in North West Iran. In this study, 194 positive cultures of M. tuberculosis in North West Iran were evaluated by the MIRU-VNTR method. MIRU-12 differentiated the 194 isolates into 138 different patterns, comprising 30 clusters and 108 unique patterns (HGDI=0.9930). The largest cluster contained twelve isolates. The results showed that the majority of TB cases in North West Iran are due to reactivation and the 12-MIRU typing method can be used as a first-line method for strain differentiation of M. tuberculosis.

Molecular fingerprinting of meticillin-resistant Staphylococcus aureus strains isolated from patients and staff of two Iranian hospitals.

Meticillin-resistant Staphylococcus aureus (MRSA) is an important cause of hospital-acquired infection. Methods for typing and epidemiological investigation of MRSA isolates have an important impact in detection of MRSA strains, source, transmission and control of these micro-organisms. The aims of this study were to study molecular diversity of MRSA isolates by randomly amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR), the surveillance efficacy of this method and determination of antibiotic resistance patterns of MRSA isolates. MRSA isolates were collected from clinical specimens and noses of 460 staff and inpatients admitted to Imam Khomeini and Paediatric Hospitals during a six-month period (2004-2005). Eighty MRSA strains, in which the presence of mecA gene had been confirmed by PCR, were subjected to RAPD-PCR using five primers and the results were summarised in a dendrogram to show the relationships between the test isolates. Antibiotic resistance patterns of MRSA isolates were also determined by disc agar diffusion method using 13 antibiotic discs according to Clinical and Laboratory Standards Institute guidelines. Forty-three RAPD-PCR profiles were detected. The test isolates were clustered into 18 taxa with 50% similarity, indicating the heterogeneity of our test isolates. MRSA isolates fell into 41 antibiotic resistance patterns. There was correlation between antibiotic resistance patterns and results of RAPD-PCR. Most of the MRSA isolates were multi-resistant.