Occurrence and molecular characteristics of carbapenem-resistant Enterobacteriaceae recovered from wildlife: a systematic review and meta-analysis

Deep in the guts of wild birds, bats, and boars, scientists are finding bacteria that shrug off one of medicine’s most precious weapons. A new systematic review and meta-analysis, published in Frontiers in Microbiology, has pulled together the scattered evidence on carbapenem-resistant Enterobacteriaceae (CRE) recovered from wildlife, and the picture it paints is striking: these last-resort antibiotic killers are not confined to hospital wards and intensive care units. They are turning up in free-living animals across every inhabited continent, carrying the very same resistance genes that keep infectious disease physicians awake at night.

The research team, led by Ji-hwan Yim, Maryum Tanveer, and Gayeon Won at Jeonbuk National University in the Republic of Korea, followed the PRISMA reporting framework to sift through 6,988 records published between January 2000 and July 2025, drawn from PubMed, Scopus, and Web of Science. After removing duplicates and screening titles, abstracts, and full texts, only 19 studies made the cut. That small yield is itself telling. While CRE have been exhaustively documented in clinical settings and livestock, the ecological distribution of these bacteria outside managed systems has remained largely unmapped, leaving scientists with fragmented clues about how far the resistance problem has penetrated the natural world.

The pooled estimate that emerged from the random-effects meta-analysis was 74.49 percent, with a 95 percent confidence interval stretching from 49.75 to 94.04 percent, and a staggering I-squared statistic of 96 percent. But the authors are careful, and rightly so, about what this number actually means. The figure represents the proportion of recovered Enterobacteriaceae isolates that tested positive for carbapenem resistance under the laboratory procedures of the included studies. It is not the prevalence of CRE carriage among wild animals. Because many studies used selective or enrichment culture methods designed to favor the recovery of resistant organisms, susceptible bacteria may have been suppressed in the lab, inflating the apparent proportion. The estimate reflects what happens to isolates once they reach the petri dish, not what is happening inside every fox or gull in the wild.

Stratifying the data by bacterial species revealed CRE-positive proportions of 76.51 percent for Escherichia coli, 72.41 percent for Klebsiella species, and 86.46 percent for other Enterobacteriaceae genera, including Citrobacter and Enterobacter. These subgroup estimates, however, come with wide confidence intervals and substantial heterogeneity, so they should be read with caution. The prominence of carbapenem-resistant E. coli is epidemiologically significant for a different reason: E. coli is both a common intestinal commensal and a notorious reservoir of resistance genes, capable of picking up new genetic material through horizontal gene transfer. Its repeated recovery from wildlife suggests that these animals are being exposed to bacteria that have already learned to survive in human-altered environments.

When the researchers examined sampling environments, the highest descriptive estimate appeared in water-associated sites, at 84.49 percent, followed by captive settings at 79.65 percent, natural habitats at 77.06 percent, and human-associated environments at 72.36 percent. Yet none of these differences reached statistical significance. The only moderator that did was sample type. Fecal samples showed a pooled CRE-positive proportion of 89.29 percent, dramatically higher than the 23.04 percent seen in rectal, cloacal, or wound swabs, a difference that was statistically significant at p less than 0.01. In univariate meta-regression, sample type explained 33.1 percent of the between-study heterogeneity, making it the clearest signal in an otherwise noisy dataset. The authors note that fecal sampling may simply capture more of the gut-associated Enterobacteriaceae where resistance determinants accumulate, or that swab-based methods recover fewer organisms overall, complicating direct comparison.

The molecular findings are where the story turns genuinely alarming. Across the included studies, researchers identified clinically important carbapenemase-encoding genes from all five major families: blaNDM, blaKPC, blaOXA-48-like, blaVIM, and blaIMP. These genes encode enzymes that hydrolyze carbapenem antibiotics before they can kill the bacterial cell, and many of them ride on plasmids, the mobile genetic elements that shuttle resistance between bacterial lineages with alarming efficiency. The geographic patterns broadly mirror those seen in human medicine. NDM variants, particularly NDM-5, dominated in Asia, appearing in studies from Pakistan, India, and China. KPC-lineage enzymes, especially KPC-2, were the most common finding in North and South America, detected in isolates from the United States, Brazil, and Chile. OXA-48 was prominent in Algeria, while Tunisia reported both VIM and IMP genes. Europe showed the broadest diversity, with Spain alone yielding KPC-2, KPC-3, VIM-1, OXA-48, OXA-245, NDM-1, and NDM-5 in E. coli and Klebsiella pneumoniae. Australia contributed a single study identifying IMP-4-producing E. coli.

Sequence type analysis added another layer of concern. Multilocus sequence typing revealed that while most lineages were country-specific, a handful of internationally recognized clones appeared repeatedly across distant regions. E. coli ST38, one of the most recurrent sequence types, was identified in Spain, Algeria, Turkey, and Alaska. ST410, a lineage previously associated with high-risk international dissemination, was detected in Spain and Alaska. ST744 appeared in both Spain and Chile. Among Klebsiella pneumoniae, Spain reported ST11 and ST307, both globally significant hospital-associated lineages, alongside a diverse array of other sequence types. China contributed an unusually rich catalogue of K. pneumoniae and K. quasipneumoniae lineages. The repeated identification of these lineages in wildlife suggests that the same resistant clones circulating in human and environmental settings are also present in wild animals, although the direction of transmission remains unresolved.

That caveat is central to how the authors want their findings interpreted. Carbapenems are almost never used in veterinary medicine; their use is tightly restricted to preserve their effectiveness for the most severe human infections. So how do wild animals, which have never received these drugs, end up carrying bacteria that resist them? The most plausible explanation, the researchers argue, is exposure to resistant bacteria or resistance determinants originating from anthropogenically influenced environments. Wastewater treatment plants do not completely eliminate resistant bacteria or resistance genes, allowing them to persist and spread into surrounding ecosystems. Wildlife species that inhabit or frequent aquatic environments, particularly migratory birds like gulls and storks that move between wetlands, coastal zones, and wastewater-associated habitats, may experience repeated exposure to these contamination sources. The descriptively elevated CRE-positive proportion among Charadriiformes, the taxonomic order that includes many water-associated and migratory species, fits this pattern, even though the difference was not statistically significant.

The methodological scrutiny applied to the evidence base reveals both strengths and weaknesses. Risk of bias was assessed using the Joanna Briggs Institute critical appraisal checklist for prevalence studies, with three reviewers independently evaluating each study. Only three of the 19 studies were classified as low risk across all evaluated domains. Nine studies met or exceeded the recommended minimum sample size of 140, while ten fell short. Statistical analysis methods were adequately described in only seven studies. Publication bias assessment added further nuance: the funnel plot showed asymmetry, and the trim-and-fill method estimated four potentially missing studies, which would lower the pooled estimate from 74.49 percent to 59.64 percent if those studies were included. However, Egger’s regression test did not reach statistical significance, and heterogeneity remained stubbornly high even after adjustment, suggesting that the asymmetry may reflect genuine methodological and ecological diversity rather than selective publication alone.

What emerges from this synthesis is not a declaration that wildlife are driving the CRE crisis, but a sober recognition that they are embedded in the same contaminated landscapes that humans have created. The authors are explicit that transmission direction cannot be established from the available evidence and that wildlife should not be interpreted as confirmed primary reservoirs or active drivers of dissemination. Instead, they propose that wild animals may serve as useful sentinels, biological barometers that reflect the extent of environmental CRE contamination in aquatic, wastewater-associated, and anthropogenically influenced ecosystems. Future surveillance studies, the researchers argue, should report detailed culture and enrichment procedures, distinguish between selective and non-selective isolation approaches, and clearly document the number of individual animals screened alongside the number of isolates recovered. Longitudinal monitoring and genomic transmission studies will be needed to determine whether wildlife play an active role in the persistence and spread of these bacteria, or whether they are simply reflecting, with uncomfortable fidelity, the resistance problem that human activity has seeded into the environment. Either way, the message from the wild is unambiguous: the genes that defeat our last-line antibiotics are already out there, circulating in animals that have never seen a hospital.

Subject of Research: Occurrence and molecular characteristics of carbapenem-resistant Enterobacteriaceae recovered from wildlife: a systematic review and meta-analysis

Article Title: Occurrence and molecular characteristics of carbapenem-resistant Enterobacteriaceae recovered from wildlife: a systematic review and meta-analysis

Article References: Yim, J.-H., Tanveer, M., Ntakiyisumba, E., Hur, J., & Won, G. (2026). Occurrence and molecular characteristics of carbapenem-resistant Enterobacteriaceae recovered from wildlife: a systematic review and meta-analysis. Frontiers in Microbiology, 17, Article 1897815. https://doi.org/10.3389/fmicb.2026.1897815

Image Credits: AI Generated

DOI: 10.3389/fmicb.2026.1897815

Keywords: Occurrence, molecular, characteristics, carbapenem-resistant, Enterobacteriaceae, recovered, wildlife, systematic, review, meta-analysis, scientific research