High burden of ESBL and carbapenemase-producing gram-negative bacteria in bloodstream infection patients at a tertiary care hospital in Addis Ababa, Ethiopia

Molecular identification and antimicrobial resistance profiling of pathogenic E. coli isolates from smallholder livestock households in Central Ethiopia

Escherichia coli of different pathotypes are frequently involved in morbidity and mortality in animals and humans. The study aimed to identify E. coli pathotypes and determine antimicrobial resistance (AMR) profiles in Ethiopian smallholder livestock households. The pathotyping included 198 E. coli isolates identified from human and environmental samples collected from 98 households. AMR profiling was conducted on selected E. coli pathotypes from 89 households, along with known isolates from calf samples obtained from the same households. Morphological and biochemical tests were used to identify presumptive E. coli isolates. DNA was extracted and then singleplex PCR was used to amplify virulence genes. A disc diffusion test was applied for AMR profilings in E. coli pathotypes. Data were evaluated using chi-square tests and logistic regression. Calf (79.8 %) and human (73.7 %) samples were more likely to contain pathotypes (OR 3.2; 95 % CI: 1.7, 5.9; p=0.001 and OR 2.3; 95 % CI: 1.2, 4.1; p=0.008, respectively) than the environmental samples (55.6 %). ETEC (32.3 %) and STEC (15.2 %) were the most common pathotypes detected in the study samples. Out of the 176 isolates selected for AMR profiling, 85 % were resistant to at least one drug and 36 % were multi-drug resistant (MDR). The MDR isolates were found in 44 households, with 11 sharing identical pathotypes and resistance profiles among the different samples. Thus, E. coli strains were likely circulated among humans, animals, and the environment. This in turn calls for a One-health approach to improve antimicrobial usage standards and promote proper waste disposal practices.

Investigation of methicillin, beta lactam, carbapenem, and multidrug resistant bacteria from blood cultures of septicemia suspected patients in Northwest Ethiopia

The presence of microorganisms in the bloodstream can result in severe, potentially life-threatening conditions, which are a significant cause of morbidity and mortality worldwide. The rise of antimicrobial-resistant strains further exacerbates these outcomes. However, the data concerning bacterial profiles and resistance to antimicrobials, particularly against extended-spectrum beta-lactams and carbapenems, are limited. Aimed to characterize pathogens isolated from positive blood cultures, including bacterial profiles and antibiotic susceptibility patterns, and to identify predictors of blood culture positivity in septicemia-suspected patients at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. A hospital-based cross-sectional study was conducted from February 15 to May 30, 2023. The study involved 341 patients suspected of having septicaemia who were selected consecutively through a convenience sampling technique. Blood samples were collected aseptically from each patient (10 ml from adults, 5 ml from children, and 1 ml from neonates) and inoculated into bottles containing tryptic soy broth in volumes appropriate for the patient's age. The samples were incubated at 35-37 °C for up to 7 days to detect bacterial growth. Positive blood cultures were subcultured onto various media, including chocolate agar, blood agar, modified Thayer-Martin agar, MacConkey agar, and mannitol salt agar, and incubated again at 35-37 °C for 24 h. The suspected bacteria were identified on the basis of colony morphology, Gram staining, and biochemical tests. Antimicrobial susceptibility testing was conducted via both the Kirby-Bauer and modified Kirby-Bauer disk diffusion methods. Resistance to methicillin, extended-spectrum beta-lactams, and carbapenems was determined via the cefoxitin disc test, combined-disk diffusion method, and modified carbapenem inactivation method, respectively. The data were entered into Epi-Data version 4.6 and analysed via SPSS version 25. Binary logistic regression analyses were employed to identify factors associated with bloodstream infections (BSI), with a P value of less than 0.05 considered statistically significant. Out of 341 patients suspected of septicemia, 196 (57.5%) were male and 145 (42.5%) were female, with a mean (± SD) age of 16.5 (± 7.5) years. Bloodstream infection was identified in 87 (25.5%) patients (95% CI: 21.1-30.4). Among these positive cases, 67 (77%) were from ward patients, while 20 (23%) were from those visiting outpatient departments. The primary gram-positive bacteria identified included S. aureus 27 (31.0%), CoNS 14 (16.1%), S. viridans 8 (9.2%), and S. agalactiae 4 (4.6%). The gram-negative isolates were predominantly K. pneumoniae 11 (12.6%), followed by E. coli 9 (10.3%), E. cloacae 6 (6.9%), Acinetobacter spp. 3 (3.5%), N. meningitidis 3 (3.5%), and P. aeruginosa 2 (2.3%). Methicillin resistance was detected in 17/27 (63.0%) S. aureus strains and 2/14 (14.3%) CoNS strains. Multidrug resistance was detected in 63/87 (72.4%, 95% CI: 67.2-84.7%) of the isolates. Extended-spectrum beta-lactamase and carbapenemase production were observed in 12/31 (38.7%) and 5/31 (16.1%) of isolates, respectively. The factors associated with BSI were the presence of wounds and burns (AOR = 2.103, 95% CI: 1.365-3.241, P = 0.041), length of hospital stay (≥ 5) (AOR = 2.209, 95% CI: 1.122-4.347, P = 0.022), and prior medical procedures (AOR = 1.982, 95% CI: 1.125-3.492, P = 0.018). Bloodstream infection was identified in 25.5% of suspected septicemia cases, with multidrug-resistant bacteria present in 72.4% of isolates. Gram-positive bacteria, particularly S. aureus, and gram-negative bacteria like K. pneumoniae and E. coli were predominant. High rates of methicillin, beta-lactam, and carbapenem resistance were observed, emphasizing the magnitude of antimicrobial resistance. Risk factors such as wounds, extended hospital stays, and prior medical procedures significantly increased the likelihood of culture positivity. This suggests the need for regular antimicrobial susceptibility testing to guide antibiotic selection and track resistance trends, proper wound care and medical device usage to reduce the risk of BSI in healthcare settings.

Phenotypic bacterial epidemiology and antimicrobial resistance profiles in neonatal sepsis at Jimma medical center, Ethiopia: Insights from prospective study

BACKGROUND

Epidemiological profiles and the rundown crisis of antimicrobial resistance from bacterial isolates in neonatal sepsis compel regular surveillance to enhance data-driven decision-making. Accordingly, this study aimed to assess the phenotypic epidemiology and antimicrobial resistance profiles of bacteria isolated from clinically suspected neonatal sepsis in Ethiopia.

METHODS

A total of 342 neonates suspected of clinical sepsis were randomly included in a prospective observational study conducted at the neonatal intensive care unit (NICU) of Jimma medical center (JMC) from May 2022 to July 2023. Blood samples were collected from each neonate and subjected to a culture test for identification of bacterial isolates and their antibiotic resistance profiles following the standardized guidelines. The laboratory results, along with relevant clinical data, were recorded using WHONET and analyzed using STATA software.

RESULTS

Out of the 342 blood samples that were analyzed, 138 samples (40.4%, 95% CI: 35.1-45.6, P<0.01) exhibited proven bacterial infection. The infection rates were notably higher in males with 85/138 (61.6%, 95% CI: 53.4-69.8, P<0.01) and neonates aged 0-3 days with 81/138 (58.7%, 95% CI: 50.5-66.9, P<0.01). The majority of the infections were attributed to Gram-negative bacteria, accounting for 101/138(73.2%, 95% CI: 65.6-80.7) cases, with 69/101(68.3%, 95% CI: 63.8-72.8) cases involving ESBL-producing strains, while Gram-positive bacteria were responsible for 26.8% (95% CI: 19.3-34.4) of the infections. The predominant isolates included Klebsiella pneumoniae (37.7%, 95% CI: 29.6-45.8), Coagulase-negative Staphylococci (CoNs) (20.3%, 95% CI: 13.6-27.0), and Acinetobacter species (11.6%, 95% CI: 6.0-17.1). Of the total cases, 43/72 (59.7%, 95% CI: 48.4-71.1, P<0.01) resulted in mortality, with 28/72 (38.9%, 95% CI: 27.70-50.1, P<0.03) deaths linked to Extended-Spectrum Beta-Lactamase (ESBL)-producing strains. Klebsiella pneumoniae displayed high resistance rates to trimethoprim-sulfamethoxazole (100%), ceftriaxone (100%), cefotaxime (98.1%), ceftazidime (90.4%), and gentamicin (84.6%). Acinetobacter species showed resistance to ampicillin (100%), cefotaxime (100%), trimethoprim-sulfamethoxazole (75%), ceftazidime (68.8%), chloramphenicol (68.8%), and ceftriaxone (68.8%). Likewise, CoNs displayed resistance to ampicillin (100%), penicillin (100%), cefotaxime (86.0%), gentamicin (57.2%), and oxacillin (32.2%). Multidrug resistance was observed in 88.4% (95% CI: 81.8-93.0) of isolates, with ESBL-producers significantly contributing (49.3%, 95% CI: 45.1-53.5). Furthermore, 23.0% (95% CI: 15.8-31.6) exhibited a prevalent resistance pattern to seven distinct antibiotic classes.

CONCLUSION

The prevalence and mortality rates of neonatal sepsis were significantly high at JMC, with a notable surge in antibiotic and multidrug resistance among bacterial strains isolated from infected neonates, specifically ESBL-producers. These resistant strains have a significant impact on infection rates and resistance profiles, highlighting the requisite for enhanced diagnostic and antimicrobial stewardship, stringent infection control, and further molecular characterization of isolates to enhance neonatal survival.

Prevalence of meropenem-resistant Pseudomonas Aeruginosa in Ethiopia: a systematic review and meta‑analysis

INTRODUCTION

Antimicrobial resistance (AMR) is a pressing global health concern, particularly pronounced in low-resource settings. In Ethiopia, the escalating prevalence of carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) poses a substantial threat to public health.

METHODS

A comprehensive search of databases, including PubMed, Scopus, Embase, Hinari, and Google Scholar, identified relevant studies. Inclusion criteria encompassed observational studies reporting the prevalence of meropenem-resistant P. aeruginosa in Ethiopia. Quality assessment utilized JBI checklists. A random-effects meta-analysis pooled data on study characteristics and prevalence estimates, with subsequent subgroup and sensitivity analyses. Publication bias was assessed graphically and statistically.

RESULTS

Out of 433 studies, nineteen, comprising a total sample of 11,131, met inclusion criteria. The pooled prevalence of meropenem-resistant P. aeruginosa was 15% (95% CI: 10-21%). Significant heterogeneity (I2 = 83.6%) was observed, with the number of P. aeruginosa isolates identified as the primary source of heterogeneity (p = 0.127). Subgroup analysis by infection source revealed a higher prevalence in hospital-acquired infections (28%, 95% CI: 10, 46) compared to community settings (6%, 95% CI: 2, 11). Geographic based subgroup analysis indicated the highest prevalence in the Amhara region (23%, 95% CI: 8, 38), followed by Addis Ababa (21%, 95% CI: 11, 32), and lower prevalence in the Oromia region (7%, 95% CI: 4, 19). Wound samples exhibited the highest resistance (25%, 95% CI: 25, 78), while sputum samples showed the lowest prevalence. Publication bias, identified through funnel plot examination and Egger's regression test (p < 0.001), execution of trim and fill analysis resulted in an adjusted pooled prevalence of (3.7%, 95% CI: 2.3, 9.6).

CONCLUSION

The noteworthy prevalence of meropenem resistance among P. aeruginosa isolates in Ethiopia, particularly in healthcare settings, underscores the urgency of implementing strict infection control practices and antibiotic stewardship. Further research is imperative to address and mitigate the challenges posed by antimicrobial resistance in the country.

The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden

Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015-2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.

Molecular characterization of carbapenem-resistance in Gram-negative isolates obtained from clinical samples at Jimma Medical Center, Ethiopia

Background

In resource-constrained settings, limited antibiotic options make treating carbapenem-resistant bacterial infections difficult for healthcare providers. This study aimed to assess carbapenemase expression in Gram-negative bacteria isolated from clinical samples in Jimma, Ethiopia.

Methods

A cross-sectional study was conducted to assess carbapenemase expression in Gram-negative bacteria isolated from patients attending Jimma Medical Center. Totally, 846 Gram-negative bacteria were isolated and identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Phenotypic antibiotic resistance patterns were determined using the Kirby-Bauer disk diffusion method and Etest strips. Extended-spectrum β-lactamase phenotype was determined using MAST disks, and carbapenemases were characterized using multiplex polymerase chain reactions (PCR).

Results

Among the isolates, 19% (157/846) showed phenotypic resistance to carbapenem antibiotics. PCR analysis revealed that at least one carbapenemase gene was detected in 69% (107/155) of these strains. The most frequently detected acquired genes were blaNDM in 35% (37/107), blaVIM in 24% (26/107), and blaKPC42 in 13% (14/107) of the isolates. Coexistence of two or more acquired genes was observed in 31% (33/107) of the isolates. The most common coexisting acquired genes were blaNDM + blaOXA-23, detected in 24% (8/33) of these isolates. No carbapenemase-encoding genes could be detected in 31% (48/155) of carbapenem-resistant isolates, with P. aeruginosa accounting for 85% (41/48) thereof.

Conclusion

This study revealed high and incremental rates of carbapenem-resistant bacteria in clinical samples with various carbapenemase-encoding genes. This imposes a severe challenge to effective patient care in the context of already limited treatment options against Gram-negative bacterial infections in resource-constrained settings.

Distribution of ß-Lactamase Genes Among Multidrug-Resistant and Extended-Spectrum ß-Lactamase-Producing Diarrheagenic Escherichia coli from Under-Five Children in Ethiopia

Purpose

Escherichia coli strains that produce extended-spectrum ß-lactamase (ESBL) and carbapenemase are among the major threats to global health. The objective of the present study was to determine the distribution of ß-lactamase genes among multidrug-resistant (MDR) and ESBL-producing Diarrheagenic E. coli (DEC) pathotypes isolated from under-five children in Ethiopia.

Patients and Methods

A cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia. It was a health-facility-based study and conducted between December 2020 and August 2021. A total of 476 under-five children participated in the study. DEC pathotypes were detected by conventional Polymerase Chain Reaction (PCR) assay. After evaluating the antimicrobial susceptibility profile of the DEC strains by disk diffusion method, confirmation test was done for ESBL and carbapenemase production. ß-lactamase encoding genes were identified from phenotypically ESBLs and carbapenemase positive DEC strains using PCR assay.

Results

In total, 183 DEC pathotypes were isolated from the 476 under-five children. Seventy-nine (43%, 79/183) MDR-DEC pathotypes were identified. MDR was common among enteroaggregative E. coli (EAEC) (58%, 44/76), followed by enterotoxigenic E. coli (ETEC) (44%, 17/39)) and enteroinvasive E. coli (EIEC) (30%, 7/23). Phenotypically, a total of 30 MDR-DEC pathotypes (16.4%, 30/183) were tested positive for ESBLs. Few ETEC (5.1%, 2/39) and EAEC (2.6%, 2/76) were carbapenemase producers. The predominant β-lactamase genes identified was blaTEM (80%, 24/30) followed by blaCTX-M (73%, 22/30), blaSHV (60%, 18/30), blaNDM (13%, 4/30), and blaOXA-48 (13%, 4/30). Majority of the ß-lactamase encoding genes were detected in EAEC (50%) and ETEC (20%). Co-existence of different β-lactamase genes was found in the present study.

Conclusion

The blaTEM, blaCTX-M, blaSHV, blaNDM, and blaOXA-48, that are associated with serious and urgent threats globally, were detected in diarrheagenic E. coli isolates from under-five children in Ethiopia. This study also revealed the coexistence of the β-lactamase genes.