First Standardized Antibiogram from Somaliland Reveals Alarming Antibiotic Resistance

In a modest laboratory in Hargeisa, researchers have quietly achieved something that has never been done before in Somaliland: the production of a standardized, internationally comparable cumulative antibiogram. The study, published in New Microbes and New Infections, documents a full year of bacterial susceptibility data from the country’s principal public tertiary referral hospital, analyzed according to the Clinical and Laboratory Standards Institute’s M39-A4 guideline and processed through WHONET, the free epidemiological software developed by the World Health Organization. The results paint a sobering picture of antimicrobial resistance in a region that has long remained a blind spot on the global surveillance map, and they demonstrate that even severely resource-constrained laboratories can generate data rigorous enough to inform both local prescribing and international monitoring frameworks such as GLASS.

The research team, led by Nouh Botan and colleagues, conducted a retrospective cross-sectional review of routine microbiology records collected between January 1 and December 31, 2025. From the laboratory registry, they identified 286 positive bacterial culture records with antimicrobial susceptibility results, which together generated 1,787 individual test records because each isolate was challenged against multiple drugs. Applying the M39-A4 deduplication rule, which counts only the first unique isolate per patient per species to avoid statistical distortion from repeated sampling, the team excluded nine repeat isolates and arrived at a final analytic cohort of 277 unique clinical isolates. Intermediate susceptibility results were conservatively categorized as resistant for antibiogram purposes, in line with the guideline’s recommendations, while routine patient care continued to follow the laboratory’s standard reporting procedures.

The identity of the organisms tells its own story. Escherichia coli dominated the dataset, accounting for 50.9 percent of all isolates, followed by Staphylococcus aureus at 33.6 percent. Pseudomonas species made up 6.9 percent, and other enteric organisms, primarily Proteus and Klebsiella species, contributed 8.6 percent. Half of the isolates came from urine specimens and 39 percent from wound or pus samples, with blood cultures representing only 2.2 percent. The cohort was almost perfectly balanced by sex, and a slight majority of isolates originated from outpatient services. Notably, patient age and detailed clinical diagnoses were unavailable, because the retrospective laboratory database captured only microbiological surveillance variables, a limitation that reflects the sparse data infrastructure typical of the setting.

The susceptibility findings are where the study becomes genuinely alarming. Ampicillin, a legacy frontline agent, showed a susceptibility rate of just 7.3 percent among E. coli isolates, meaning it is essentially useless as an empirical option. Ciprofloxacin, a fluoroquinolone once considered a reliable workhorse, maintained susceptibility in only 19.0 percent of E. coli isolates, translating into an overall resistance burden of 81 percent. Among the broader Enterobacteriaceae pool, ciprofloxacin susceptibility fell to 16.3 percent. These figures align with disturbing trends reported from tertiary hospitals in Ethiopia, Kenya, and elsewhere in East Africa, where Gram-negative organisms have steadily accumulated resistance to fluoroquinolones, aminoglycosides, and third-generation cephalosporins.

Not every result was bleak. Nitrofurantoin, an older drug largely reserved for urinary infections, retained a susceptibility footprint of 78.5 percent among E. coli isolates and performed even better against S. aureus at 88.3 percent, supporting its continued role in empirical treatment of uncomplicated urinary tract infections. Gentamicin offered moderate coverage, with E. coli showing 60.4 percent susceptibility, although the Enterobacteriaceae pool fared worse at 51.1 percent. These patterns suggest that carefully chosen older, inexpensive agents can still deliver clinical value in the region, provided that prescribing decisions are anchored to locally generated susceptibility data rather than habit or availability.

Perhaps the most consequential finding concerns meropenem, a carbapenem antibiotic typically held in reserve as a last-line option for serious Gram-negative infections. Only 30.5 percent of tested E. coli isolates and 30.5 percent of the Enterobacteriaceae pool were classified as susceptible, with an overall susceptibility of 40.0 percent across organisms. The authors are careful to caution that reduced phenotypic susceptibility to meropenem should not be interpreted as evidence of specific carbapenemase-producing organisms without species-level identification and molecular confirmation, tools that were not available in this setting. Nevertheless, the signal is worrying enough that the researchers call urgently for confirmatory molecular characterization and continued prospective surveillance before any definitive epidemiological conclusions about carbapenem resistance in Somaliland can be drawn.

An exploratory subgroup analysis compared urinary and wound E. coli isolates and revealed intriguing heterogeneity. Wound isolates showed higher ciprofloxacin susceptibility than urinary isolates, 30.8 percent versus 17.2 percent, and higher gentamicin susceptibility at 68.2 percent versus 58.7 percent, but markedly lower meropenem susceptibility at 13.3 percent versus 35.4 percent. Because the subgroup sample sizes were small, the team used Fisher’s exact test and reported p-values of 0.267, 0.479, and 0.128 respectively, none reaching statistical significance. The authors emphasize that these comparisons are hypothesis-generating rather than conclusive, but they illustrate how specimen source can shape resistance profiles even within a single institution, a nuance that cumulative antibiograms stratified by specimen type can capture and communicate to prescribers.

Methodological honesty is a defining feature of the paper. Antibiotic-specific denominators varied throughout the dataset because susceptibility testing reflected routine clinical practice rather than a uniform research protocol: organism-specific panels, selective testing such as nitrofurantoin applied mainly to urinary isolates, individual clinician requests, and intermittent shortages of susceptibility disks and other consumables all meant that not every isolate was tested against every drug. Species-level identification relied on routine phenotypic and basic biochemical methods, since advanced techniques such as MALDI-TOF mass spectrometry and molecular assays were unavailable, and some organisms were therefore reported only at the genus level. Standardized daily internal quality control with ATCC reference strains could not be performed due to resource limitations, and breakpoint interpretation followed the CLSI- or EUCAST-based criteria accompanying whichever products were procurable. The authors explicitly acknowledge these constraints, arguing that transparent documentation of real-world laboratory conditions is itself a contribution toward building sustainable diagnostic capacity.

Beyond the numbers, the study is a proof of concept. The relatively modest culture volume of 286 positive records over a full year likely reflects broader diagnostic barriers: out-of-pocket costs for patients, heavy reliance on empirical therapy, intermittent supply constraints, and limited culture-guided prescribing. In Somaliland and neighboring Somali territories, healthcare is financed largely through direct patient payments, and antimicrobials are frequently obtainable without prescription oversight, while regional literature has documented incomplete counseling on dosing intervals and treatment duration. The authors also point to wider drivers of resistance that hospital data alone cannot capture, including unregulated retail antibiotic sales, veterinary antimicrobial use in pastoral livestock systems, and environmental exposures, arguing that long-term containment will require integrated collaboration across human health, veterinary medicine, and public health surveillance, consistent with a One Health approach.

What emerges from Hargeisa is both a warning and a template. The warning is that resistance to commonly used and even last-resort antibiotics is already substantial in a population previously invisible to global surveillance, and that without intervention, prescribers in the region are effectively practicing blind. The template is the demonstration that WHONET software, CLSI M39-A4 methodology, and disciplined deduplication of routine laboratory records can produce a credible, facility-specific antibiogram without expensive infrastructure. The researchers conclude that strengthening sustainable laboratory capacity, including reliable procurement of culture media, susceptibility testing materials, and equipment, should accompany routine antibiogram surveillance to support antimicrobial stewardship and evidence-based prescribing. For a region where no standardized cumulative antibiogram existed before, this baseline dataset is a small dataset with outsized significance, offering clinicians their first locally grounded map of which drugs still work and which no longer do.

Subject of Research: Antimicrobial resistance surveillance and cumulative antibiogram development at a tertiary referral hospital in Somaliland

Article Title: Standardized antimicrobial resistance surveillance in Somaliland: A hospital-based baseline evaluation using CLSI M39 and WHONET

Article References: Botan, N., Ali, A. S. O., Warsame, H. A., & Ali, Z. (2026). Standardized antimicrobial resistance surveillance in Somaliland: A hospital-based baseline evaluation using CLSI M39 and WHONET. New Microbes and New Infections, 74, Article 101861. https://doi.org/10.1016/j.nmni.2026.101861

Image Credits: AI Generated

DOI: 10.1016/j.nmni.2026.101861

Keywords: antimicrobial resistance, Somaliland, cumulative antibiogram, CLSI M39-A4, WHONET, Escherichia coli, meropenem, ciprofloxacin, nitrofurantoin, surveillance, Hargeisa, East Africa