نشریه میکروب شناسی پزشکی ایران
سال هفدهم شماره 5 (مهر و آبان 1402)

Mycobacterium tuberculosis is the bacterium that causes tuberculosis. In this bacteria, long non-coding RNAs (lncRNA) can positively and negatively alter the expression of various genes through various mechanisms, such as activating transcription factors or binding to DNA targets of the chromatin complex. The  current study's purpose was to review the lncRNAs in M. tuberculosis.  The search was done with the keyword including lncRNAs, lncRNA, Long ncRNA, LincRNAs, Long ncRNA, long noncoding RNA, TB, Pulmonary Tuberculosis, Pulmonary TB, Mycobacterium tuberculosis in Pub Med, Web of Science Direct, Scopus, Scientific Information Databases, and Google scholar between 2000 and 2020. A total of 124 articles were found in PubMed,Science Direct, Scopus, Ovid,  Cochrane, and Google Scholar, of which 20  papers were selected from the databases. In revising the title and abstract, 84 articles were excluded from our study. Finally, 19 articles were included in our study, which included 4444 patients with tuberculosis. All studies were performed in China using the qRT-PCR method. The  present study's results showed an acceptable association between lncRNA and SNP with tuberculosis and M. tuberculosis. Also, these regulatory factors play an essential  role as diagnostic biomarkers and the development of new therapies.

Latent tuberculosis infection (LTBI) prevalence varies dramatically by region, with one-fourth of the world's population infected. The number of people with LTBI progressing to active tuberculosis illness (aTB) should be decreased to meet the WHO End TB Strategy objective of decreasing worldwide tuberculosis incidence by 2030. Current tuberculosis (TB) diagnostic methods are based on detecting an immune response to mycobacterial antigens injected into the skin or in vitro simulations in interferon-gamma release assays. Both tests have low sensitivity, which cannot distinguish between LTBI and aTB. Therefore, various techniques, such as alternate cytokine detection and employing novel antigens, are being studied to increase the accuracy of these tests.  In addition, novel antigens can be used to monitor aTB progression and response to treatment. This review aims to assess current available diagnostic tools and evidence on novel Mycobacterium tuberculosis (Mtb) antigens for LTBI diagnosis and select the most promising antigens for future research.

 The study aimed to detect SARS-CoV-2 using custom-designed primers in conventional PCR, targeting RdRp, E, and N genes, and assess regional isolate genetic diversity compared to global strains.

 In Sulaimani City, Iraq, from September 2020 to September 2021, 200 positive nasopharyngeal samples were collected, and 17 known variants with the S gene were randomly selected for whole RdRp, E, and N gene sequencing. To facilitate sequencing, six primer sets were designed for the RdRp gene (RdRp1, RdRp2, RdRp3), two for the N gene (N1, N2), and one for the E gene.

 Twelve mutations in the RdRp gene were identified, with the most common mutation being 14408C>T (P323L). In the N gene, a unique mutation, 28977C>T (S235F), was detected in eight samples of various variants alongside other amino acid-altering point mutations (28280-2GAT>CTA and 2881-3GGG>AAC). The E gene exhibited amino acid-altering mutations (S68F and I13L) in two samples. The most frequent mutation, 28977C>T (S235F), was identified in eight samples representing alpha, gamma, and cluster 5 variants.

 A novel mutation, specifically 28280-2GAT>CTA, resulting in D3L, along with three other mutations (28484G>A, 29129T>G, 29131T>C) causing amino acid substitutions (G70S, N284K, F285L) were identified in the N gene. Additionally, a unique mutation at 26281 A>T in the E gene was observed in the Wuhan variant.

 Helicobacter pylori is found in the stomach and the oral cavity, which plays a significant role in oral diseases and recurrent gastric infections. This study aimed to detect the presence of oral H. pylori and investigate its potential association with dental caries and erosion.

 Saliva and plaque samples were collected from two groups: a study group of 40 H. pylori-infected patients, confirmed by immunological tests, and a control group included 40 subjects who were given negative results after laboratory examination. Molecular detection of H. pylori was performed using the polymerase chain reaction (PCR). Additionally, clinical assessments of dental caries and erosions were conducted.

 The study group showed a higher prevalence of H. pylori in saliva (62.5%) compared to dental plaque (45.0%). Among the study group, 70% tested positive for H. pylori by PCR, while 30% tested negative. Dental caries experience (DMFS) was slightly higher in the study group compared to the control group, and significant differences in (DS) and (DMFT) (p<0.05). The prevalence of dental erosion was also higher in the study group compared to the control group.

 The presence of H. pylori in the oral cavity represents an important risk factor for dental caries and erosion.

 Children under five years are susceptible to being infected by Acute gastroenteritis (AGE) pathogens. Therefore, the main objective of the present research is to study the epidemiology and the etiology of AGE among children in Saudi Arabia.

 In this retrospective study, multiplex PCR was used to detect the gastroenteric viruses, including RoVA (Rotavirus A), NoVGI (Norovirus Group I), NoVGII (Norovirus Group II), HAstV (Human Astrovirus), EAdV (Enteric Adenovirus), and HEV (Human Enterovirus) in 92 stool samples collected from pediatric children aged ≤7 admitted to hospitals in Al-Ahsa province in Saudi Arabia, during December 2021 to June 2022.

 Out of the 92 samples tested, 63 (68.4%) showed positive results, indicating the presence of at least one gastroenteric virus infection. RoV group A was the most detected virus at 54%, followed by HAstV at 27%, EAdV at 22.2%, NoVGI at 9.5%, and HEV at 6.3%. Gastroenteric virus mono-infection was much higher than co-infection, at 79.3%. Children in the age group (1Y-2Y) were the most infected with viral AGE at 41.3% compared with other groups. Male children were more infected than females at 38%. The main viral AGE symptoms revealed in all positive children were diarrhea, vomiting, nausea, and fever, with rates of 100%, 95.2%, 92.1%, and 81%, respectively.

 Results demonstrated that the prevalence of gastroenteric infections among children is relevant and should be considered by the national health authority. This study is the first work conducted in the province of Al-Ahsa in Saudi Arabia. It could improve epidemiological and etiological data on children's AGE in the province.

 All Coxiella burnetii isolates carry one of four large, conserved, autonomously replicating plasmids or a plasmid-like chromosomally integrated sequence.

 In Sulaimani City, Iraq, from September 2020 to September 2021, 200 positive nasopharyngeal samples were collected, and 17 known variants with the S gene were randomly selected for whole RdRp, E, and N gene sequencing. To facilitate sequencing, six primer sets were designed for the RdRp gene (RdRp1, RdRp2, RdRp3), two for the N gene (N1, N2), and one for the E gene.

 In total, out of 400 milk samples collected from cow, buffalo, sheep, and goats based on the IS1111 gene, 62 (15.5%), (95% CI: 12.3%–19.4%) samples were positive for C. burnetii. Out of 62 positive samples, 16 (25.8%), (95% CI: 16.6%–37.9%) samples contained QpH1 plasmid gene and 5 (8%), (95% CI: 3.5%–17.5%) samples contained QpRS plasmid gene. Also, there were 7 (11.3%), (95% CI: 5.6%–21.5%) positive samples for QpDG and 5 (11.3%), (95% CI: 3.5%–17.5%) positive to QpDV gene. The Phylogenetic analysis of plasmid sequences showed that all obtained sequences have 100% similarity. A phylogenetic tree constructed based on neighbor-joining analysis of partial genes revealed that 20 sequenced isolates were closely clustered together showing 99.9% similarity which can be considered identical and also revealed the 100% similarly of these sequences with more sequences in the gene bank from different sources.

 Our results indicated that nested PCR has high sensitivity in detecting plasmids.

 Methicillin Resistance Staphylococcus aureus (MRSA) causes staph infections, produces numerous toxins and virulence factors, and displays antibiotic resistance. Therefore, this study aimed to detect MRSA and its antibiotic-resistant patterns and evaluate the toxins genes in S. aureus isolates from Baghdad, Iraq.

 Two hundred twenty bacterial samples were collected from different clinical sources in Iraq, 2022-2023. The diagnosis was made using traditional culture, microscopic examinations, and molecular diagnosis using the 16srRNA gene and mecA gene used for Methicillin Resistance detection. In addition, Antibiotic resistance patterns were detected using VITEK-2. Also, the toxins genes were determined by sequencing.

 Fifty isolates were identified as S. aureus, and the strains showed high resistance to Benzylpenicillin, Erythromycin, Oxacillin, and Clindamycin. PCR showed a prevalence of the mecA gene in methicillin resistance S. aureus isolates by 100%, while toxin genes that were present in S. aureus were LukD/E gene 50(100%), eta gene 50(100%), etd gene 47(94%), LukS/F gene 34(68%) and tst gene 21(42%). All isolates tested negative for the etb gene. The results of the sequencing analysis of the studied genes showed that there were no genetic mutations. They were 100% identical except for the eta gene, and the results indicated three genetic mutations.

 All S. aureus isolates had the mecA gene for methicillin resistance, and S. aureus possessed toxin genes. The sequencing analysis of the eta gene indicated the presence of various mutations, including the silent mutations.

 Antibiotic resistance is recognized as a major threat to global health that can result in increased morbidity and mortality. On February 27, 2017, the first list of antibiotic-resistant priority pathogens was published by the World Health Organization (WHO). These pathogens, including Pseudomonas aeruginosa, pose the greatest threat to human health. This research was conducted in order to introduce viable candidate vaccine proteins against P. aeruginosa outer membrane proteins (OMPs) using reverse vaccinology approaches.

 Fifty-eight clinical isolates and 9982 outer membrane protein sequences were retrieved for vaxign2 calculation of sequence-derived features. First, 30 proteins with the highest adhesion probability were selected, and in the next step, 10 candidates common among the 58 strains with the highest scores were introduced as candidates for further studies. After determining the physicochemical characteristics of these vaccine candidates, the presence of protected domains was predicted in 2 out of 10 proteins.

 Based on the results obtained from the bioinformatics analysis of the antigenic properties of these proteins, we identified 10 outer membrane proteins that have the highest antigenic scores, are common among all 58 clinical isolates, have no human protein homologs, and have less than 1 transmembrane helix. These candidate proteins have optimal physicochemical properties. The presence of conserved domains was predicted only in the outer membrane porin F and enterobactin iron receptor.

 We suggested 10 candidate proteins that showed suitable characteristics including outer membrane protein F (OprF) and ferric enterobactin receptor.

 Proteus vulgaris, a Gram-negative bacterium, is a common cause of human infections, particularly urinary tract infections (UTIs). This study aimed to assess the multidrug resistance patterns of Proteus vulgaris isolated from diverse clinical samples, shedding light on its impact on healthcare-associated infections.

 In this cross-sectional study, 300 clinical samples were collected, including 100 urine samples, 50 wound samples, 50 vaginal samples, 50 blood cultures, and 50 sputum samples. All samples were selected in the same number (50:50), except the urine samples (100) because the urine samples in this study were more available in the collection from the study patients, which gave more advanced UTIs. Phenotypic and molecular techniques were employed to identify and characterize these bacteria, focusing on detecting resistance genes such as UreC and blaCTX-M.

 Among the 300 clinical samples, 150 yielded positive cultures for Proteus species. These isolates were obtained from various clinical samples, including 48% from urine, 32% from wounds, 10% from vagina, 8% from blood, and 2% from sputum. Of the 100 P. vulgaris isolates, 88% harbored resistance genes on chromosomal DNA and plasmids. Specifically, 75% carried the UreC gene, and 50% carried the blaCTX-M gene. The highest prevalence of these resistant genes was observed in urine and wound pus samples.

 This study revealed a concerning prevalence of highly resistant multidrug-resistant (MDR) P. vulgaris isolates, particularly in female urinary tract infections. The genomic presence of the UreC gene, which encodes the urease enzyme, and the blaCTX-M gene, which confers resistance to cefotaxime, underscores the urgency of effective antimicrobial strategies in combating these infections.

 Antibiotic resistance has a major contribution to human health. As reported in 2009, Indonesia ranked 8th out of 27 countries with the highest MDRO rate in the world. To determine the risk factors of infection due to MDROs at Dr.M.Djamil General Hospital in sepsis patients, it is necessary to identify the factors that cause MDROs; thus, effective prevention and control methods can be planned.

 This was a cross-sectional study conducted on 101 patients with 124 isolates diagnosed with sepsis who were treated at Dr.M.Djamil General Hospital. The characteristics and factors associated with MDROs in sepsis patients were recorded for each subject. Then, a bacterial culture examination was performed with blood culture and other cultures depending on the focus of infection. A descriptive analysis was conducted to analyze the frequency distribution of each research variable. Bivariate analysis was performed to determine the relationship between each variable and infection due to MDROs in sepsis patients, and multivariate logistic regression analysis was performed to find the most dominant variable.

 History of antibiotic use (P<0.05) and urinary catheter use (P<0.05) had a significant correlation with infection due to MDROs, and urinary catheter use and history of antibiotic use were the strongest risk factors associated with infection due to MDROs in sepsis patients admitted to Dr.M.Djamil General Hospital. Antibiotics should be used wisely and rationally in managing infectious patients, and the use of urinary catheters should be done more selectively for inpatients to prevent the development of MDROs as a cause of infection.

 WHONET software is a database for analyzing microbiology data, specifically antibiotic resistance patterns. Pseudomonas aeruginosa is a significant agent of nosocomial infections and has been identified as a critical priority by the World Health Organization (WHO). The aim of this study was to monitor the resistance patterns of imipenem and meropenem over one year (February 2022-February 2023) using WHONET software 2022.

 A total of 95 P. aeruginosa isolates were obtained from Kowsar Hospital in Sanandaj, Iran. After verification through biochemical tests and 16sRNA PCR, an antibiogram test was performed for each isolate based on The Clinical & Laboratory Standards Institute (CLSI) guidelines. Data were analyzed using WHONET 2022.

 Pseudomonas aeruginosa isolates were obtained from 44 females and 51 males. Of all isolates, the WHONET analysis showed that resistance to imipenem and meropenem was 87.4% and 64.2%, respectively. The WHONET database can be an appropriate software for analyzing and monitoring bacterial susceptibility and resistance, especially for critical priority bugs such as P. aeruginosa.

 Blueberries, scientifically known as Vaccinium corymbosum L., contain various secondary metabolites such as flavonoids and phenolic acids. These compounds are recognized for their potential in preventing cancer and antimicrobial properties.

 The extract's antibacterial activity was assessed using the time-killing assay, while its anticancer activity was evaluated using the MTT assay.

 The findings from the antibacterial tests revealed that the fruit extracts exhibited minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) at concentrations of 3.5-4.2 mg/mL and 5.6-5.9 mg/mL, respectively. Furthermore, the MTT assay demonstrated that the blueberry extract displayed cytotoxic effects on cancer cell lines (HeLa and MCF7), while it showed no significant cytotoxicity on normal cells (L929). Treatment with the unripe blueberry fruit extract significantly decreased the viability of cancer cells compared to the other extracts. Specifically, the highest level of cellular toxicity among all extracts was observed in the HeLa cancer cell line at a concentration of 1.5 mg/L after 72 hours (more than 90%). Based on these findings, it can be concluded that blueberry fruit extract possesses enhanced antibacterial and anticancer properties. Moreover, this study indicated that the early stages of fruit growth exhibit greater cytotoxic effects against cancer and bacterial cells. These results significantly affect the food, pharmaceutical, and plant biotechnology industries.