Highly clonal carbapenem-resistant Acinetobacter baumannii isolates from a Peruvian hospital.

UNLABELLED: Acinetobacter baumannii is an opportunistic pathogen of great clinical concern, showing high levels of resistance to several antimicrobials, including carbapenems. This study aimed to characterize carbapenem-resistant A. baumannii recovered from a tertiary care hospital (Lima, Peru) in January-February 2021 (during the coronavirus disease 2019 pandemic). Antimicrobial susceptibility was determined by VITEK-2, and the presence of carbapenem-resistance genes by PCR. All 40 A. baumannii isolates were extensively drug-resistant, showing full resistance to all antibiotics tested except ampicillin/sulbactam (95% of resistance) and colistin (10%). The bla OXA-24-like gene was detected in 90% of isolates, and the remaining 10% isolates harbored the bla OXA-23-like gene. Pulsed-field gel electrophoresis classified isolates into three different pulsotypes, grouping 8, 2, and 30 isolates, respectively. Additionally, whole-genome sequencing of two isolates of the main pulsotype revealed that they belonged to ST2 and ST2724 (international clone II) and harbored the bla TEM-1, bla OXA-66, bla OXA-72, and bla ADC-30 β-lactamase genes; mutations in gyrA and parC, aminoglycoside, tetracycline, and sulfonamide resistance genes; and a class 1 integron (In439) containing aac(6')-Ib', catB8, and aadA1 located inside the AbGRI3 genomic resistance island. These findings highlight the presence of highly resistant and clonally related ST2 of A. baumannii and their relationship with genomes of ST2 of South America.

IMPORTANCE: Acinetobacter baumannii is a critical pathogen known for causing severe infections in hospitalized patients and for its remarkable ability to develop resistance to multiple antibiotics, including last-line treatments such as carbapenems. In Latin America, data on the genetic background and spread of these resistant strains remain limited. Our study provides a detailed molecular and genomic characterization of extensively drug-resistant A. baumannii isolates collected from a Peruvian hospital during the coronavirus disease 2019 pandemic. We identified a predominant clone belonging to international clone II, which carried multiple resistance genes and a complex resistance island. These findings raise public health concerns, as they highlight the silent spread of high-risk clones in regions with limited surveillance capacity. By contributing valuable local genomic data, our study supports global efforts to track antimicrobial resistance and underscores the urgent need to strengthen molecular monitoring of hospital-associated pathogens also in low- and middle-income countries.