Dominant drug-resistant Acinetobacter baumannii lineage traced in northern Peru hospital

A single, closely related lineage of multidrug-resistant Acinetobacter baumannii appears to have circulated for years among intensive care patients at a tertiary hospital in northern Peru, according to a new molecular surveillance study published in New Microbes and New Infections. Researchers from the Pontificia Universidad Católica del Perú and Lambayeque Regional Hospital combined three DNA fingerprinting techniques with protein mass spectrometry to compare clinical isolates collected between April 2015 and September 2021. Their results point to one dominant group of genetically similar bacteria alongside a strikingly divergent isolate that resisted every antibiotic tested, a finding that underscores how little is known about the strain-level epidemiology of one of the world’s most dangerous hospital pathogens in South America.

Acinetobacter baumannii is an aerobic, Gram-negative coccobacillus that has earned a place on the World Health Organization’s bacterial priority pathogens list as a critical-priority organism. It belongs to the so-called ESKAPE group of nosocomial bacteria, a shorthand for the pathogens that effectively escape the effects of most available antibiotics. The species thrives in hospital environments, colonizing patients and healthcare workers and surviving for prolonged periods on dry surfaces and medical equipment. It causes pneumonia, bloodstream infections, urinary tract infections, meningitis, endocarditis, and wound infections, and it disproportionately strikes immunocompromised, older, and critically ill patients, particularly those with long intensive care unit stays or extensive prior antimicrobial exposure. Nearly sixty percent of isolates recovered from hospitalized patients have been reported as multidrug-resistant.

The bacterium’s arsenal of resistance mechanisms is a major reason for concern. It possesses intrinsic resistance to several antimicrobial classes and readily acquires additional determinants through mobile genetic elements such as plasmids, transposons, and genomic islands. Its principal defenses include reduced cell wall permeability, active efflux pumps that expel drugs, modification of antimicrobial targets, and enzymatic inactivation of antibiotics. Beta-lactamase production is especially important, and metallo-beta-lactamases of the New Delhi type, which destroy carbapenem antibiotics, are heavily concentrated in Asia and Africa according to recent meta-analyses. Resistance to colistin, a last-line polymyxin, has been estimated at roughly seventeen percent in Southeast Asia and the Eastern Mediterranean but only about three percent in the Americas, although ICU outbreaks of highly resistant, genetically related isolates make strain-level surveillance essential everywhere.

Peru’s own data remain sparse. Hospital isolates, particularly from intensive care units in Lima, show resistance to multiple antimicrobial classes, with carbapenemase production frequently reported. Studies from Lambayeque and Trujillo found A. baumannii in twenty-seven percent and seventeen percent of hospital-derived bacterial isolate collections, respectively. Previous work in Lima identified international clones II and III among carbapenem-resistant isolates, and a later whole-genome study documented a highly clonal international clone II population in a Peruvian hospital. Across the wider region, a multicentre study of nine hospitals in Argentina, Bolivia, Chile, Ecuador, Paraguay, and Uruguay associated most carbapenem-resistant isolates with sequence types ST79, ST25, or ST15 and frequently detected the blaOXA-23 carbapenemase gene, while genomic surveillance in Chile and Paraguay has revealed both region-specific and internationally disseminated high-risk lineages.

The new study began with twenty-four multidrug-resistant isolates available from the study period. Preliminary fingerprinting showed that more than seventy percent of them grouped within a single subclade with highly similar banding patterns. To avoid redundant characterization while preserving the diversity of the collection, the team purposively selected seven representative isolates for full analysis: six from the predominant subclade and one with a divergent preliminary profile. All seven came from patients in the intensive care unit of Lambayeque Regional Hospital and were recovered from specimens associated with hospital-acquired infections, defined as infections developing at least seventy-two hours after admission. The specimens included urine, pus, bronchial fluid, and a vaginal swab.

Antimicrobial susceptibility testing by disk diffusion, interpreted according to Clinical and Laboratory Standards Institute guidelines, revealed a bleak picture. Every isolate was resistant to piperacillin-tazobactam, ceftazidime, imipenem, meropenem, ciprofloxacin, and trimethoprim-sulfamethoxazole, confirming multidrug resistance across the board. Responses to aminoglycosides varied, with several isolates remaining susceptible to amikacin or gentamicin, and levofloxacin susceptibility was similarly mixed. One isolate, designated Ac-4268, was resistant to every single agent tested and was classified as extensively drug-resistant, or XDR. Notably, the six isolates belonging to the principal genetic group all retained susceptibility to at least one tested drug, whereas the divergent Ac-4268 did not, a partial agreement between genetic relatedness and resistance phenotype that the authors interpret cautiously given the small sample size.

To assess genetic relatedness, the researchers employed three complementary repetitive-element PCR techniques: BOX-PCR, ERIC-PCR, and REP-PCR. These methods amplify genomic regions between repetitive DNA motifs, producing banding fingerprints that can be compared quantitatively. Binary band-presence matrices were analyzed using the Dice similarity coefficient and UPGMA clustering, with isolates scoring at or above a coefficient of 0.85 assigned to the same genotype. All three methods converged on the same result: six isolates, Ac-913, Ac-954, Ac-891, Ac-409, Ac-389, and Ac-1062, formed one group, while Ac-4268 stood apart in every analysis. This consistency across three independent fingerprinting assays strengthens the inference that a single related lineage dominated the hospital’s multidrug-resistant population during the study window.

The team then turned to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, or MALDI-TOF MS, which identifies bacteria by the mass spectrum of their abundant proteins. All seven isolates were confirmed as A. baumannii with reliable log scores above 2.0. The main spectral profile dendrogram revealed a five-isolate cluster and two individual profiles, Ac-954 and Ac-4268, at an arbitrary distance cutoff of 200. The composite correlation index, which ranges from zero to one, showed the highest pairwise similarity between Ac-389 and Ac-409 at 0.85, followed by Ac-891 and Ac-1062 at 0.80, while Ac-4268 scored roughly 0.50 against all others. Interestingly, Ac-954 clustered with the main group by PCR but appeared as an individual profile by mass spectrometry, illustrating that the two methods measure different biological features and should be treated as complementary rather than interchangeable.

The authors are careful about what these results do and do not demonstrate. The six-isolate PCR group is consistent with a predominant related lineage persisting or expanding within the hospital, but genomic identity and direct patient-to-patient transmission were not established, and the fingerprint and proteomic differences should not be read as phylogenetic distance. The divergence of Ac-4268, which was also recovered from the same patient as Ac-1062 at another anatomical site, may reflect the presence of a distinct lineage, plausibly shaped by the acquisition of mutations and mobile genetic elements. The study’s limitations are explicit: only seven of twenty-four isolates underwent full characterization, selection was non-random, the isolates span 2015 to 2021 and may not reflect the current situation, and whole-genome sequencing was not performed, so sequence types, resistance genes, and transmission chains remain undefined.

Even so, the findings carry practical weight. Repetitive-element PCR and MALDI-TOF MS are affordable, accessible tools that can support preliminary strain surveillance in resource-limited settings where whole-genome sequencing is not routinely available, and they can flag emerging clusters for infection control teams before outbreaks escalate. The resistance profiles documented here illustrate the shrinking therapeutic options for multidrug- and extensively drug-resistant A. baumannii, a pathogen associated with high mortality in intensive care cohorts across the region. The authors call for prospective surveillance incorporating isolates collected after 2021, ideally combined with whole-genome sequencing, to determine whether the predominant lineage and its resistance profile remain in circulation and to inform antimicrobial stewardship and infection control decisions in northern Peru and beyond.

Subject of Research: Molecular epidemiology and antimicrobial resistance of multidrug-resistant Acinetobacter baumannii isolates from a tertiary hospital in northern Peru

Article Title: Molecular evidence of a dominant multidrug resistant Acinetobacter baumannii lineage in a tertiary hospital in northern Peru

Article References: Quispe-Choque, K. G., Ruiz-Quiñones, N., Binatti-Ferreira, M., Perini-Leme-Giordano, A. L., Zaninelli-Schreiber, A., Fantinatti-Garboggini, F., Casado-Pena, F. L., & Clavo, R. F. (2026). Molecular evidence of a dominant multidrug resistant Acinetobacter baumannii lineage in a tertiary hospital in northern Peru. New Microbes and New Infections, Article 101864. https://doi.org/10.1016/j.nmni.2026.101864

Image Credits: AI Generated

DOI: 10.1016/j.nmni.2026.101864

Keywords: Acinetobacter baumannii, antimicrobial resistance, multidrug-resistant bacteria, hospital-acquired infections, Peru, molecular epidemiology, MALDI-TOF mass spectrometry, repetitive-element PCR, intensive care unit, extensively drug-resistant, carbapenem resistance, infection control