Prevalence, multidrug resistance patterns, and carbapenemase-encoding genes of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli from clinical and non-clinical samples in Ethiopia: Systematic review and meta-analysis

Chalachew Genet; Wendemagegn Enbiale; Anna Rommerskirchen; Addisu Melese; Baye Yirga Adugna; Zeleke Ayenew; Hiwot Tadesse; Bayeh Abera; Endalkachew Nibret; Abaineh Munshea Abitew

doi:10.1177/20503121261488385

. 2026 Sep 7;14:20503121261488385. doi: 10.1177/20503121261488385

Prevalence, multidrug resistance patterns, and carbapenemase-encoding genes of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli from clinical and non-clinical samples in Ethiopia: Systematic review and meta-analysis

Chalachew Genet ^1,^2,^3,^✉, Wendemagegn Enbiale ^3,^4,⁵, Anna Rommerskirchen ^6,⁷, Addisu Melese ², Baye Yirga Adugna ^1,⁸, Zeleke Ayenew ⁹, Hiwot Tadesse ², Bayeh Abera ², Endalkachew Nibret ^1,^10,¹¹, Abaineh Munshea Abitew ^1,¹⁰

PMCID: PMC13554686 PMID: 42719521

Abstract

Background

Carbapenems are considered the last resort to treat life-threatening bacterial infections. However, their efficacy is increasingly compromised by carbapenemase-producing K. pneumoniae (CPKP) and Escherichia coli (CPEC). Although these organisms have been reported in Ethiopia, the overall burden and distribution of carbapenemase-encoding genes remain unclear. This study aims to determine the pooled prevalence of CPKP and CPEC from both clinical and non-clinical samples in Ethiopia and to identify the most common carbapenemase-encoding genes.

Methods

A systematic search was conducted in electronic databases for studies published in English up to June 30, 2025. The review followed PRISMA guidelines and included 44 eligible studies. Quality assessment was performed using the Joanna Briggs Institute (JBI) checklist. The meta-analysis was performed using Comprehensive Meta-Analysis (CMA) software version 2, applying a random-effects model to estimate pooled prevalence. Heterogeneity and publication bias were evaluated using the I² statistic, funnel plot, and Egger’s test.

Results

The pooled prevalence of CPKP and/or CPEC in Ethiopia was 8.3% (95% CI: 6.3–10.9; I² = 86.41, p < 0.001), with a higher prevalence in non-clinical samples (13.3%) than in clinical ones (8%). Six studies reported 60 carbapenemase-encoding genes in 51 K. pneumoniae isolates. The most dominant resistant gene was the bla_NDM metallo-β-lactamase type, accounting for 85%. The pooled prevalence of multidrug-resistant E. coli and/or K. pneumoniae reported by studies included in the review was 78.4% (95% CI = 71-84.2, I² = 96.10, p< 0.001).

Conclusions

This study reveals a high pooled prevalence of CPKP and CPEC in Ethiopia and high dominance of the bla_NDM carbapenemase gene. These findings underscore the need for enhanced antimicrobial resistance surveillance, infection prevention strategies, and stewardship interventions across both clinical and environmental settings.

Keywords: Escherichia coli, K. pneumoniae, carbapenem-resistance, metallo-β-lactamase, Enterobacteriaceae, one health, Ethiopia

Introduction

K. pneumoniae and E. coli are responsible for a wide spectrum of infections, ranging from mild to severe, life-threatening diseases such as wound infection, urinary tract infection, gastroenteritis, pneumonia, sepsis, and meningitis. These infections were previously manageable with commonly available antibiotics.^1,2 However, the global emergence of multidrug resistance (MDR), particularly resistance to third- and fourth-generation cephalosporins, has resulted reliance on carbapenems, which are widely considered as the last-resort antibiotics for treating MDR Gram-negative bacterial infections.^3,4

Unfortunately, K. pneumoniae and E. coli have developed resistance to carbapenems, further complicating treatment and elevating their clinical significance. These organisms have become increasingly prevalent and are associated with growing burden of antimicrobial resistance, prompting the World Health Organization to classify them as “critical priority” pathogens for research and new drug development.^5,6 Among the various mechanisms of carbapenem resistance, carbapenemase-mediated enzymatic inactivation is the most predominant and clinically concerning in E. coli and K. pneumoniae.⁷ This enzymatic inactivation, mainly encoded by plasmids, enables rapid horizontal gene transfer, facilitating more efficient dissemination than non-enzymatic resistant mechanisms.^8,9

Infections caused by carbapenemase-producing E. coli (CPEC) and carbapenemase-producing K. pneumoniae (CPKP) are a growing public health crisis, leaving few treatment options and a narrow, promising future for new antibiotics in the pipeline.^10,11 Compared to their carbapenem-susceptible counterparts, CPEC and CPKP are associated with longer hospital stays, increased health care costs, and mortality^12,13 and have higher MDR rates.^14–16

Though there are different carbapenemase types and variants reported globally, the most common include K. pneumoniae carbapenemase (KPC), New Delhi metallo-β-lactamase (NDM), imipenemase (IMP), Veronica Integron Metallo-β-lactamase types (VIM), oxacillinase-48 (OXA-48), and OXA-23, with variable geographical distribution and spectrum of β-lactam hydrolysis.^17,18 Carbapenemase production in K. pneumoniae and E. coli can be detected using various molecular methods, including polymerase chain reaction (PCR), microarray, and whole genome sequencing (WGS). Phenotypic tests, including modified Hodge test (MHT), modified carbapenem inactivation method (mCIM), Carba NP test, matrix-assisted laser desorption–ionization time of flight mass spectrometry (MALDI-TOF MS), and lateral flow immunoassay, can identify enzymatic activity or the enzymes themselves.^9,19 Among these, molecular assay, mCIM, and Carba NP are recommended by the Clinical Laboratory Standard Institute (CLSI)²⁰ and the European Committee on Antimicrobial Susceptibility Testing (EUCAST).²¹

For effective patient care, infection prevention, and antimicrobial resistance (AMR) control, it is critical to adopt reliable detection methods tailored to the local epidemiology of carbapenemase-encoding genes.²² Understanding the local prevalence of CPEC and CPKP and the distribution of carbapenemase genes is critical for guiding treatment choices, refining diagnostic algorithms, and informing public health policy.^19,23 Therefore, national-level data on the prevalence of carbapenemase-producing bacteria and the distribution of gene variants are essential to inform antimicrobial stewardship strategies and infection control protocols.^24–27

In Ethiopia, there is a dearth of data on the national CPEC, and CPKP prevalence and dominant carbapenemase-encoding gene variants circulating in Ethiopia, which is crucial to implement appropriate carbapenemase detection methods and provide input to revise treatment guidelines and infection prevention protocols accordingly.¹⁷ Despite the growing threat posed by these pathogens, there has been no systematic synthesis of the available evidence in Ethiopia from clinical and non-clinical samples. Therefore, the present study is the first systematic review and meta-analysis, which identified the predominant circulating carbapenemase-encoding genes and estimate the pooled prevalence of CPEC and CPKP and MDR level of the isolates in Ethiopia, using published data derived from clinical and non-clinical sources.

Methods

Study period and setting

This systematic review and meta-analysis were conducted in Ethiopia, East Africa, from July 1 to December 31, 2025. Administratively, the country is divided into 12 regional states (Afar, Amhara, Benishangul-Gumuz, Central Ethiopia, Gambella, Harari, Oromia, Sidama, Somalia, South Ethiopia, South West Ethiopia Peoples’ Region, and Tigray regional states) and two city administrations (the country’s capital, Addis Ababa city administration, and Dire Dawa city administration).

Literature sources and search strategy

A comprehensive literature search was done on PubMed, Google Scholar, and African journals online databases following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guideline²⁸ using Medical Subject Headings (MeSH) terms, Boolean operators (AND, OR) and truncation (“*”). The completed PRISMA 2020 checklist is provided in Supplementary File 1. MeSH terms used to search PubMed were: carbapenemase* OR carbapenem-resistant OR “beta-lactamase producer” OR “beta-lactam resistance” AND (“Escherichia coli” OR “Klebsiella spp.” OR “Klebsiella pneumoniae” OR Enterobacteriaceae) AND Ethiopia. Additional studies were identified by manually screening the reference lists of included articles.

Screening of studies and eligibility record identification process

All search results were exported into EndNote version 20 (Thomson Reuters, USA) reference manager, and duplications were removed using the software and manually by looking at each record. Then, abstract and title screening and full text evaluation for eligibility based on the predefined inclusion and exclusion criteria were done by CG and AM (Figure 1). Studies conducted in Ethiopia and published up to June 30, 2025, and that fulfilled the eligibility criteria were included.

Figure 1. — PRISMA flow diagram illustrating the process of literature identification, screening, eligibility assessment, and final inclusion of studies in the systematic review and meta-analysis.

Inclusion and exclusion criteria

For initial screening of the article title, abstract, and eligibility assessment of the full text, the authors set the following predefined inclusion and exclusion criteria.

Inclusion criteria: Studies published in English and available as freely accessible full text articles from local or international journals were included. Eligible studies were those conducted in any health facility or community setting involving human participants, animal subjects, or environmental samples, and that tested E. coli and/or K. pneumoniae for carbapenemase production using phenotypic and/or genotypic tests. No eligible study excluded due to unavailability of full text during the screening process. The study must also identify and quantify E. coli and K. pneumoniae tested for carbapenemase to the species level.

Exclusion criteria: Studies were excluded if carbapenemase production was not confirmed by phenotypic and/or genotypic methods. Moreover, studies with no total bacteria isolated, screened, and confirmed for carbapenemase production. Additionally, duplicate studies were excluded.

Quality assessment and data extraction

The quality of articles included for analysis was assessed by the Joanna Briggs Institute (JBI) critical appraisal checklist for prevalence studies.²⁹ The assessment was independently performed by the authors CG and AM, and disagreements were resolved through discussion with a third author, BY. Since all studies scored more than five out of nine points, they were all included (Supplementary file 2). Then, two reviewers (CG and AM) independently extracted data about the characteristics of included studies, such as author name, year of publication, study area, study design, study period, study subject, sample size, specimen type, and carbapenemase detection method, using a Microsoft Excel 2013 data abstraction sheet. When disagreement occurred in the process of data extraction, it was resolved by discussion and consensus. The third author (BY) was consulted when consensus could not be achieved.

Data processing and statistical analysis

The outcome of interest is the prevalence of CPEC and CPKP isolated from clinical and non-clinical samples (human, animal, food, or environmental samples) in Ethiopia, as well as the MDR level of E. coli and K. pneumoniae isolates included in this review. If the prevalence of carbapenemase-producing isolates were not possible to extract directly from studies, it was determined by dividing the CPEC and CPKP by the total isolates tested multiplied by 100. Before including studies reporting zero CPEC and CPKP in the meta-analysis, a constant 0.5 value is added as a continuity correction. The pooled prevalence and subgroup prevalence of carbapenemase-producing isolates by publication year, region, sample type, study participant type, and carbapenemase detection method were determined using comprehensive meta-analysis version 2 (CMA 2.0) software. The random effect model was used to determine the pooled prevalence of CPEC and CPKP. Heterogeneity of studies was determined by the Cochran’s Q-test and I² statistics.

Publication bias assessment

To see the presence of publication bias among studies included, a funnel plot was drawn. To include any missing studies and estimate the adjusted effect size, the Trim-and-Fill method was applied. Egger’s regression asymmetry tests were performed, and a p-value of less than 0.05 was considered as having significant publication bias.

Results

Study selection

Out of 205 research articles retrieved from databases, 161 articles were removed because of duplication (n = 58), unrelated title and abstract (n = 92), not detected carbapenemase production (n = 2), not indicated screened and carbapenemase producer (n = 7), and included multiple countries without specifically indicating CPEC and CPKP in each country (n = 2). The remaining 44 articles were included in the study^30–73 (Table 1).

Table 1.

Characteristics of studies included for prevalence of CPEC and CPKP isolated from clinical and non-clinical samples in Ethiopia.

Author, publication year	Study area	Study design	Study subject	Sample size^¥	Specimen type	CDM	Prevalence of CPEC and/or CPKP: N (%)
Abdeta et al., 2021³¹	AA	CS	Patient	1,337	MS	mCIM	11 (4.2)
Abera et al., 2024³²	AA	CS	AHI	261	Stool	mCIM	2 (0.8)
Aklilu et al., 2020³³	SERS	CS	Patient	421	Stool	meropenem/cloxacillin combination discs test	6 (2.1)
Alebel et al., 2021³⁴	ARS	CS	Patients	270	MS	mCIM	10 (18.5)
Alelign et al., 2023³⁵	SERS	CS	Food	100	Street foods	mCIM	7 (12.3)
Alemayehu et al., 2021³⁷	SRS	CS	Patients	103	MS	mCIM	4 (6.2)
Alemayehu et al., 2025³⁶	SRS	CS	Patient	153	MS	mCIM	7 (9.3)
Amare et al., 2022³⁸	ARS	CS	AHI	290	Stool	mCIM	7 (2.2)
Asmare et al., 2024³⁹	ARS	LS	Patient	363	Urine	Chromatic CRE	2 (9.1)
Assefa et al., 2024⁴⁰	SERS	CS	Patient	386	Sputum	mCIM	9 (14.5)
Awoke et al., 2022⁴¹	AA	CS	Patient	132	MS	mCIM	28 (21.2)
Ayalneh et al., 2024⁴²	ORS	CS	Patient	423	Stool	mCIM	12 (31.6)
Befikadu et al., 2024⁴³	ORS	CS	Patient	344	Stool	Combi Carba plus Mast discs	11 (3.8)
Beshah et al., 2023⁴⁴	AA	CS	Patients	1486	Blood	mCIM	19 (16.8)
Beyene et al., 2019⁴⁵	AA	CS	Patient	947	MS	MHT	4 (1.9)
Birhanu et al., 2025⁴⁶	ARS	CS	Patient	341	Blood	mCIM	4 (20)
Desta et al., 2016⁴⁷	AA	CS	Patient	267	Fecal sample/swab	ROSCO Neo-Sensitabs	5 (1.7)
Eshetie et al., 2015⁴⁸	ARS	CS	Patient	442	Urine	CHROMagar KPC medium	4 (2.8)
Gebremedhin et al., 2023⁴⁹	TRS	CS	Patients	297	Urine	MHT	5 (8.2)
Kindu et al., 2023⁵⁰	ARS	CS	Environment	384	Environmental swab	mCIM	26 (26.5)
Kiros et al., 2023⁵¹	ARS	CS	Patient	383	Stool	mCIM	47 (33.6)
Legese et al., 2017⁵³	AA	CS	Patient	322	Blood, urine	MHT	2 (8)
Legese et al., 2022⁵²	MC	CS	Patient	1,416	Blood	WGS	17 (10.9)
Mekonnen et al., 2023⁵⁴	AA	CS	Patients	384	Rectal swab	mCIM	60 (13.2)
Mitiku et al., 2022⁵⁵	SERS	CS	Patient	422	Urine	mCIM	7 (8.6)
Moges et al., 2019⁵⁶	ARS	CS	Patients	532	MS	MHT	18 (15)
Moges et al., 2021⁵⁷	ARS	CS	Patient	833	MS	MHT	1 (5.6)
Mussema et al., 2022⁵⁸	ORS	CS	Patient	39	Sputum	MASTTM D73C combination disc sets	2 (20)
Negeri et al., 2021⁵⁹	MC	CS	Patients	204	MS	PCR	0.5^⁋ (0.25)
Odoko et al., 2024³⁰	SERS	CS	Patient	1337	Wound swab	MHT	11 (25.6)
Seman et al., 2021⁶¹	AA	CS	Patient	120	Urine	MHT	6 (9.2)
Seman et al., 2022⁶⁰	AA	CS	Patient	2397	Blood	mCIM	5 (6.7)
Sharew et al., 2025⁶²	ARS	CS	Environment	226	Gown swab	mCIM	6 (9.7)
Shibabaw et al., 2023⁶³	ARS	CS	Patients	384	MS	mCIM	16 (13.2)
Sisay et al., 2025⁶⁴	ARS	CS	Patient	384	MS	mCIM	15 (14.9)
Tadesse et al., 2022⁶⁵	ARS	CS	Patient	384	MS	mCIM	4 (6.1)
Tekele et al., 2021⁶⁶	AA	CS	Patient	312	MS^∞	mCIM	7 (2.6)
Tesfaye et al., 2019⁶⁷	AA	CS	Water	24	Water	mCIM	0.5^⁋ (1.7)
Tilahun et al., 2022⁶⁸	ARS	Cohort study	Patient	384	Wound swab	MHT	13 (11.8)
Tufa et al., 2022⁶⁹	ORS	CS	Patients	684	MS	PCR	2 (10.5)
Woldeteklie et al., 2022⁷⁰	AA	CS	Patient	130	Wound swab	MHT	8 (29.6)
Worku et al., 2022⁷¹	ARS	CS	Patient	384	Stool	mCIM	1 (1.7)
Zakir et al., 2021⁷²	SERS	CS	Patient	212	Rectal swab	mCIM	3 (2.1)
Zelelie et al., 2023⁷³	MC	CS	Patient and AHI	476	Stool	mCIM	4 (2.2)

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Note. AA→ Addis Ababa; AHI→ Apparently Healthy Individuals; ARS→ Amhara Regional State; AST→ Antimicrobial Susceptibility Testing; CDM→ Carbapenemase Detection Method; CPEC→ Carbapenemase producing E. coli; CPKP→ Carbapenemase Producing K. pneumoniae; CS→ Cross Sectional; LS→ Longitudinal Study; MC→ Multi Center (Conducted in more than 1 region or/and city administration); MS→ Multiple Specimen (at least two of the specimens among blood, urine, ear discharge, nasal/wound swabs, sputum, pus, stool, tracheal aspirates cerebrospinal fluid and other body fluids); ORS→ Oromia Regional State; SERS→ Southern Ethiopia Regional State; SRS→ Sidama Regional State; TRS→ Tigray Regional State.

^⁋Continuity correction of 0.5 added for studies reporting 0 CPEC and/or CPKP.

^¥the sample size can be the total number of patients/individuals/water source, food samples, environmental samples included or total bacterial isolates processed in the study.

Study characteristics

Out of 44 studies included, 42 (95.5%) were conducted using a cross-sectional study design, and the majority of the studies were from Amhara Regional State (15/44, 34.1%), followed by Addis Ababa (AA) city administration (13/44, 29.5%), and Southern Ethiopia Regional State (6/44, 13.6%).

The study revealed that 90.5% (38/42) of studies included in this review were conducted among patients with various disease conditions, whereas the remaining 6 studies were conducted on environmental samples (3/44, 6.8%), apparently healthy humans (2/44, 4.5%), and food (1/44, 2.3%). Twenty-six (26/44, 59.1%) and nine (9/44, 20.5%) of the included studies confirmed carbapenemase production in K. pneumoniae and E. coli, phenotypically using mCIM and modified Hodge test (MHT), respectively. The remaining 11 studies reported CPEC and/or CPKP using WGS,⁵² PCR,^59,69 chromogenic culture media,⁴⁸,³⁹ and combined antibiotic discs designed for carbapenemase detection^33,43,47,58 (Table 1).

Pooled prevalence of carbapenemase-producing E. coli and K. pneumoniae

The pooled prevalence of CPEC and/or CPKP was 8.3% (95% CI: 6.3-10.9) with a significant level of heterogeneity among studies (Q = 316.42, I²= 86. 1, p< 0.001) (Figure 2). The funnel plot drawn to assess publication bias was asymmetrical (Figure 3(A)), indicating the presence of publication bias. Egger’s regression asymmetry tests (p< 0.001) indicated that the publication bias was statistically significant. A funnel plot was drawn after applying a trim and fill technique, in which five asymmetrical studies on the left side of the pooled estimate were trimmed to identify and fill their missing counter parts in the right side (Figure 3(B)). After applying the trim and fill techniques, the adjusted pooled prevalence of CPEC and/or CPKP was 9.6% (95% CI = 7.4-12.5), a value that was similar to the original pooled prevalence of 8.3 %, indicating a minimal impact of publication bias.

Figure 3. — (A) Funnel plots assessing publication bias among studies reporting the prevalence of carbapenemase-producing *Escherichia coli* (CPEC) and *Klebsiella pneumoniae* (CPKP) isolated from clinical and non-clinical samples in Ethiopia before applying the trim-and-fill method, indicating potential asymmetry suggestive of publication bias. (B) Funnel plots assessing publication bias among studies reporting the prevalence of CPEC and CPKP isolated from clinical and non-clinical samples in Ethiopia after applying the trim-and-fill technique, which estimates and accounts for potentially missing studies to correct for publication bias. ***Note*** . CPEC: carbapenemase-producing *Escherichia coli*; CPKP: carbapenemase-producing *Klebsiella pneumoniae*.

Subgroup prevalence of carbapenemase producing E. coli and K. pneumoniae

Subgroup analysis was performed by publication year, region, sample type, study participant type, and carbapenemase detection method, provided that there were at least two studies in each subgroup⁷⁴ (Figure 4 and Table 2). Among the studies included in this review, the highest number was published in 2022 (11 studies), followed by 2021 and 2023, each contributing 8 studies. The highest pooled prevalence of CPKP was reported among studies published in 2024 (24.3, 95% CI: 10.5-46.7), whereas the highest pooled prevalence of CPEC was observed in 2023 (9.8%, 95% CI: 5-18.2). The prevalence of CPKP showed a sharp increase among studies published since 2021 (Figure 4).

Figure 4. — Subgroup analysis of the prevalence of carbapenemase-producing *Escherichia coli* and *Klebsiella pneumoniae* in Ethiopia, stratified by year of publication for studies published up to June 30, 2025. This analysis highlights temporal trends in the reported prevalence over time. ***Note*** . CPEC: carbapenemase-producing Escherichia coli; CPKP: carbapenemase-producing Klebsiella pneumoniae.

Table 2.

Sub-group analysis of carbapenemase-producing E. coli and K. pneumoniae in Ethiopia.

Subgroup type	Number of studies	Pooled prevalence (95% CI)	Heterogeneity:
Subgroup type	Number of studies	Pooled prevalence (95% CI)	I² (p-value)
Region/city administration
Addis Ababa city	13	6.4 % (3.7-10.8)	I²= 88.75 (<0.001)
Amhara regional state	15	16.2 % (14.1-18.6)	I²= 85.81 (<0.001)
Multiple study site^⁋	3	2.8% (0.5-14.2)	I²= 86.79 (0.001)
Oromia regional state	4	13% (3.4-38.9)	I²= 89.67 (<0.001)
Sidama regional state	2	8% (4.5-13.9)	I²=0.00 (0.489)
South Ethiopia Regional State	6	8.1% (3.6-17.4)	I²=85.92 (<0.001)
Tigray	1	-	-
Sample source
Clinical samples	40	8% (6-10.7)	I²=86.78 (<0.001)
Non-clinical samples	4	13.3% (6.1-26.8)	I²=74.61 ( 0.008)
Bacterial species
E. coli	43	5.5% (3.7-7.9)	I²=79.11 (<0.001)
K. pneumoniae	39	14.9% (12.1-18.2)	I²=61.33 (<0.001)
Sample type
Blood	4	12.7% (8.4-18.7)	I²= 44.85 (0.142)
Food and environmental sample^⸙	4	13.3% (6.1-26.8)	I²=74.61 (0.008)
Sputum	2	15.4% (8.7-25.7)	I²= 0.00 (0.656)
Stool	11	4.4% (2-9.7)	I²= 94.67 (<0.001)
Urine	5	7.2% (4.7-10.8)	I²= 12.47 (0.334)
Wound swab	4	19.8% (12.8-29.2)	I²= 55.36 (0.081)
Multiple samples^¥	14	7.3% (4.6-11.5)	I²= 81.33 (<0.001)
Study participant
Apparently healthy human	2	1.5 (0.6-4.2)	I²= 46.04 (0.173)
Patients	38	8.8 (6.6-11.5)	I²= 85.64 (<0.001)
Food and environment	4	13.3. (6.1.-26.8)	I²= 74.61 (0.008)
Carbapenemase detection method
CLSI/EUCAST recommended	30	8.5% (6.1-11.6)	8.1% (4.9-13.3)
CLSI/EUCAST not recommended	11	I²= 87.62 (<0.001)	I²= 82.17 (<0.001)

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Note. “-“→ since only one study reported, it is not eligible for subgroup analysis. CLSI→ Clinical Laboratory Standards Institute, EUCAST→ European Committee on Antimicrobial Susceptibility Testing.

^¥include studies that collected at least two different clinical specimens such as urine, blood, ear swabs, sputum, stool, pus, cerebrospinal fluid, and tracheal aspirates. Others: four studies included, each collecting one clinical sample of a different type (water, sputum, wound sample, and aspirates/pus.

^⁋One study was conducted in two regional states (Amhara and Sidama) and Addis Ababa city administration; the second study was conducted in Tigray regional state, Addis Ababa, and Oromia regional state, and the 3^rd study was conducted in Addis Ababa and Amhara Regional State.

^⸙Environmental samples include water and environmental swab samples.

Among 44 studies included in this review, the highest number of studies were from Amhara Regional State (15/44, 34.1%), followed by Addis Ababa city administration (13/44, 29.5%). In the subgroup analysis, the highest pooled prevalence of CPEC and/or CPKP was observed in ARS, 16.22% (95% CI: 14.1-18.6), followed by Oromia Regional State (ORS), 13% (95% CI: 3.4-38.9). Among different samples processed, the highest sub-group prevalence of CPEC and/or CPKP was observed in wound swab (19.8%, 95% CI: 12.8-29.2). Meanwhile, among different sample sources, the prevalence of CPEC and/or CPKP was higher in non-clinical (11.8%, 95% CI: 7.1-19.1) than clinical (8.1%, 95% CI: 6.1-10.8) samples (Table 2).

Carbapenemase encoding gene types reported in Ethiopia

The majority of the studies (36/44, 81.8%) identified carbapenemase production using phenotypic methods only, without detecting carbapenemase-encoding genes or characterizing specific carbapenemase enzyme types. Among the eight studies that reported the types of carbapenemase genes or enzymes, two studies (one from AA⁶⁶ and the other from ORS⁴³) used phenotypic methods to characterize carbapenemase types. In contrast, six studies (6/44, 13.6%) identified carbapenemase-encoding genes using WGS⁵² and PCR.^{32,41,59,60,69} The studies reported a total of 60 carbapenemase genes detected in 51 K. pneumoniae or E. coli isolates, with the bla_NDM-type being the most frequent gene, accounting 85% (51/60) (Table 3).

Table 3.

Carbapenemase-encoding genes detected in E. coli and K. pneumoniae isolated from clinical and non-clinical samples.

Study name	Study area	E. coli and/or K. pneumoniae		Detection method	Total gene detected^⁋	Carbapenemase gene types
Study name	Study area	Total screened (n=777)	Gene detected: n (%)	Detection method	Total gene detected^⁋	bla_NDM type: n (%)	bla_OXA type: n (%)	bla_KPC type n (%)
Abera, 2024³²	AA	264	2 (0.8)	PCR	6	2 (33.3)	2 (33.3)	2 (33.3)
Awoke, 2022⁴¹	AA	132	26 (19.7)	PCR	27	26 (96.3)	-	1 (3.7)
Legese, 2022⁵²	AA, Dessie, Hawassa	103	17 (16.5)	WGS	21	17 (81)	4 (19)	-
Negeri, 2021⁵⁹	AA, Jimma, Mekelle	204	0 (0)	PCR	0	-	-	-
Seman, 2022⁶⁰	AA	55	5 (9.1)	PCR	5	5 (100)	-	-
Tufa, 2022⁶⁹	Asella	19	1 (5.3)	PCR	1	1 (100)	-	-

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Note. “-“→ not detected; AA→ Addis Ababa, WGS→ Whole genome sequencing; PCR→ Polymerase Chain Reaction.

^⁋include multiple or single gene types detected in a single E. coli and/or K. pneumoniae.

Multi drug resistant profile of E. coli and K. pneumoniae reported by studies included in the review

Among 44 studies included in this review, 31 (70.5%) reported the MDR level for K. pneumoniae and/or E. coli isolates.^{30–34,36–43,45–50,55,56,58,59,61,62,64,66,68,71,73} However, 13 studies (29.5%) did not include the MDR level of E. coli and/or K. pneumoniae because of the study scope, did not perform antimicrobial susceptibility testing or did not report MDR results. The pooled prevalence of MDR K. pneumoniae and/or E. coli reported in 31 studies were 78.4% (95% CI= 71-84.2) with a significant level of heterogeneity among studies (Q= 762.60, I²= 96.10, p< 0.001). Sub-group analysis of MDR E. coli and K. pneumoniae was done on 20 studies (20/31, 43.5%) based on study periods. The remaining 11 studies each reported data on E. coli and/or K. pneumoniae at different time periods, and therefore were not eligible for sub-group analysis.^{31–33,38,41,43,47,48,59,66,73}

The pooled MDR level was high throughout the study period for both E. coli and K. pneumoniae, ranging from 69.2% to 92.3%. The highest pooled MDR rate for K. pneumoniae was reported by studies conducted in 2023 as 92% (95% CI: 79.6-97.1), while it was 86.4% (95% CI: 77.6-92.1) for E. coli in the same year. In the sub-group analysis, both the pooled MDR rate and the pooled prevalence of CPEC and/or CPKP showed an increasing trend from 2017/18 to 2023 (Figure 5).

Figure 5. — Pooled prevalence of MDR rate and CPEC and/or CPKP conducted in different study periods in Ethiopia and published up to June 30, 2025. ***Note*** . CPEC: carbapenemase-producing *Escherichia coli*; CPKP: carbapenemase-producing *Klebsiella pneumoniae;* MDR: Multidrug resistance.

Discussion

This systematic review and meta-analysis synthesized data from 44 studies that reported on CPEC and CPKP across various regions and city administrations in Ethiopia. However, only 13.6% (6/44) of these studies identified the specific carbapenemase-encoding genes^{32,41,52,59,60,69} despite the critical importance of this information for patient management, infection prevention, and antimicrobial stewardship.^75,76

The overwhelming majority of included studies (90.9%) focused on human subjects, reflecting a significant research gap in surveillance in animal and environmental sources of CPEC and CPKP. This underrepresentation is concerning, particularly in light of the growing evidence that animals and the environment serve as significant reservoirs of multidrug-resistant (MDR) organisms in Ethiopia and across sub-Saharan Africa.^77–79 These findings underscore the urgent need to incorporate One Health approaches to effectively control the spread of carbapenem-resistant organisms.⁸⁰

The pooled prevalence of CPEC and/or CPKP in Ethiopia was 8.3% (95% CI: 6.3-10.9), which was higher than figures reported from Ghana (5.6%),⁸¹ Gabon (1.61%),⁸² and Belgium (0.57%).⁸³ This relatively higher prevalence may reflect inadequate infection-prevention practices and the widespread use of self-medication, including inappropriate antibiotic use, in Ethiopia.^84,85 Conversely, the prevalence in the present review was lower than that observed in Pakistan (28%),⁸⁶ in other sub-Saharan African countries (9-60%), and the majority of North African countries (2.3-67.7%).⁸⁷ Such variation may partly result from differences in diagnostic methods, for example, 20.5% of included studies in the present review used the modified Hodge test (MHT), which has low sensitivity and was removed from CLSI recommendations in 2018, potentially underestimating prevalence.⁹

In the sub-group analysis by bacterial species, the pooled prevalence of CPKP and CPEC was 14.9% and 5.5%, respectively. This was significantly higher than the pooled prevalence of carbapenem-resistant K. pneumoniae (5.8%) and E. coli (4.1%) in West Africa.⁸⁸ However, the prevalence in our review was lower than the global estimate, where the pooled prevalence reported 49.4% for carbapenem-resistant K. pneumoniae and 26.42% for carbapenem-resistant E. coli.⁸⁹ Meanwhile, a study from Pakistan also reported a higher prevalence than our study, as 24% and 9% for carbapenem-resistant K. pneumoniae and E. coli, respectively.⁹⁰ These differences may be attributable to regional variation, differences in carbapenemase detection methods, or the inclusion of non-carbapenemase resistance mechanisms in estimating prevalence.

Our review also showed that the pooled prevalence of CPEC and/or CPKP in clinical samples was 8%, which is higher than that reported in a previous systematic review conducted in Ethiopia on clinical samples (5.44%).⁹¹ This variation may be associated with the rapidly increasing prevalence of CPEC and CPKP in developing countries.⁹² Regionally in Ethiopia, the highest pooled carbapenemase prevalence was observed in the Amhara regional state (16.2%), followed by Oromia regional state (13%). These variations may reflect the true epidemiological differences across regions or may be influenced by differences in IPC practices among hospitals, as well as methodological variations among the studies included in this review. In a previous study in Ethiopia, the highest pooled prevalence was reported in the country’s capital, Addis Ababa (6.45%), followed by ARS (5.27%).⁹¹ Finding more than triple the prevalence of ARS in this review than in the previous study,⁹¹ coupled with a higher prevalence in regional states than in the country capital, might indicate a widespread and imminent threat due to CPEC and CPKP in Ethiopia. If not properly managed, a similar increase may occur in other parts of the country, as evidenced in other parts of the world.^93,94 Higher pooled prevalence of ARS might be associated with significant knowledge and practice gaps regarding AMR among the general public, patients, and livestock producers.⁹⁵ Since obtaining antibiotics without a prescription is easy in the ARS,⁹⁶ this creates favorable conditions for frequent exposure to broad-spectrum antibiotics, an identified risk factor for CPEC and CPKP infection and carriage.^97,98

The subgroup analysis showed that the pooled prevalence of CPEC and/or CPKP among studies published during the first 6 months of 2025 was 12. 8%, representing an approximately threefold increase compared with the 2019 subgroup pooled prevalence reported in this study (4.4%). Though there is an increasing trend globally,⁹² the amount of increase in the present study was alarming, which might be associated with the use of carbapenem as empiric therapy, a weak regulatory system on antibiotic use, a lack of AMR surveillance based on a One Health approach, and inadequate infection prevention and control measures.^84,85

In the present review, bla_NDM-type was the most frequent gene identified, accounting for 85% of gene types reported by articles included in this review. This indicates a significant public health threat, given that infections caused by metallo-β-lactamase (MBL) type of carbapenemase-producing bacteria often did not respond to conventional and newer β-lactamase inhibitor combination therapies, unlike infections caused by serine carbapenemase-producing bacteria.⁹⁹ The bla_NDM carbapenemase gene has frequently been identified on highly transmissible plasmids with high evolution potential¹⁰⁰ and has been associated with outbreaks.¹⁰¹ This may further facilitate the dissemination of bla_NDM-type variants throughout the country unless effective and sustained surveillance and infection prevention measures are implemented. Thus, in the absence of effective control measures, the dominant bla_NDM carbapenemase-encoding gene in clinical isolates may disseminate to environmental reservoirs, thereby increasing the overall burden of infection and establishing the environment, water, and food as potential sources of carbapenemase-producing bacterial infections.

The predominance of the bla_NDM carbapenemase gene observed in this study aligns with reports from Central and West Africa^88,102 and Pakistan.⁸⁶ This trend likely reflects the global spread of bla_NDM originally endemic to the Indian subcontinent.^99,103 In contrast, studies from Ghana,⁸¹ Saudi Arabia,¹⁰⁴ Iran,¹⁰⁵ Switzerland,¹⁰⁶ and Belgium⁸³ reported bla_OXA-48 as the predominant carbapenemase gene. This variation might be explained by the rapid international spread of the bla_OXA-48 gene⁹³ rather than restricting itself to the Middle East and North Africa.¹⁰⁷ The low-level bla_OXA genes reported in our study may also be attributed to their low level of in vitro carbapenem resistance ability, leading to a low detection rate by the phenotypic method.^76,93 Since 93.2% of studies in this review relied on phenotypic techniques, such underestimation is plausible.

The pooled prevalence of MDR K. pneumoniae in the present study was 81.9%. This was higher than the pooled MDR prevalence of studies published from 2015 to 2020, as 68%.¹⁰⁸ The difference might be associated with the true reflection of an increasing trend in MDR, as evidence by a comparable finding in 2022, Ethiopian (86%).¹⁰⁹ The result in our review was also higher than a study in Nepal¹¹⁰ reporting 55%. The variation might be associated with differences in infection prevention and control measures. The pooled MDR prevalence of E. coli in the present study was 72.9%. This was comparable with a previous study in Ethiopia, 70%,¹⁰⁸ but higher than Asia, 66.3%,¹¹¹ and global pooled prevalence¹¹² reporting 5.7%, 22%, and 31.3% for animal, human, and environmental isolates, respectively. The variations might be due to the difference in the number of studies, the number of samples analyzed, and the infection prevention and control measures in place.

The present systematic review and meta-analysis were the first to determine the pooled prevalence of CPEC and CPKP isolated from clinical and non-clinical samples and identify the dominant type of carbapenemase-encoding genes in Ethiopia by searching databases without study period and population (human, animal, and environmental samples) restriction. The majority of the studies included (84.1%) were recent reports published since 2021, allowing for the recent pooled prevalence of carbapenemase production in Ethiopia. On the other hand, the present review has limitations. The search was limited to PubMed, Google scholar, and African Journal Online, without inclusion of databases such as Embase, Scopus, and Web of Science, which may have introduced potential selection bias. Moreover, the majority of the studies (81.8%) included in our systematic review relied solely on phenotypic methods for the detection of carbapenemase production without characterizing carbapenemase-encoding genes. This limitation may have reduced the ability of these studies to determine the diversity and distribution of carbapenemase-encoding genes in Ethiopia. Since carbapenemase enzymes differ in their spectrum of activity, understanding the distributions of the enzymes and their encoding genes is clinically important. However, these data were not reported in the majority of studies included in this review. Although full-text availability was an inclusion criteria, no eligible studies were excluded due to lack of access to full text, however, the potential for selection bias due to inaccessible studies cannot be completely ruled out. Furthermore, the high heterogeneity observed among the included studies should be considered when interpreting the pooled estimate.

Conclusions

The pooled prevalence of carbapenemase-producing E. coli and K. pneumoniae in Ethiopia is high and rising, posing a significant public health challenge. Notably, non-clinical sources reported slightly higher prevalence rates than clinical sources, underscoring the neglected role of environmental and animal reservoirs. The dominance of bla_NDM metallo-β-lactamase, which is not susceptible to β-lactamase inhibitor combination therapies, further limits treatment options. The higher prevalence of MDR E. coli and K. pneumoniae in Ethiopia, together with the elevated subgroup prevalence of CPEC and CPKP in ARS and ORS, highlights a major public health challenge and underscores the potential for further dissemination across other regions of the country, urging close attention. Future research should focus on large-scale, multicenter genomic studies to elucidate the full diversity of carbapenemase genes, their transmission dynamics, and risk factors across human, animal, and environmental sectors. Implementation of established CPEC and CPKP prevention and control strategies, including strict infection control practices, use of molecular diagnostic methods, strengthened antimicrobial surveillance and stewardship programs, can help to reduce and tackle further increases and potential outbreaks.

Supplemental material

Supplemental material - Prevalence, multidrug resistance patterns, and carbapenemase-encoding genes of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli from clinical and non-clinical samples in Ethiopia: Systematic review and meta-analysis

sj-pdf-1-smo-10.1177_20503121261488385.pdf^{(176.2KB, pdf)}

Supplemental material for Prevalence, multidrug resistance patterns, and carbapenemase-encoding genes of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli from clinical and non-clinical samples in Ethiopia: Systematic review and meta-analysis by Chalachew Genet, Wendemagegn Enbiale, Anna Rommerskirchen, Addisu Melese, Baye Yirga Adugna, Zeleke Ayenew, Hiwot Tadesse, Bayeh Abera, Endalkachew Nibret, Abaineh Munshea Abitew in Sage Open Medicine

sj-pdf-2-smo-10.1177_20503121261488385.pdf^{(373.4KB, pdf)}

Appendix.

List of abbreviations

AMR: Antimicrobial Resistance
CLSI: Clinical Laboratory Standard Institute
CPEC: Carbapenemase Producing E. coli
CPKP: Carbapenemase Producing K. pneumoniae
EUCAST: European Committee on Antimicrobial Susceptibility Testing
MDR: Multidrug resistance
mCIM: Modified Carbapenemase Inactivation Method
MHT: Modified Hodge Test
NDM: New Delhi metallo-β-lactamase
PCR: Polymerase Chain Reaction
WGS: Whole Genome Sequencing

Authors’ contribution: Conceptualization and designing the study was done by C.G., W.E., A.R., E.N., and A.M. Literature search, article quality assessment, data extraction was done by C.G., A.M. and B.Y. Analyzing, interpreting the data and writing the draft was done by CG. Reviewing the manuscript was done by CG, W.E., A.R., A.M., B.Y.A, Z.A., H.T., B.A., E.N., and A.M.A.

Funding: The authors received no financial support for the research, authorship, and/or publication of this article.

The authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Supplemental material: Supplemental material for this article is available online.

ORCID iDs

Chalachew Genet https://orcid.org/0000-0001-8631-5094

Endalkachew Nibret https://orcid.org/0000-0002-7063-2877

Abaineh Munshea Abitew https://orcid.org/0000-0002-1469-2189

Data Availability Statement

All data is included within the manuscript.*

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PERMALINK

Prevalence, multidrug resistance patterns, and carbapenemase-encoding genes of carbapenemase-producing Klebsiella pneumoniae and Escherichia coli from clinical and non-clinical samples in Ethiopia: Systematic review and meta-analysis

Chalachew Genet

Wendemagegn Enbiale

Anna Rommerskirchen

Addisu Melese

Baye Yirga Adugna

Zeleke Ayenew

Hiwot Tadesse

Bayeh Abera

Endalkachew Nibret

Abaineh Munshea Abitew

Abstract

Background

Methods

Results

Conclusions

Introduction

Methods

Study period and setting

Literature sources and search strategy

Screening of studies and eligibility record identification process

Figure 1.

Inclusion and exclusion criteria

Quality assessment and data extraction

Data processing and statistical analysis

Publication bias assessment

Results

Study selection

Table 1.

Study characteristics

Pooled prevalence of carbapenemase-producing E. coli and K. pneumoniae

Figure 2.

Figure 3.

Subgroup prevalence of carbapenemase producing E. coli and K. pneumoniae

Figure 4.

Table 2.

Carbapenemase encoding gene types reported in Ethiopia

Table 3.

Multi drug resistant profile of E. coli and K. pneumoniae reported by studies included in the review

Figure 5.

Discussion

Conclusions

Supplemental material

Appendix.

List of abbreviations

ORCID iDs

Data Availability Statement

References

Associated Data

Supplementary Materials

Data Availability Statement

ACTIONS

PERMALINK

RESOURCES

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