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.

Multilocus sequence typing analysis and molecular characterization of carbapenemase related genes in Acinetobacter baumannii isolated from hospitalized patients in Erbil city, Iraq.

Acinetobacter baumannii, has been recognized by (WHO) as a global priority pathogen. It has been demonstrated to quickly pick up antimicrobial resistance genes. Multilocus sequence typing (MLST) is an unambiguous typing method for identifying accurate and portable nucleotide sequences of internal fragments of multiple housekeeping genes. The present study aimed to determine the sequence type using MLST, genetically define the carbapenem resistance phenotype and clarify the epidemiology of multidrug resistant (MDR) A. baumannii in the Kurdistan region of Iraq. Clinical samples were collected from ICU patients. VITEK 2 compact system was used for bacterial identification and antimicrobial susceptibility profile. PCR was used for detecting carbapenemase-related genes. Additionally, MLST was used to evaluate the genetic diversity of carbapenem-resistant isolates using Oxford scheme primers. In this investigation, 63 non-duplicate A. baumannii isolates from hospitalized patients were identified. According to CLSI standards, 75% and 73.4% of isolates were resistant to meropenem and imipenem respectively. Tigecycline and colistin were the most effective antibacterial agents. Of the various combinations of carbapenemase genes identified, the most common co-existence of genes present among clinical isolates were BlaOXA-23, and BlaOXA-51 (95.31%). While the less common combination of genes was detected in 4 isolates  (6.25 %) consisting of the co-existence of all tested carbapenemase genes in the present study (BlaOXA-23, BlaOXA-51, BlaOXA-58, BlaIMP, BlaVIM, BlaNDM). Regarding MLST analysis, the results confirmed that ST 556 (n=4) had the greatest frequency rate among clinical isolates, followed by ST 218 (n=3). Notably, the most common worldwide clonal lineage was CC92, which corresponded to (ICII). Only two isolates from ST 441, on the other hand, matched CC109/ ICI.  The present investigation revealed a significant level of diversity among A. baumannii isolates.

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.

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.