Antimicrobial resistance profiles of bacterial isolates from clinical specimens referred to Ethiopian Public Health Institute: analysis of 5-year data.

BACKGROUND: Antimicrobial resistance is one of the common global public health problems. The emergence of antimicrobial resistance is multifactorial, and tackling its development is challenging. Consequently, infections caused by resistant bacteria are unresponsive to conventional drugs, resulting in prolonged and severe illnesses, higher mortality rates, and considerable healthcare costs. Therefore, understanding the antimicrobial resistance profiles of bacterial pathogens is essential to optimize treatments and reduce the risks associated with infections. This study aimed to determine the antimicrobial resistance patterns of bacterial isolates from different clinical specimens at the Ethiopian Public Health Institute (EPHI). MATERIALS AND METHODS: The retrospective cross-sectional study was conducted on the bacterial culture and antibiotic susceptibility reports of different clinical specimens referred to the Bacteriology Laboratory of EPHI from September 2015 to August 2019. Standard bacteriological techniques were used for the isolation and identification of the bacteria. Data were extracted from 840 patients' records, which included the type of clinical sample cultured, the name of the bacteria, the representations of the antibiotics used for susceptibility testing, and the susceptibility results. Descriptive statistics were used to describe the bacterial isolates and the antimicrobial resistance profiles. RESULTS: Eight types of clinical specimens were analyzed for bacterial isolates and urine specimens were the most analyzed. Ten different genera of bacteria were identified by culture. Almost all the isolates were gram-negative bacteria, while only one species of gram-positive (Staphylococcus aureus) was reported. Antibiotic sensitivity patterns were tested on 840 culture isolates. Escherichia coli strains revealed more than 57% resistance to seventeen antibiotics. Klebsiella pneumoniae showed nearly 70% or greater resistance rates for 17 of the antibiotics used. The overall detected multidrug resistance (MDR) was 64.29%. The highest MDR was reported in Acinetobacter strains (84%) followed by K. pneumoniae (80%). CONCLUSIONS: The multidrug resistance rates found in this study were alarming. Strengthening antimicrobial resistance surveillance at the national level is mandatory, and antimicrobial sensitivity testing should be accessible at local diagnostic centers.

Antimicrobial Resistance Patterns of Staphylococcus aureus and Enterococcus Species at the Ethiopian Public Health Institute, Ethiopia: A Five-Year Retrospective Analysis.

Purpose: The study aimed to investigate the antimicrobial resistance patterns of Staphylococcus aureus and Enterococcus species isolated from clinical specimens over a period of five years, including resistance to methicillin and vancomycin. Patients and Methods: Bacterial identification and antimicrobial susceptibility testing reports from 2017 to 2021 at the Ethiopian Public Health Institute were used for this retrospective study. The organisms were identified using either BD Phoenix M50, Vitek 2 compact, or conventional biochemical methods, whichever was available at the time of testing. The antimicrobial susceptibility profiles of the isolates were determined using either Kirby-Bauer disc diffusion, BD phoenix M50, or Vitek 2 compact. WHONET software was used to analyze the antimicrobial resistance patterns of both organisms. The p-values of ≤0.05 were considered statistically significant. Results: During the study period, a total of 315 Staphylococcus aureus and 92 Enterococcus species were isolated. Out of 315 Staphylococcus aureus isolates, 27% and 5.1% were methicillin and vancomycin resistant, respectively. Staphylococcus aureus showed very high resistance to Penicillin G (86.7%). Out of 92 Enterococcus species recovered, 8.7% were vancomycin-resistant. Enterococcus species showed very high resistance to Penicillin G (71.4%) and tetracyclines (83.3%). Methicillin-resistant Staphylococcus aureus shows 100% resistance to penicillin followed by ciprofloxacin (50%), erythromycin (45.6%), and tetracycline (44.2%) and lower resistance to vancomycin (18.8%). All vancomycin-resistant isolates of both organisms were fully resistant (100%) to all antibiotics tested, except for linezolid and daptomycin, to which they were susceptible. Conclusion: This study found a high prevalence of methicillin and vancomycin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus species between 2017 and 2021. However, there were no statistically significant changes in the prevalence of these organisms during the study period. This suggests that larger and more representative nationwide data is needed to show trends of these pathogens.

Characterization of plasmids carrying blaCTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia.

CTX-Ms are encoded by blaCTX-M genes and are widely distributed extended-spectrum ß-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to ß-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of blaCTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of blaCTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of blaCTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.

Prevalence and Trends of Carbapenem-Resistant Pseudomonas aeruginosa and Acinetobacter Species Isolated from Clinical Specimens at the Ethiopian Public Health Institute, Addis Ababa, Ethiopia: A Retrospective Analysis.

Purpose: Carbapenem-resistant Acinetobacter species and P. aeruginosa are the leading cause of nosocomial infections. Therefore, the objective of this study was to analyze the prevalence, antimicrobial susceptibility profile, and trends of carbapenem-resistant P. aeruginosa and Acinetobacter species isolated from clinical specimens. Patients and Methods: This retrospective study included data from Ethiopian Public Health Institute from 2017 to 2021. BD phoenix M50, Vitek 2 compact, and conventional identification methods were used to identify the organisms. The Kirby-Bauer disc diffusion, BD phoenix M50, and Vitek 2 compact methods were used to determine the antimicrobial susceptibility profiles of the isolates. Chi-square for linear trends using Epi Info was employed to test the significance of carbapenem resistance trends over time. The p-values of ≤0.05 were considered statistically significant. Results: Following data cleaning, 7110 reports were used. Out of this, (N=185, 2.6%) and (N=142, 2%), Acinetobacter species and P. aeruginosa were isolated, respectively. Twenty-four Acinetobacter species and fourteen P. aeruginosa species were omitted because carbapenem antimicrobial agents were not tested for them. The overall prevalence of carbapenem-resistant Acinetobacter species and P. aeruginosa were 61% and 22%, respectively. The prevalence of carbapenem-resistant Acinetobacter species increased significantly from 50% in 2017 to 76.2% in 2021 (p=0.013). The trend of carbapenem-resistant P. aeruginosa was fluctuating (p=0.99). Carbapenem-resistant Acinetobacter had a lower resistance rate to amikacin (44%) and tobramycin (55%); similarly, carbapenem-resistant P. aeruginosa had a lower resistance rate to amikacin (27%) and tobramycin (47%). Conclusion: This study revealed a high prevalence of carbapenem-resistant Acinetobacter species and P. aeruginosa, both of which showed better sensitivity to amikacin and tobramycin. Furthermore, Acinetobacter species showed a statistically significant increasing trend in carbapenem resistance.

Bacterial and fungal profile, drug resistance pattern and associated factors of isolates recovered from blood samples of patients referred to Ethiopian Public Health Institute: cross-sectional study.

BACKGROUND: Blood stream infections are serious infections that usually induce prolongation of hospital stay, morbidity and mortality in several countries including Ethiopia. The aim of this study was to determine bacterial and fungal profile, their drug resistance patterns, and risk factors associated with blood stream infections. METHODS: A cross sectional study design was conducted from February 23 to June 23, 2020 at Ethiopian public health. A structured questionnaire was used to collect data on socio-demographic factors and clinical conditions. Blood specimens were analyzed using standard microbiological techniques. Antimicrobial susceptibility tests were performed using Kirby-Bauer disc diffusion technique and Vitek compact 2. Simple and multiple logistic regressions were used to assess the potential risk factors. RESULTS: A total of 175 pathogens isolated from 346 blood specimens. Of these, 60% Gram-negative bacteria, 30.86% Gram-positive bacteria and 9.14% fungal isolates were identified. Burkholderia cepacia and Coagulase negative staphylococcus were the predominant pathogen among Gram-negative and Gram-positive bacteria respectively. Among fungus, Candida krusei (56.25%) was the most predominant isolate. The highest proportions of antibacterial resistance were observed among 3rd generation cephalosporin and penicillin. Most fungal isolates expressed resistance to fluconazole. Sex (P = 0.007), age (P < 0.001) and use of invasive medical devices (P = 0.003) were identified as risk factors for bacterial blood stream infections. CONCLUSION: The study showed high prevalence of blood stream infection was due to B. cepacia and non-C. albicans spp. This finding alarming ongoing investigation of blood stream infection is important for recognizing future potential preventive strategies including environmental hygiene and management of comorbid medical diseases to reduce the problem.

Antimicrobial Resistance Profiling and Molecular Epidemiological Analysis of Extended Spectrum ß-Lactamases Produced by Extraintestinal Invasive Escherichia coli Isolates From Ethiopia: The Presence of International High-Risk Clones ST131 and ST410 Revealed.

The treatment of invasive Escherichia coli infections is a challenge because of the emergence and rapid spread of multidrug resistant strains. Particular problems are those strains that produce extended spectrum ß-lactamases (ESBL's). Although the global characterization of these enzymes is advanced, knowledge of their molecular basis among clinical E. coli isolates in Ethiopia is extremely limited. This study intends to address this knowledge gap. The study combines antimicrobial resistance profiling and molecular epidemiology of ESBL genes among 204 E. coli clinical isolates collected from patient urine, blood, and pus at four geographically distinct health facilities in Ethiopia. All isolates exhibited multidrug resistance, with extensive resistance to ampicillin and first to fourth line generation cephalosporins and sulfamethoxazole-trimethoprim and ciprofloxacin. Extended spectrum ß-lactamase genes were detected in 189 strains, and all but one were positive for CTX-Ms ß-lactamases. Genes encoding for the group-1 CTX-Ms enzymes were most prolific, and CTX-M-15 was the most common ESBL identified. Group-9 CTX-Ms including CTX-M-14 and CTX-27 were detected only in 12 isolates and SHV ESBL types were identified in just 8 isolates. Bacterial typing revealed a high amount of strains associated with the B2 phylogenetic group. Crucially, the international high risk clones ST131 and ST410 were among the sequence types identified. This first time study revealed a high prevalence of CTX-M type ESBL's circulating among E. coli clinical isolates in Ethiopia. Critically, they are associated with multidrug resistance phenotypes and high-risk clones first characterized in other parts of the world.

Extended-spectrum beta-lactamase production and multi-drug resistance among Enterobacteriaceae isolated in Addis Ababa, Ethiopia.

Background: The global emergence and spread of extended-spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae have been threatening the ability to treat an infection. Hence, this study aimed to determine the prevalence of ESBL-producing and multi-drug resistance (MDR) Enterobacteriaceae (ESBLs-E) from different clinical specimens in Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted from January 1 to May 30, 2017. A total of 426 Enterobacteriaceae isolates were identified from clinical specimens. The isolates were collected from four laboratories. Antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method on Muller Hinton agar (MHA). All Enterobacteriaceae were screened for ESBLs production using cefotaxime and ceftazidime as per CLSI guideline. Each ESBL screening positive Enterobacteriaceae were confirmed by a combination disk test (CDT). Data were entered and analyzed by using SPSS version-20. Result: The most frequent Enterobacteriaceae were E. coli 228 (53.5%) and K. pneumoniae 103 (24.1%). The magnitude of ESBLs-E was 57.7% (246/426). The highest frequencies of ESBLs-E were observed in blood specimesns (84.4%) and the highest ESBLs production was observed in K. pneumoniae (85.4%). The highest resistance level was seen to sulfamethoxazole-trimethoprim (77.0%), amoxicillin with clavulanic acid (71.6%), cefotaxime (62.2%), cefepime (60.3%) and ceftazidime (60.8%). The overall magnitude of multi-drug resistance (MDR) level was 68.3%. Of ESBLs-E, 96.3% of them were MDR (P < 0.001). Conclusion: There was a high prevalence of ESBLs-E and MDR isolate in Addis Ababa. Most of ESBLs-E was isolated primarily in blood and urine. The highest ESBLs production was observed among K. pneumoniae. Hence, strong infection control strategies must be implemented in hospital settings of the country.