Jundishapur Journal of Microbiology
Year:2020 | Volume:13 | Issue:6|Papers Count:9

Background: Approximately 3% of the population worldwide is infected with Hepatitis C Virus (HCV). Different regimens have been used to treat HCV, each of which has its side effects and efficacy. Sofosbuvir, a direct-acting antiviral drug, has replaced all previous regimens with the highest response rate. However, its response is not fully covered in Pakistan, especially Khyber Pakhtunkhwa. Objectives: The study aimed to examine the response to Sofosbuvir and Ribavirin combination therapy in chronic HCV patients infected with various HCV genotypes. Methods: This study was conducted in Tertiary Care Hospitals, Peshawar, Pakistan. The patients were enrolled from January 2016 to March 2017. A total of 80 patients (57 naï ve and 23 non-responder) were enrolled in this study. The age range was 16-70 years, and the mean age was 36 2 years. Genotyping, biochemical profile, PCR tests, and liver ultrasounds were done for all of the enrolled subjects at the start and end of therapy. All patients were given direct-acting antiviral drugs for six months and then, the end of treatment response was noted. Results: A total of 80 subjects with HCV infection took part in the study, including 57 (71. 25%) treatment-naï ve and 23 (28. 75%) treatment non-responding patients. The end of therapy response was reported after 24 weeks of treatment. Among the 80 patients, 72 (90%) patients achieved the end of therapy response. The highest end of therapy response (100%) was noted in genotype 1 and mixed genotypes and patients with normal liver ultrasound. The lowest end of therapy response (70%) was found in un-type genotype and patients with an abnormal texture of liver ultrasound. The end of therapy response rate was higher in females than in males. Conclusions: In the current study, the minimal response was found in un-type genotypes and genotypes that did not respond to INF, as compared to treatment-naï ve subjects. Further research is needed to understand the relevant host and viral factors, with particular attention to relapsed patients and non-responders that are difficult to treat in the Pakistani population.

Background: Nosocomial infections are acquired during hospital treatment or in a hospitalenvironment. Onesuch infecting agent is uropathogenic Escherichia coli and many virulence genes enable it to become pathogenic, thereby causing damage to the host. Objectives: This study aimed to identify aer, traT, and PAI genes in E. coli isolates collected from fecal and urinary tract infection (UTI) specimens and determine the relationship between them in both populations studied in a center in Iran by multiplex polymerase chain reaction (PCR) assay. Methods: Seventy-five isolates of E. coli from the urine of inpatients and 75 isolates from commensal fecal without UTI and diarrhea were collected. The E. coli bacteria were detected and isolated, using biochemical techniques and supplementary tests in the Microbiology Laboratory of Shahrekord University of Medical Sciences. Antibiotic susceptibility pattern for 14 antibiotics was done utilizing the disc diffusion method. The existence of aer, traT, and PAI virulence genes among all isolates was investigated by multiplex PCR. Results: Among the urinary pathogenic E. coli isolates, the highest antibiotic resistance was observed in cefazolin, ampicillin, and cotrimoxazole antibiotics. The prevalence rates of aer, traT, andPAI genes in the fecal isolates were 92%, 90. 6%, and46. 6%, respectively. Further, their prevalence rates in urine isolates were 96%, 97. 3%, and 41. 3%, in that order. Conclusions: The presence of the high frequency of pathogenic islands (PAIs), especially in fecal samples, is important because these genes are easily transmitted and convert a commensal bacterium into a pathogen. Because only the genome of pathogenic bacteria has been unwrapped, little attention has been paid to PAIs in commensal bacteria.

Context: Neisseria meningitidis is the causative agent of a life-threatening infection with high mortality and morbidity worldwide. The most common types of this bacterium are serogroups A, B, C, W135, X, and Y. Although in some countries, such as Iran, the meningococcal meningitis has been well monitored and controlled by the use of divalent and quadrivalent vaccines, other fatal infections caused by these bacteria are still an important threat. For the above reason, this review focused on the differences of Neisseria characteristics, particularly in capsular composition, pathogenic and commensal stages to a better understanding of how to manage Neisseria infections. Evidence Acquisition: In this review, PubMed, EMBASE, ScienceDirect, Scopus, and Google Scholar were searched for Englishlanguage publications on pathogenic or commensal strains of Neisseria, meningococcal disease, Neisseria biology, genetic diversity, molecular typing, serogroups, diagnostic, and epidemiology around the world up to July 2019. All articles and academic reports in the defined area of this research were considered too. The data were extracted and descriptively discussed. Results: We included 85 studies in the survey. The data analysis revealed that the distribution of meningococcal serogroups was different regionally. For example, the serogroups C and W-135 accounted for Africa and Latin America regions, serogroup B in the European countries, and rarely in theWestern Pacific, and serogroups A and C were dominant in Asian countries. Although data set for laboratory-based diagnosis of N. meningitidis are available for all countries, only 30% of the countries rely on reference laboratories for serogroup determination, and more than half of the countries lack the ability of surveillance system. Nevertheless, molecular detection procedure is also available for all countries. The use of the meningococcal vaccine is a variable country by country, but most countries have applied the meningococcal vaccine, either divalent or quadrivalent, for the protection of high-risk groups. Conclusions: Owing to the geographical distribution of N. meningitidis serogroups in circulating, each country has to monitor for changes in serogroups diversity and its control management. Furthermore, laboratories should scale up the epidemiology and disease burden. It should be mentioned that quadrivalent meningococcal vaccines reduce the meningococcal disease burden sharply.

Background: GyrA and gyrB genes encodeDNAgyrase subunits. This enzymeregulatesDNAsupercoiling. Inhibitors of this enzyme, such as ciprofloxacin, may change the level of supercoiling and the expression level of genes, including gyrA and gyrB. Objectives: The aims of this research were first to select some transcription factors, which regulate the expression of gyrA and gyrB. Secondly, the effect of these transcription factors was investigated on the expression of these genes in Escherichia coli mutants with different levels of resistance to ciprofloxacin in the presence and absence of these transcription factors. Methods: For this purpose, the online software called Promoter Analyzer in Virtual Footprint version 3 was used to find and select some transcription factors. The relative expression of genes was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Results: Theoretical results showed that CspA, FhlA, and SoxS transcription factors (with a score of match higher than 6), could be selected for further analysis. The expression of gyrA and gyrB genes remained unchanged in the presence and absence of CspA and FhlA transcription factors following exposure to the low amount of ciprofloxacin. However, SoxS transcription activator might have indirect effects on the expression of these genes, as soxS gene was overexpressed following treatment with a higher amount of ciprofloxacin. Conclusions: It is concluded that overexpression of gyrA and gyrB genes is not dependent on CspA and FhlA transcription factors, but may be dependent indirectly on regulatory proteins involved in oxidative stress following exposure to ciprofloxacin.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) has emerged as a significant pathogen in community and hospital environments and is associated with high mortality and morbidity. Both polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) methods are sensitive and acceptable molecular methods for the diagnosis of infectious diseases. Objectives: This study aimed to develop detection assays for Staphylococcal mecA and spa using multiplex PCR and LAMP. Methods: Both methods were standardized, and detection limits were determined using serial dilutions of S. aureus DNA samples. Fifty-three clinical isolates of S. aureus were confirmed to the species level using biochemical tests and multiplex PCR and multiplex LAMP for the spa gene, while disk diffusion, minimum inhibitory concentration, and detection of mecA genes were used for the assessment of methicillin resistance. Results: The PCR could detect the mecA and spa genes at 1 fg/mL and 10 fg/mL of bacterial DNA, which were equal to 35 and 350 gene copy numbers, respectively. Similarly, multiplex LAMP detected the spa and mecA genes at 0. 1 fg/mL and 1 fg/mL of bacterial DNA, which were equal to 3. 5 and 35 genome copy numbers, respectively. According to MIC and disk diffusion methods, four (7. 54%) cases were oxacillin-sensitive methicillin-resistant S. aureus, 16 isolates were methicillin-sensitive, and 37 isolates were methicillinresistant. According to multiplex PCR, 47. 75% of the isolates were mecA-positive while in multiplex LAMP, 41 (35. 77%) isolates were mecA-positive. Conclusions: The sensitivity and specificity of the multiplex LAMP were higher than those of multiplex PCR and biochemical methods. Thus, we can apply the LAMP for the routine detection of MRSA.

Background: Infertility is one of the serious problems in gynecology and one of the most important issues of concern in couples. Meanwhile, a significant rise in infertility is recently reported in Iran due to the infections and harsh environmental conditions. Objectives: The current study aimed to detect Chlamydia trachomatis and Listeria monocytogenes in males with infertility using PCR, and to evaluate bacteriospermia effects of the studied bacteria on semen parameters. Methods: Semen specimens of 100 infertile men were collected. Then, each specimen was divided into two parts: the first part was tested by semen analysis according to the WHO guidelines and the second was tested using the PCR method. The PCR intended to identify C. trachomatis and L. monocytogenes. Results: Out of 100 semen samples, 20% were positive for C. trachomatis, 3% were positive for L. monocytogenes, and 3% were positive for both bacteria (co-infection). The leukocyte count was higher than the normal range (0-1 Mil/mL) in all semen specimens. The prevalence of C. trachomatis in azoospermic patients was significantly higher than that of nonazoospermic (P < 0. 05). However, there was no significant difference between the two groups in terms of the detection of L. monocytogenes (P > 0. 05). Detection of C. trachomatis and L. monocytogenes had no significant association with abnormal semen parameters in asymptomatic patients (P > 0. 05). Conclusions: The results indicated that precise analysis of semen parameters and diagnosis of leukocytospermia in patients using the PCR can be considered as a rapid and accurate technique to detect bacteria such as C. trachomatis and L. monocytogenes in semen specimens. Therefore, the utilization of this technique in the screening programs for asymptomatic infertile couples can be helpful for early treatment.

Background: Cryptosporidium species are recognized as one of the most important gastrointestinal pathogens of humans and livestock. Objectives: This study aimed to determine the prevalence and sub-genotypes of Cryptosporidium spp. among diarrheic patients in Bandar Abbas City, Iran. Methods: Diarrheic fecal samples were collected from 170 patients in three hospitals of Bandar Abbas, Iran, from October 2018 to May 2019. Initial parasitological identification of Cryptosporidium spp. was performed by modified Ziehl-Neelsen (ZN) staining. For molecular analysis, the positive specimens and the suspected ones of Cryptosporidium spp. were evaluated by sequence analysis of the 60-kDa glycoprotein gene (gp60). The collected data were analyzed using SPSS software and the relationship between the variables and the presence of Cryptosporidium spp. assessed by the chi-square test. To assess the degree of agreement between PCR and ZN staining, Cohen’ s kappa-index was applied. Results: Of the 170 diarrheic patients, 98 (57. 6%) were male, and 72 (42. 4%) were female. Prevalence of Cryptosporidium spp. by parasitological examination was 1. 8% (3/170). However, using PCR, Cryptosporidium spp. was detected in 12% (6/50) of the positive microscopically samples (3 samples) and 47 suspected specimens. Sequence analysis of the gp60 gene showed that all of the positive isolates were Cryptosporidium parvum in which all subtypes belonged to allele family IId. Twodistinct nucleotide sequences obtained from this study were deposited in GenBank under the accession numbers MN820453 and MN820454. Conclusions: The predominance of C. parvum (subtype family IId) in this study emphasizes the importance of zoonotic Cryptosporidium transmission in Bandar Abbas, Southern Iran.

Background: Helicobacter pylori is an important pathogen in the upper digestive tract. It is of great significance to properly understand the risk factors for the transformation of Barrett esophagus into esophageal carcinoma. However, the relationship between H. pylori and gastroesophageal reflux disease (GERD) and Barrett esophagus remains controversial, and the correlation with immune function has been rarely reported. Objectives: This study investigated the effect of H. pylori infection on Barrett esophagus and its correlation with immune function. Methods: We recruited 40 patients with Barrett esophagus (Barrett esophagus group) and 40 patients with GERD (GERD group). In addition, 40 healthy controls were selected for the control group. Esophageal function and its correlation with immune function were measured in each group. Results: The positivity rate of H. pylori (P< 0. 05)andsphincter pressure were lower in both Barrett esophagusandGERDgroups than in the control group, while the levels of PGI, PGII, PGI/II, and G-17 were higher (P < 0. 05). The levels of CD3+, CD4+, and CD4+/CD8+ were lower in the Barrett esophagus group than in the GERD group, but they were negatively correlated (P < 0. 05) with H. pylori infection. The level of CD8+ was higher in the Barrett esophagus group, and it was positively correlated (P < 0. 05) with H. pylori infection. Conclusions: Helicobacter pylori infection may protect against Barrett esophagus by reducing gastric acid secretion and increasing lower esophageal sphincter pressure. Besides, it has a certain correlation with immune function.

In December 2019, in Wuhan, China began the outbreak of the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) epidemic. As a result of rapid spread, it turned into a pandemic announced by WHO on March 11, 2020. SARS-CoV-2 is an etiological factor of a new disease called COVID-19. The virus is transmitted mainly through the droplet route. In most cases, it causes mild symptoms such as fever, dry cough, weakness, and muscle pain; less common symptoms include sore throat, runny nose, diarrhea, and chills. However, among people with impaired immunity and comorbidities, as well as among older people, it leads to lifethreatening complications in the form of acute respiratory distress syndrome (ARDS), sepsis, and septic shock. Moreover, SARS-CoV-2 is the third highly pathogenic in humans and easily spreading coronavirus after the virus of a severe acute respiratory syndrome (SARS) in 2002-2003 and virus of the Middle East respiratory syndrome (MERS) in 2012. This review summarizes current information on the emergence, origin, diversity, and common characteristics, as well as the epidemiology of the above three highly contagious coronaviruses.