The research, led by Tizazu Zelelie, Biniam Mekonnen, and Demiss Nigussie and published in Public Health in Practice, was designed around the One Health framework, the internationally endorsed recognition that human, animal, and environmental health are inseparable. First formalized in 2015 by the tripartite coalition of the Food and Agriculture Organization, the World Health Organization, and the World Organization for Animal Health, and later expanded to include the United Nations Environment Programme, the approach acknowledges that resistant bacteria and their genes do not respect the boundaries between hospital wards, farms, and waterways. Resistant organisms shed into the environment can transfer their resistance genes horizontally to other bacteria infecting humans and animals, creating reservoirs of resistance that no single-sector intervention can drain. East Africa presents particularly fertile ground for this dynamic, combining agricultural and pastoral livelihoods with patterns of antimicrobial misuse, limited access to clean water, poor sanitation, and inadequate infection prevention infrastructure.

To capture the full scope of the problem, the authors searched PubMed, ScienceDirect, and Google Scholar for studies reporting carbapenem-resistant E. coli isolated from humans, animals, food, or the environment in thirteen East African countries. Following the PRISMA reporting guidelines and registered prospectively on PROSPERO, the review screened more than 4,300 records, ultimately retaining twenty-nine studies that met rigorous eligibility criteria. Each study was assessed for bias by two independent reviewers using the Newcastle Ottawa Scale, and all were judged to carry low risk of bias, scoring at or above the six-star threshold. The researchers then performed a random-effects meta-analysis using restricted maximum likelihood estimation in the R statistical environment, quantifying heterogeneity with the I-squared statistic and probing publication bias with funnel plots and Egger’s test.

The numbers underlying the headline finding are substantial. Across the included studies, the combined sample size reached 11,581 participants and specimens, from which 3,908 E. coli isolates were recovered. Of those, 442 strains proved resistant to carbapenem antibiotics. The studies were heavily weighted toward clinical settings, with seventy-six percent hospital-based and human samples accounting for nearly eighty percent of all sources, but the remainder drew from environmental reservoirs, food, and animals, giving the analysis its distinctive cross-sector character. Geographically, Ethiopia dominated the evidence base with fourteen studies, followed by Uganda with seven, Sudan with four, Tanzania with two, and single studies from Djibouti and Kenya. No eligible studies emerged from the other seven countries in the region, itself a telling indicator of surveillance gaps.

Beneath the pooled estimate of 12.7 percent lies a sobering spread. The lowest reported prevalence was 0.5 percent in an Ethiopian study, while the highest, drawn from sewage at a Ugandan referral hospital, reached a remarkable 50 percent. In subgroup analyses, Sudan recorded the highest country-level pooled prevalence at 24.7 percent, followed by Uganda at 17.4 percent and Ethiopia at 9.9 percent. More striking still was the finding that the environment emerged as the most contaminated interface of all, with a pooled prevalence of 24.2 percent among environmental isolates, compared with 11.9 percent in humans, 7.7 percent in food, and 4.2 percent in animals. Clinical samples of multiple types yielded a pooled prevalence of 15.8 percent. These figures suggest that hospitals, farms, and communities are continuously seeding the environment with resistant organisms, which in turn serve as a reservoir capable of reinfecting the human population.

Genetic analysis revealed the molecular arsenal behind this resistance. Half of the included studies, 51.7 percent, reported the detection of carbapenemase-encoding genes, including KPC and GES from the class A serine beta-lactamases, NDM-1 and NDM-5, VIM, IMP, and SPM among the metallo-beta-lactamases, and OXA-48 and OXA-181 oxacillinases. These genes encode enzymes that destroy carbapenems and are readily transferred between bacterial species on mobile genetic elements, meaning a resistance trait that emerges in one organism can rapidly colonize others. The World Health Organization ranks carbapenem-resistant pathogens first on its global priority list of antibiotic-resistant bacteria precisely because treatment options for them are so desperately limited: essentially reduced to polymyxins, fosfomycin, and tigecycline, older or more toxic drugs that represent imperfect substitutes for an entire antibiotic class.

The stakes of this trend are measured in lives. Global modeling published in the Lancet estimates that bacterial antimicrobial resistance was associated with nearly 5 million deaths in 2021, contributing to roughly one in eight deaths worldwide, and projects that as many as 8.22 million deaths annually could be attributable to AMR by 2050 if current trajectories continue. In the WHO African region alone, more than one million deaths were associated with resistant bacteria in 2019. Among Gram-negative bacteria, resistance to carbapenems has climbed faster than to any other antibiotic class, with associated deaths rising from 619,000 in 1990 to 1.03 million in 2021. Carbapenem-resistant Enterobacteriaceae infections are linked to longer hospital stays, higher healthcare costs, and elevated mortality, burdens that fall hardest on health systems with the least capacity to absorb them.

The review also captured a subtle temporal signal. Prevalence in studies published between 2021 and 2025 was marginally lower, at 12.6 percent, than in the 2015 to 2020 window, which averaged 13.5 percent, though the authors note this difference was not statistically significant and may simply reflect variation in study designs, settings, and target populations. Regional trend data from Ethiopia’s Amhara Public Health Institute, which showed resistance climbing to a peak in 2019 before declining, offers tentative grounds for the hope that sustained interventions can bend the curve. At the same time, the extraordinarily high statistical heterogeneity among the studies, with an I-squared value of 93.3 percent, underscores how differently the epidemic of resistance is unfolding across countries, populations, and sample types, and the authors caution that significant publication bias was detected and statistically adjusted in their estimates.

Perhaps the most consequential implication of the study is what it says about surveillance and regional coordination. The authors attribute the region’s elevated burden to weak laboratory capacity, poor health system governance, limited diagnostic infrastructure, and the destabilizing effects of conflict in countries such as Sudan and Ethiopia, all compounded by prolonged and often inappropriate antimicrobial use in both human and animal populations. Because routine testing for carbapenemase production is rarely performed in African clinical laboratories, the true prevalence may well exceed what published studies capture. The authors call for effective implementation of the One Health approach across sectors, strengthened routine diagnostic capacity, national and regional surveillance programs, rapid detection methods, and integration that extends beyond health policy alone. Without such coordinated action, the environmental reservoirs documented at prevalence rates approaching one in four isolates will continue to replenish the human burden, ensuring that one of medicine’s final antibiotics loses its power across one of the world’s most vulnerable regions.

Subject of Research: Prevalence and molecular epidemiology of carbapenem-resistant E. coli across human, animal, and environmental interfaces in East Africa

Article Title: Carbapenem-resistant E. coli with one-health approach in East Africa: Systematic review and meta-analysis

Article References: Zelelie, T., Mekonnen, B., & Nigussie, D. (2026). Carbapenem-resistant E. coli with one-health approach in East Africa: Systematic review and meta-analysis. Public Health in Practice, 12, Article 100843. https://doi.org/10.1016/j.puhip.2026.100843

Image Credits: AI Generated

DOI: 10.1016/j.puhip.2026.100843

Keywords: carbapenem-resistant E. coli, antimicrobial resistance, One Health, East Africa, systematic review, meta-analysis, carbapenemase genes, NDM, public health surveillance, Ethiopia, Uganda, Sudan

Antimicrobial resistance, often abbreviated as AMR, has become one of the defining health challenges of the twenty-first century, and its reach now extends well beyond hospitals and farms. Wildlife populations across the globe are increasingly recognised as reservoirs of resistance genes, prompting concern under the One Health framework, which recognises that human, animal, and environmental health are deeply interconnected. Most studies to date have focused on animals in close contact with human activity, such as urban wildlife, livestock, and captive animals, where antibiotic residues and resistant bacteria flow readily between species and environments. Far less is known about what happens when resistance elements appear in animals that have never encountered clinical antibiotics, and whether their mere presence leaves any detectable imprint on the host’s microbial communities.

At the centre of the new study sits a piece of bacterial genetics with a formidable clinical reputation. The class 1 integron, identified by the presence of the intI1 gene, is a DNA platform that acts as a capture-and-dissemination system for antibiotic resistance genes, primarily among Gram-negative bacteria. Integrons function by using an enzyme called integrase to snip gene cassettes out of one location and slot them into another, allowing bacteria to accumulate and shuffle resistance determinants with remarkable efficiency. Because class 1 integrons thrive in environments shaped by human activity, from wastewater treatment plants to agricultural runoff, their presence in wildlife is often interpreted as a biomarker of anthropogenic influence. In the gut, which is widely regarded as one of the most important reservoirs of antibiotic resistance genes in any animal, the question of whether integron carriage reshapes the microbial community is central to understanding how resistance integrates, persists, and evolves.

To address this question, a research team led by Laura Marshall of Macquarie University, working with colleagues including Sabrina Haque, Wayne Boardman of the University of Adelaide, Fiona McDougall, and Michelle Power, analysed faecal samples from 62 wild koalas living in Belair National Park. The samples were collected in October 2022 with the assistance of researchers from Flinders University and veterinary students from the University of Adelaide, under approvals from the Flinders University Animal Ethics Committee and the South Australian Department for Environment and Water. Crucially, each sample could be categorised according to whether the class 1 integron was present or absent, allowing the team to directly compare the gut microbial communities of integron-positive and integron-negative animals within the same population.

The analytical backbone of the study was 16S rRNA gene amplicon sequencing, a technique that targets a slowly evolving component of the bacterial ribosome to profile which microbes are present in a sample and in what relative proportions. By amplifying and sequencing this marker gene from the faecal DNA, the researchers could construct a snapshot of each koala’s gut microbiome without needing to culture the organisms, a critical advantage given that the majority of gut bacteria resist laboratory cultivation. The resulting datasets were then interrogated with a battery of standard community ecology tools designed to detect even subtle differences between microbial assemblages.

The results were strikingly uniform in their message. When the team measured alpha diversity, a family of metrics that captures the richness and evenness of species within a single sample, they found no significant differences between koalas carrying the class 1 integron and those lacking it. Beta diversity analyses, which quantify how communities differ from one another across samples, likewise revealed no meaningful separation between the two groups. Non-metric multidimensional scaling, an ordination technique that arranges samples in a low-dimensional space based on the similarity of their microbial profiles, showed no clustering pattern associated with integron status, indicating that community composition was essentially unrelated to whether the resistance element was present.

Differential abundance analysis, which tests whether particular bacterial taxa are enriched or depleted in one group relative to another, delivered the same verdict: no single taxon was significantly different between integron-positive and integron-negative koalas. Taken together, the findings indicate that the class 1 integron, at least on its own, is not associated with significant shifts in the gut microbiome of this antibiotic-naïve koala population. In other words, the presence of a clinically important resistance element does not appear to require, nor to produce, any substantial reorganisation of the microbial ecosystem in which it resides.

The significance of this null result lies in what it tells us about the ecology of resistance in the absence of antibiotics. A persistent worry in the field is that the acquisition of resistance elements might impose fitness costs on bacteria, potentially reshaping microbial communities, or conversely that certain microbial contexts might favour the spread of resistance once it arrives. If integron carriage were tied to particular microbial backgrounds, it could hint at conditions that promote or constrain the element’s persistence. The koala data suggest that, in a population with no history of antibiotic exposure, the integron can persist without such ecological entanglement, raising important questions about the baseline state of resistance in wildlife before anthropogenic selection pressures take hold.

Koalas make a particularly compelling subject for this kind of work. As an iconic Australian marsupial with a specialised diet of eucalyptus leaves and a gut microbiome adapted to detoxifying the plant’s chemical defences, the koala occupies a relatively contained ecological niche. Populations such as the one in Belair National Park experience some degree of proximity to urban areas, yet the animals themselves are not treated with antibiotics and are unlikely to encounter significant pharmaceutical residues in their food or water. This makes them a useful natural experiment for asking what resistance carriage looks like in a microbiome that has not been sculpted by clinical drug use, and whether the genetic markers of human influence can appear in wildlife without any accompanying microbial disruption.

The study also carries practical implications for conservation and disease management. If integron carriage in wildlife is ecologically neutral in the absence of antibiotic selection, then monitoring programmes may be able to treat the intI1 gene as a standalone indicator of anthropogenic exposure without needing to account for cascading effects on host microbiome health, at least in antibiotic-naïve animals. Conversely, the result underscores that the arrival of antibiotic residues into an environment could change the picture entirely, potentially converting a benign passenger into an active participant in the evolution and spread of resistance. Understanding the pre-antibiotic baseline, as this study does, is an essential reference point against which future environmental perturbations can be measured.

The research was funded by the Morris Animal Foundation under grant D21ZO-507 awarded to Michelle Power, with open access funding organised by the Council of Australian University Librarians and its member institutions. The work was published as an open access article in Microbial Ecology, accepted on 25 August 2026 and published on 4 September 2026, allowing researchers, wildlife managers, and the public to freely examine the full dataset and methods. The authors acknowledged the Wallumattagal clan of the Dharug Nation as the traditional custodians of the lands where laboratory analyses were performed at Macquarie University, and the Kaurna people as custodians of the Belair National Park lands where the samples were collected.

As antimicrobial resistance continues to spread through human, animal, and environmental compartments, studies like this one are helping to map the terrain on which that spread occurs. The message from Belair National Park is a measured one: a resistance element born of human medicine can settle quietly into the gut of a wild animal without leaving a microbial fingerprint, a reminder that the ecology of antibiotic resistance is complex, context-dependent, and far from fully understood. Whether that quiet coexistence survives contact with real-world antibiotic pollution remains a question for future research, but the koalas of South Australia have now provided a rare and carefully documented baseline for answering it.

This comprehensive investigation zeroed in on Klebsiella pneumoniae, a formidable member of the ESKAPE group of bacteria, which are known for their capacity to evade many frontline antimicrobials. K. pneumoniae is a familiar pathogen implicated in life-threatening infections, and alarming trends reveal its dissemination beyond human healthcare settings. Dr. Mauro Conter, an associate professor at the University of Parma’s Department of Veterinary Medical Sciences, led the examination of over 500 wildlife fecal samples collected from Northern Italy. These samples originated from species including red foxes, crows, magpies, and various water birds — animals that traverse urban, rural, and wilderness areas, forming conduits for the silent transmission of resistant bacteria.

The research highlights that wildlife, despite lack of direct antibiotic administration, can act as reservoirs for AMR bacteria and resistance genes. Foxes contribute to localized, ground-based spread, fragmenting resistance across short distances, whereas migratory birds can serve as vectors for long-range dissemination via natural flight patterns. This dual modality primes resistance genes for broader ecological infiltration, intertwining human, animal, and environmental health in a complex resistance matrix. Notably, Klebsiella species were isolated from 32 samples, with K. pneumoniae present in approximately 2% of all wildlife fecal specimens, signaling concerning environmental contamination by high-risk bacterial strains.

A particularly disturbing finding from the study was that K. pneumoniae isolates recovered from wildlife exhibited nearly complete resistance to third-generation cephalosporins—a stark contrast to clinical isolates. While clinical surveillance in Italy reports a 19.6% resistance rate to 3GCs among K. pneumoniae strains, this study revealed 100% resistance among wildlife isolates. This disparity not only underscores the wilderness as a reservoir of potent resistance but also foreshadows the insidious spread of these formidable pathogens into human populations, potentially undermining current therapeutic options.

Equally worrisome was the absolute resistance to fluoroquinolones observed in wildlife isolates. These antibiotics serve as critical tools to manage serious urinary tract infections and pneumonia. Human infections in Italy currently demonstrate a more moderate resistance percentage of 17.4%, highlighting a troubling escalation in resistance outside clinical surveillance and raising questions about environmental pressures selecting for multidrug-resistant phenotypes outside hospitals.

The genetic backbone for these alarming resistance profiles includes enzyme variants such as NDM-5 carbapenemase found in the isolated high-risk ST307 clone of K. pneumoniae. Carbapenemases degrade carbapenem antibiotics — often the last line of defense against resistant infections. The presence of such enzymes in wildlife signifies an unprecedented environmental dissemination of resistance mechanisms previously thought to be confined to clinical settings. This mechanism allows bacteria to circumvent even the most potent antimicrobial therapies, raising the stakes in global AMR management.

The study emphasizes that antibiotic resistance is not merely a clinical or hospital problem but rather an ecological challenge necessitating a ‘One Health’ approach. The interconnectedness of human, animal, and environmental health manifests through bacterial gene flow via water sources, waste management systems, and natural wildlife behavior. Surveillance of wildlife populations thus emerges as a valuable early warning system, capable of detecting emergent resistance patterns before they become widespread in clinical environments. Monitoring these environmental reservoirs could empower public health authorities to intervene proactively.

To stem the tide of resistance proliferation across ecosystems, the researchers advocate for multifaceted interventions. Reducing antibiotic pollution in wastewater streams, refining sewage treatment protocols, and encouraging judicious antimicrobial usage in agriculture and livestock are critical strategies. Furthermore, restricting the use of critically important antibiotics exclusively to human medicine could prevent environmental reservoirs from becoming breeding grounds for multidrug-resistant bacteria, including those harboring carbapenemases.

However, the authors caution that this study’s sampling methodology and scope impose limitations on fully extrapolating the data. The actual diversity and prevalence of resistant bacteria in the environment may be underestimated, and direct transmission chains between wildlife and humans remain to be conclusively established. Larger scale studies bridging human clinical isolates, animals, and environmental samples across national and international contexts will be vital to unravel the complexities of resistance transmission dynamics, although such endeavors are inherently challenging.

Emerging evidence also suggests that climate change and its impact on wildlife behavior could compound the spread of antimicrobial resistance. Shifts in migratory routes, altered habitats, and ecosystem disruptions may intensify interspecies bacterial exchanges, thereby accelerating the evolution and dissemination of resistant strains. Addressing AMR requires integrating these ecological factors into a holistic strategy that transcends traditional siloed approaches.

Ultimately, Dr. Conter’s team drove home the message that combating antimicrobial resistance demands coordinated, interdisciplinary solutions embracing microbiology, ecology, veterinary science, and public health. Their findings provide a compelling case for incorporating routine wildlife monitoring into global AMR surveillance systems. By doing so, policies can be better informed, interventions more timely, and resistance threats curtailed before overwhelming healthcare infrastructures worldwide.

The sobering reality of AMR spilling into the environment beyond clinics exposes the fragility of current antibiotic stewardship efforts. Only by recognizing wildlife as sentinels and reservoirs of resistance can we hope to anticipate and mitigate the relentless march of resistant pathogens. This study offers a clarion call to scientists, policymakers, and medical professionals alike: the war against antibiotic resistance is a battle that extends far beyond hospital walls into the very ecosystems where human and animal lives intersect.

Subject of Research: Animals

Article Title: Wildlife as sentinel of antimicrobial resistance in Klebsiella spp. with genomic insights into Klebsiella pneumoniae in Northern Italy

News Publication Date: 16-Apr-2026

Web References:
https://doi.org/10.3389/fmicb.2026.1716432

Keywords: Antimicrobial resistance, Klebsiella pneumoniae, third-generation cephalosporins, carbapenemase, wildlife reservoirs, environmental contamination, One Health, antibiotic stewardship, NDM-5, ESKAPE bacteria, fluoroquinolones, AMR surveillance