Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection.

BACKGROUND: Escherichia coli (E. coli) is a multidrug resistant opportunistic pathogen that can cause secondary bacterial infections in patients with COVID-19. This study aimed to determine the antimicrobial resistance profile of E. coli as a secondary bacterial infection in patients with COVID-19 and to assess the prevalence and characterization of genes related to efflux pumps and porin. METHODS: A total of 50 nonduplicate E. coli isolates were collected as secondary bacterial infections in COVID-19 patients. The isolates were cultured from sputum samples. Confirmation and antibiotic susceptibility testing were conducted by Vitek 2. PCR was used to assess the prevalence of the efflux pump and porin-related genes in the isolates. The phenotypic and genotypic evolution of antibiotic resistance genes related to the efflux pump was evaluated. RESULTS: The E. coli isolates demonstrated high resistance to ampicillin (100%), cefixime (62%), cefepime (62%), amoxicillin-clavulanic acid (60%), cefuroxime (60%), and ceftriaxone (58%). The susceptibility of E. coli to ertapenem was greatest (92%), followed by imipenem (88%), meropenem (86%), tigecycline (80%), and levofloxacin (76%). Regarding efflux pump gene combinations, there was a significant association between the acrA gene and increased resistance to levofloxacin, between the acrB gene and decreased resistance to meropenem and increased resistance to levofloxacin, and between the ompF and ompC genes and increased resistance to gentamicin. CONCLUSIONS: The antibiotics ertapenem, imipenem, meropenem, tigecycline, and levofloxacin were effective against E. coli in patients with COVID-19. Genes encoding efflux pumps and porins, such as acrA, acrB, and outer membrane porins, were highly distributed among all the isolates. Efflux pump inhibitors could be alternative antibiotics for restoring tetracycline activity in E. coli isolates.

Anti H. pylori, anti-secretory and gastroprotective effects of Thymus vulgaris on ethanol-induced gastric ulcer in Sprague Dawley rats.

The objectives of the present study were to evaluate the acute toxicity, gastroprotective, therapeutic, anti-inflammatory and anti H. pylori activities of T. vulgaris total plant extract against ethanol-induced gastric ulcers in Sprague Dawley rats. Animals were divided into five groups i.e G-1 (Normal Control), Group 2 (ulcer control) were administered orally with 0.5% Carboxymethylcellulose (CMC), Group 3 (omeprazole treated) was administered orally with 20 mg/kg of omeprazole and Groups 4 and 5 (Low dose and High dose of the extract) were administered orally with 250, and 500 mg/ kg of Thymus vulgaris extract, respectively. After 1 hour, the normal group was orally administered with 0.5% CMC (5 ml/kg), whereas absolute alcohol (5ml/ kg) was orally administered to the ulcer control group, omeprazole group, and experimental groups. Stomachs were examined macroscopically and microscopically. Grossly, rats pre-treated with T. vulgaris demonstrated significantly decreased ulcer area and an increase in mucus secretion and pH of gastric content compared with the ulcer control group. Microscopy of gastric mucosa in the ulcer control group showed severe damage to gastric mucosa with edema and leukocytes infiltration of the submucosal layer. However, rats pretreated with omeprazole or Thyme vulgaris exhibited a mild to moderate disruption of the surface epithelium and lower level of edema and leukocyte infiltration of the submucosal layer. The T. vulgaris extract caused up-regulation of Hsp70 protein, down-regulation of Bax protein, and intense periodic acid Schiff uptake of the glandular portion of the stomach. Gastric mucosal homogenate of rats pre-treated with T. vulgaris exhibited significantly increased superoxide dismutase (SOD) and catalase (CAT) activities while malondialdehyde (MDA) level was significantly decreased. Based on the results showed in this study, Thymus vulgaris extract can be proposed as the safe medicinal plants for use and it has considerable gastroprotective potential via stomach epithelium protection against gastric ulcers and stomach lesions.

Incidence and geographical distribution of tuberculosis disease in Erbil city, Iraq.

OBJECTIVES: This study aimed to identify the geographical distribution of TB in Erbil city, Kurdistan Region, Iraq, determine potential risk factors associated with TB distribution, and provide recommendations to improve TB control programs in the region. METHODS: The records of TB patients registered at the Chest and Respiratory Disease Center in Erbil, Iraqi Kurdistan Region, from January 2012 to December 2016 were reviewed and analyzed. The number of cases by the quarter of residence within Erbil city were analyzed spatially and presented in an appropriate map. RESULTS: The estimated annual incidence of TB in Erbil city constantly increased from 16 per 100,000 inhabitants in the year 2012 to 21.7 per 100,000 inhabitants in the year 2016. Most of the TB cases were from the middle zone of Erbil city (44%), followed by the outer zone (43.8%) and the central zone (12.2%). The largest number of the cases were from Brayaty quarter (40), followed by Badawa (35) Nawroz (35) and Kurdistan (31) quarters. Clusters with a large number of cases were mainly located in the southern part of the city. CONCLUSION: The estimated TB incidence constantly increased in Erbil city from 2012 to 2016. Mapping the distribution of TB cases in Erbil city provided useful information about the epidemiological situation of TB that can be used to direct future TB control strategies.

A comprehensive review of histopathological findings of infections induced by COVID-19.

The severe acute respiratory syndrome (SARS)-Coronavirus (CoV2) virus, first identified in Wuhan, China, caused the coronavirus disease 2019 (COVID-19) which soon became a global pandemic, as labelled by the World Health Organization (WHO). The transmission method of the infection is primarily through droplets of various sizes. The SARS-CoV2 virus leads to a severe respiratory illness which in the first place causes the simulation of the acute respiratory syndrome. In order to diagnose of COVID-19 efficiently, samples with infection probability need to be examined through histopathological methods. Survival chances of the infected can remarkably increase if the virus is diagnosed timely by reverse transcription-polymerase chain reaction (RT-PCR) or computed tomography (CT) scan of the chest. One of the destructive effects of COVID-19 is the formation of ground-glass opacity (GGO) in the lungs which might be regarded to be equivalent to high-altitude pulmonary edema (HAPE). COVID-19 acts very similarly to SARS and Middle East Respiratory Syndrome (MERS) which can be inactivated by the chemical compounds of ethanol and sodium hypochlorite. Epidemiologic characteristics of COVID-19 have been indicated by numerous studies; however, there is still a lack of details of pathologic changes in the lung. The present comprehensive review is an attempt to assess and cover the current state of knowledge on COVID-19 disease based on the histopathologic studies conducted before May 2020.

Survival analysis of patients with tuberculosis in Erbil, Iraqi Kurdistan region.

BACKGROUND: Tuberculosis is an important health concern in Iraq, but limited research has examined the quality of tuberculosis care and the survival of the patients. This study aimed to assess the 12-month survival of tuberculosis patients and evaluate the effect of the associated risk factors on patients' survival. METHODS: We reviewed the records of 728 patients with tuberculosis who were registered and treated at the Chest and Respiratory Disease Center in Erbil, Iraqi Kurdistan Region, from January 2012 to December 2017. Demographic data, the site of the disease, and treatment outcomes were retrieved from patients' records. Data analysis included the use of the Kaplan-Meier method and the log-rank test to calculate the estimates of the survival and assess the differences in the survival among the patients. The Cox regression model was used for univariate and multivariate analysis. RESULTS: The mean period of the follow-up of the patients was 7.6 months. Of 728 patients with tuberculosis, 50 (6.9%) had died. The 12-month survival rate of our study was 93.1%. A statistically significant difference was detected in the survival curves of different age groups (P < 0.001) and the site of the disease (P = 0.012). In multivariate analysis, lower survival rates were only observed among patients aged ≥65 years (hazard ratio = 9.36, 95% CI 2.14-40.95) and patients with extrapulmonary disease (hazard ratio = 2.61, 95% CI 1.30-5.27). CONCLUSION: The 12-month survival rate of tuberculosis patients managed at the Chest and Respiratory Disease Center in Erbil was similar to the international rates. The high rates of extrapulmonary tuberculosis and the low survival rate necessitate further studies and action with a possible revision to the tuberculosis management strategy.