Drug-Resistant Superbugs Surge in Somali ICUs, First Long-Term Study Reveals

In the intensive care units of a 400-bed tertiary referral hospital in Mogadishu, bacteria are quietly winning an arms race against modern medicine. A five-year retrospective study published in Frontiers in Antibiotics has documented, for the first time in any Somali healthcare facility, the longitudinal trajectory of multidrug-resistant Enterobacteriaceae among critically ill patients. The findings are stark: overall multidrug resistance prevalence stood at 37.9% across 758 unique isolates collected between January 2019 and December 2024, but the temporal pattern tells a more alarming story. Resistance remained relatively stable at 24–25% during 2019 and 2020, dipped to 15% in 2021, and then escalated dramatically to 36.4% in 2022, 47.8% in 2023, and 54.2% by 2024. The Cochran-Armitage test for linear trend confirmed the escalation was statistically significant (χ² = 43.91, p < 0.001), and the 2024 estimate does not overlap the 2021 nadir, indicating a genuine deterioration rather than statistical noise.

The study team, led by researchers from Banadir University, Somali National University, Hormuud University, and the Mogadishu-Somalia-Turkey Recep Tayyip Erdoğan Training and Research Hospital, systematically reviewed 4,464 initial isolates from the laboratory information management system. After removing duplicates (n = 2,118), non-bacterial organisms (n = 54), and non-Enterobacteriaceae Gram-negative isolates (n = 1,534), 758 unique Enterobacteriaceae isolates representing individual patient episodes were retained for analysis. This deduplication strategy, retaining only the first recorded culture episode per patient, avoids over-representation of patients with repeated cultures and ensures each isolate reflects a distinct clinical event. The cohort was drawn from Emergency and General Intensive Care Units admitting approximately 2,000 to 2,500 critically ill patients annually, a population uniquely vulnerable to resistant infections owing to invasive mechanical ventilation, central venous and urinary catheterization, and repeated broad-spectrum antibiotic exposure.

Microbiologically, the cohort was dominated by two genera. Escherichia coli accounted for 48.3% of isolates and Klebsiella spp. for 45.9%, together representing 94.2% of the entire collection. Enterobacter spp. (2.2%), Proteus spp. (2.0%), Serratia spp. (0.7%), Citrobacter spp. (0.5%), Pantoea spp. (0.3%), and Morganella morganii (0.1%) made up the remainder. The demographic profile showed that 63.5% of isolates came from male patients, with the age distribution spanning 5.0% aged 20 years or younger, 37.9% aged 21–40, 24.7% aged 41–60, and 32.5% over 60. Sputum specimens predominated at 62.3% of the collection, followed by urine (21.5%) and blood (16.2%), reflecting the high burden of suspected lower respiratory tract infection among mechanically ventilated patients in this setting.

Antimicrobial susceptibility testing followed Clinical Laboratory Standards Institute (CLSI) M100 performance standards using the Kirby-Bauer disk diffusion method on Mueller-Hinton agar. Eight antimicrobials representing eight distinct classes were tested: colistin, meropenem, piperacillin-tazobactam, cefoperazone-sulbactam, amikacin, tigecycline, trimethoprim-sulfamethoxazole, and ciprofloxacin. Because disk diffusion is not recommended for colistin susceptibility testing in Enterobacteriaceae owing to poor agar diffusion, colistin interpretation relied on broth microdilution using CLSI M07 reference methodology. Under CLSI M100 criteria, only intermediate (MIC ≤2 µg/mL) and resistant (MIC ≥4 µg/mL) categories are recognized for colistin against Enterobacterales, with no susceptible category defined. A critical methodological correction was applied during the study: 21 isolates (2.8% of the cohort) belonging to Proteus spp., Serratia spp., and Morganella morganii are intrinsically resistant to polymyxins as a consequence of constitutive lipid A modification encoded by the arnBCADTEF operon, which neutralizes the anionic charge of lipopolysaccharide and prevents polymyxin binding. These isolates were excluded from the denominator used to estimate acquired colistin resistance, yielding a corrected denominator of 737.

The species-level pattern of multidrug resistance emerged as the study’s most consequential microbiological finding. Klebsiella spp. demonstrated the highest MDR prevalence at 54.9%, with over half of all Klebsiella isolates resistant to at least one agent in three or more antimicrobial classes. Enterobacter spp. followed at 52.9%, while Escherichia coli showed a markedly lower MDR rate of 22.1%. In the multivariable logistic regression model, relative to Klebsiella spp., E. coli isolates had significantly reduced odds of multidrug resistance (adjusted odds ratio 0.27; 95% confidence interval 0.19–0.38; p < 0.001), and Proteus isolates similarly showed lower odds (AOR 0.19; 95% CI 0.05–0.70; p = 0.012). Neither patient sex, age group, nor ICU type was significantly associated with MDR status in the adjusted analysis. The model explained approximately 10.5% of the variance in MDR status (pseudo R² = 0.105), indicating that bacterial species identity is the primary driver of resistance in this cohort, while demographic and specimen variables available in the retrospective laboratory database account for only a small fraction of the observed variation.

Specimen source showed a significant bivariate association with multidrug resistance (χ² = 34.81, p < 0.001). Sputum specimens harbored the highest proportion of MDR isolates at 44.9%, followed by blood at 35.8% and urine at 19.0%. In the multivariable model, sputum isolates showed a non-significant trend toward higher odds of MDR relative to blood (AOR 1.40; 95% CI 0.90–2.17; p = 0.136), while urine isolates tended toward lower odds (AOR 0.61; 95% CI 0.34–1.09; p = 0.097). The predominance of respiratory specimens carrying the highest resistance burden is consistent with the epidemiology of ventilator-associated pneumonia, in which mechanically ventilated patients undergo protracted exposure to broad-spectrum beta-lactams administered empirically for suspected lower respiratory tract infection, creating an intensely selective environment within respiratory secretions that preferentially enriches for highly resistant Gram-negative bacilli.

The antimicrobial susceptibility landscape revealed profound therapeutic constraints. Among tested multidrug-resistant isolates, ciprofloxacin resistance reached 95.4%, trimethoprim-sulfamethoxazole resistance 92.9%, and meropenem resistance 77.5%. Piperacillin-tazobactam resistance among MDR isolates was 94.3%, cefoperazone-sulbactam 83.9%, and amikacin 54.8%. These figures leave virtually no oral or first-line therapeutic option for patients infected with MDR strains. By contrast, colistin retained the greatest in vitro activity: among the 737 isolates from genera without intrinsic polymyxin resistance, acquired resistance was documented in only 1.2% (9/735 tested). All nine colistin-resistant isolates were multidrug-resistant, comprising six Klebsiella spp., two E. coli, and one Pantoea sp. The proportion of colistin resistance among MDR isolates was 3.2% (9/283) versus 0/452 among non-MDR isolates (p = 0.001), a pattern more compatible with therapy-selected chromosomal resistance within an already-resistant population than with independent plasmid acquisition, although the authors caution that with only nine isolates this observation is hypothesis-generating rather than conclusive. Because confirmatory broth microdilution was applied only to isolates screening non-susceptible on disk diffusion, the colistin figure represents a conservative lower-bound estimate, and heteroresistant subpopulations below the detection threshold of standard broth microdilution may have been misclassified as non-resistant.

Tigecycline resistance was 17.4% among the 155 isolates in which it was tested, but the agent was tested in only 20.4% of the cohort, and testing was clinically directed rather than systematic, preferentially applied to isolates already known to be extensively resistant. The authors note that resistance proportions for agents with low testing coverage are subject to ascertainment bias in the direction of overestimation and should be regarded as provisional pending systematic panel testing. Testing coverage ranged from 99.7% for colistin and 95.0% for meropenem to 15.0% for trimethoprim-sulfamethoxazole, and all susceptibility proportions reported use the number of isolates actually tested for each agent as the denominator.

The temporal trajectory spanning the pre-pandemic, pandemic, and post-pandemic periods offers unique insights into how extraordinary disruptions in healthcare delivery interact with resistance patterns in low-resource settings. The 2021 decline rests on the smallest annual sample in the series (n = 70; 95% CI 7.9–24.3%) and is temporally compatible with several explanations the dataset cannot distinguish, including transient benefits of intensified infection prevention measures during the acute COVID-19 phase, reduced patient volume, and altered specimen submission practice. Notably, the specimen mix in 2021 differed markedly from surrounding years, with sputum accounting for 20 of 70 isolates compared with 127 of 176 in 2022; since sputum isolates carried the highest MDR prevalence, part of the apparent 2021 decline may reflect this compositional shift rather than a change in underlying resistance. The subsequent resurgence to 54% by 2024 aligns with documented global post-pandemic antimicrobial resistance trends, including disruptions to stewardship programs and increased antimicrobial consumption. A 2024 analysis from the WHO Global Antimicrobial Resistance and Use Surveillance System demonstrated statistically significant positive correlations between beta-lactam and fluoroquinolone consumption and increased recovery of resistant E. coli and Klebsiella spp. from bloodstream infections across participating countries. However, the authors emphasize that antimicrobial consumption data were not available for this institution, and the temporal association documented here should be read as a signal warranting prospective investigation rather than as evidence that post-pandemic health-system disruption caused the resurgence.

Somalia currently lacks a functional national antimicrobial resistance surveillance system, established WHO GLASS participation, or a formally adopted National Action Plan on Antimicrobial Resistance. This institutional absence stands in sharp contrast to regional peers, where two-thirds of WHO African Region countries have developed national action plans and 30 of 47 countries participate in WHO GLASS. The authors call for urgent institutional responses including the establishment of a quarterly institutional antibiogram, creation of a multidisciplinary Antimicrobial Stewardship Committee, and restricted-use protocols for carbapenems and colistin requiring infectious disease consultation and documented clinical justification. At the national level, they advocate formal engagement with the WHO GLASS framework, development of a Somalia-specific National Action Plan incorporating multicenter surveillance and molecular resistance characterization, and establishment of a sentinel hospital surveillance network anchored at three to five geographically representative hospitals. The single-center design means the findings should be interpreted as indicative of high-acuity tertiary ICU settings in urban Somalia rather than nationally representative estimates, and multicenter prospective studies are essential to validate these findings across Somalia’s diverse healthcare landscape. Given that global data report 30-day mortality rates of 50–57% among ICU patients with carbapenem-resistant Enterobacteriaceae bacteremia, the clinical urgency of the resistance escalation documented in this Mogadishu ICU could not be clearer.

Subject of Research: Antimicrobial Resistance

Article Title: Epidemiology and predictors of multidrug-resistant Enterobacteriaceae in intensive care units of a tertiary hospital in Somalia: a five-year retrospective study (2019–2024)

Article References: Zubair, O. S., Abdi, Y. H., Ali, T. A., Issack, Z. I., & Ahmed, A. A. (2026). Epidemiology and predictors of multidrug-resistant Enterobacteriaceae in intensive care units of a tertiary hospital in Somalia: a five-year retrospective study (2019–2024). Frontiers in Antibiotics, 5, Article 1889216. https://doi.org/10.3389/frabi.2026.1889216

Image Credits: AI Generated

DOI: 10.3389/frabi.2026.1889216

Keywords: antimicrobial resistance, Enterobacteriaceae, intensive care units, Somalia, Klebsiella, colistin, antimicrobial stewardship, WHO GLASS, Epidemiology, predictors, multidrug-resistant, intensive