Comparative genomic insights into carbapenem-resistant versus susceptible Acinetobacter baumannii in Shanghai hospital settings: a multi-center molecular surveillance study
Jul 2026· Frontiers in Cellular and Infection Microbiology· Vol 16· 0 citations· 39 references
Medicine
TL;DR
The ICU environment was critical for CRAB control, and CRAB exhibited stronger resistance, harbored more putatively conjugative plasmids and richer virulence-associated genes than CSAB, highlighting the need for targeted disinfection and surveillance of prevalent clones.
Abstract
Background Carbapenem-resistant Acinetobacter baumannii (CRAB) is priority pathogen for nosocomial infection control worldwide. This study aimed to elucidate differences in distribution, genotyping and antimicrobial resistance patterns between CRAB and carbapenem-susceptible Acinetobacter baumannii (CSAB) strains isolated from healthcare environments. Materials and methods A total of 1,812 environmental samples were collected from 10 medical institutions in Pudong New Area between June and December 2024 for the identification of A. baumannii. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analysis were performed to reveal molecular characteristics of A. baumannii. Results A total of 81 A. baumannii strains were detected, with 39.51% CRAB (n = 32) and 60.49% CSAB (n = 49). CRAB strains were highly prevalent in intensive care units (ICUs, accounting for 83.33%) and patient-contact items, whereas CSAB were more evenly distributed. MLST analysis identified ST2 as dominant CRAB clone (78.13%), followed by ST164 (18.75%). CRAB isolates demonstrated 100% resistance to multiple antibiotics such as piperacillin/tazobactam and ciprofloxacin, whereas all CSAB isolates were susceptible to tested antibiotics except one ampicillin/sulbactam-resistant isolate. Carbapenem resistance in CRAB was predominantly mediated by class D carbapenemases, with carriage rate of the blaOXA-23 gene reaching 96.88%. Notably, six ST164 isolates co-harbored class B and class D carbapenemase genes, which may elevate resistance severity. Bioinformatic analysis indicated that 22.20% of resistance plasmids in CRAB were predicted to be conjugative. CRAB exhibited a more diverse and extensive virulence gene profile than CSAB strains. Conclusions The ICU environment was critical for CRAB control. ST2 and ST164 represented clones worthy of attention. CRAB exhibited stronger resistance, harbored more putatively conjugative plasmids and richer virulence-associated genes than CSAB, highlighting the need for targeted disinfection and surveillance of prevalent clones.
Background Carbapenem−resistant Acinetobacter baumannii (CRAB) is a major threat to hospitalised patients, particularly in intensive care units and orthopaedic wards where implant−associated infections are common. However, the genomic and biofilm characteristics of CRAB in orthopaedic specialty hospitals remain poorly understood. Methods A total of 97 non-duplicate CRAB isolates collected between 2024 and 2025 were included. Antimicrobial susceptibility testing was performed using the VITEK-2 system, and biofilm formation was quantitatively assessed by the crystal violet method. Whole-genome sequencing (WGS) was carried out on the Illumina platform to analyse multilocus sequence typing (MLST), capsular types, resistance genes and virulence genes. A phylogenetic tree was constructed based on single-nucleotide polymorphisms (SNPs). Results ST2 was the dominant clone (95.88%) among the 97 isolates, and KL3 was the most prevalent capsular type (83.51%). All isolates carried intrinsic blaOXA-51-like genes, predominantly blaOXA-66 (95.88%). The most common acquired carbapenemase gene was blaOXA-23 (98.97%), and two isolates carried metallo-β-lactamase (MBL) genes (blaNDM-1 and blaNDM-5, respectively). All isolates exhibited a multidrug-resistant phenotype, with low resistance rates to tigecycline (6.19%) and minocycline (7.22%), and all remained susceptible to colistin. Strong biofilm formers accounted for 91.75% of isolates, and the carriage rates of biofilm-associated genes (bap, csuABCDE, pgaABCD) exceeded 90%. Phylogenetic analysis grouped the isolates into three clonal clades, with the majority (88.66%) falling into Clade C (ST2/KL3). This clade had been circulating in China as an outbreak lineage since 2018, gradually replacing Clade B (ST2/KL2), and became the dominant clone in 2024–2025. Conclusion CRAB isolates in this orthopaedic specialty hospital are dominated by the ST2/KL3 clone, which carries multiple resistance and virulence genes, exhibits a remarkably strong biofilm-forming ability, and shows a capsular switch trend from KL2 to KL3. Enhanced molecular surveillance of this dominant clone and increased attention to anti-biofilm strategies for orthopaedic implant-related infections are strongly recommended.
Tengfei Shi, Shaohan Xu, Xuexin Zheng et al.· Frontiers in Cellular and In...· 0 citations
OBJECTIVE
The prevalence of carbapenem-resistant Acinetobacter baumannii (CRAb) has been increasing globally. This study aimed to investigate the risk factors, resistance gene profiles, and molecular epidemiology of CRAb bloodstream infections (BSIs) among patients in Xi'an, China, to provide evidence for clinical prevention and targeted treatment.
METHODS
We conducted a retrospective study of 139 patients with A. baumannii BSIs. Patients were categorized into a CRAb group (n = 84) and a carbapenem-susceptible A. baumannii (CSAb) group (n = 55). Independent risk factors were identified via multivariate logistic regression analysis. Carbapenemase resistance genes were detected using polymerase chain reaction (PCR), and CRAb isolates were molecularly typed by multilocus sequence typing (MLST).
RESULTS
Multivariate logistic regression analysis identified the following as independent risk factors for CRAb BSIs: inappropriate empirical antimicrobial therapy (OR = 8.620; 95% CI: 2.078-35.751), deep venous catheterization (OR = 12.625; 95% CI: 2.263-70.429), prolonged hospitalization before the onset of BSIs (OR = 1.467; 95% CI: 1.123-1.915), and ICU admission (OR = 4.981; 95% CI: 1.898-13.065). Antimicrobial susceptibility testing showed that CRAb isolates were multidrug-resistant, exhibiting resistance rates exceeding 70% to most common clinical antibiotics, with the exception of tigecycline (5.95% resistance) and colistin (27.38% resistance). All 84 CRAb isolates carried both blaOXA-51-like and blaOXA-23-like genes, while other carbapenemase genes were not detected. MLST identified 7 sequence types (STs), with ST540 (45.24%, 38/84) being the dominant clone. eBURST analysis indicated that the major STs (ST195, ST208, etc.) belonged to the same clonal complex.
CONCLUSION
Inappropriate empirical antimicrobial therapy, deep venous catheterization, prolonged hospitalization before the onset of BSIs and ICU admission are independent risk factors for CRAb BSIs. The prevalent strains produce OXA-23-like carbapenemase, and molecular typing indicates that the ST540 clone and its related clonal complex are predominant, suggesting potential nosocomial clonal spread.
Jiahao Guan, Yajuan Ren, Xiaojun Dang et al.· Microbial Drug Resistance· 0 citations
This study substantiates an escalated incidence of carbapenem-resistant, MDR A. baumannii in post-surgical infections in Pakistan, highlighting the exigency for strengthened antimicrobial stewardship and infection control strategies in the hospitals of the region.
Sana Gul, Nawab Ali, M. Qasim et al.· Antibiotics· 0 citations
Background/Objectives: Acinetobacter baumannii is a major cause of infections in Intensive Care Units (ICUs), driving mortality through high-level antimicrobial resistance. This study utilized whole-genome sequencing (WGS) to evaluate the phenotypic, genotypic and virulence features of carbapenem-resistant A. baumannii (CRAB), which has caused ventilator-associated pneumonia/tracheobronchitis (VAP/VAT) in the ICU of the University Hospital of Split, Croatia. Methods: Over 1 year, lower respiratory tract specimens from 79 VAP/VAT patients were analyzed. CRAB isolates were identified via MALDI-TOF MS and evaluated for antimicrobial susceptibility, and a representative subset underwent WGS and multilocus sequence typing (MLST). Results: Out of 106 specimens, 18 non-duplicate CRAB strains were isolated. Five isolates underwent genomic analysis, identifying two globally distributed, high-risk Pasteur lineages: ST2 and ST492. These lineages displayed distinct resistomes: ST2 carried blaOXA-23 and blaADC-73, while ST492 harbored plasmid-borne blaOXA-72 (Rep3-T1/AB082 cluster) and blaADC-30. All isolates shared aminoglycoside/macrolide-resistance genes, conserved efflux pumps, and virulence determinants (bau, bas, ent, bar) crucial for acinetobactin synthesis and respiratory colonization. Phylogenetic analysis confirmed regional circulation and genetic links to neighboring countries. Conclusions: This study highlights the evolutionary dynamics of endemic CRAB lineages in a Croatian ICU and their global dissemination, which poses a critical threat, demanding strict infection control and novel therapeutics.
Marija Čavka, Marija Kvesić Ivanković, Ana Maravić et al.· Antibiotics· 0 citations
Background Carbapenem resistant Acinetobacter baumannii (CRAB) is recognized as one of the most critical priority pathogens by the World Health Organization due to its persistence in nosocomial settings, extensive antimicrobial resistance, and increasing dissemination at the global level. Despite the escalating availability of genomic data, genotype–phenotype integrated studies exploring the genetic determinants associated with carbapenem resistance remain limited. Methods In this study, a comprehensive comparative genomics was performed using publicly available 395 clinical A. baumannii genomes, comprising of 267 CRAB and 128 carbapenem susceptible A. baumannii (CSAB). Comparative genomic analyses included sequence types (STs), virulence factors (VFs), antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) characterization. Pangenome-wide association study (PanGWAS) was performed to test the associations between genotypes and carbapenem resistance phenotype. Results CRAB genome subset demonstrated higher abundance of ARGs (acquired carbapenemases in particular), plasmids, carbapenem resistance-associated insertion sequences, and integrons than CSAB genomes. PanGWAS identified six positively associated genes (relE, umuC, hphA, hsmA, hphR, and fecI) significantly enriched in CRAB population. Core SNP phylogeny integrated with STs and acquired carbapenemase genes exhibited heterogeneous distribution of resistance genes across lineages, indicating potential role of both clonal dissemination and horizontal gene transfer. Conclusion This study provides an overall genomic architecture of CRAB integrating comparative genomics, PanGWAS, and phylogenomics approaches. The findings underscore the complex interplay between ARGs, VFs, and MGEs in the genomic evolution of CRAB, expanding current understanding of CRAB adaptation and may contribute toward enhanced surveillance, antimicrobial stewardship, and exploration of alternative therapeutic targets.
Sara Pearl, A. Anbarasu· Frontiers in Cellular and In...· 0 citations
BACKGROUND/AIMS
Acinetobacter baumannii is an opportunistic gram-negative pathogen and an increasingly important cause of hospital-acquired infections, particularly in intensive care units. Its remarkable ability to rapidly acquire resistance mechanisms, especially against carbapenems, represents a major public health concern. This study aimed to investigate the molecular detection and characterization of OXA-type carbapenemase genes in A. baumannii isolates collected from various clinical sources in Baghdad, Iraq.
METHODS
Between March and July 2025, 36 non-repetitive A. baumannii isolates were obtained from patients with different infections. Identification was performed using standard biochemical tests, CHROMagar Acinetobacter, and the VITEK 2 system and was confirmed by PCR amplification of the intrinsic blaOXA-51 gene. Antimicrobial susceptibility testing was conducted according to CLSI guidelines. The prevalence of blaOXA-23, blaOXA-24, blaOXA-51, and blaOXA-58 genes was determined by PCR. Selected PCR products were sequenced and subjected to phylogenetic analysis.
RESULTS
Extensive antimicrobial resistance was observed among the isolates, particularly to carbapenems, with resistance rates of 83.3% for imipenem and 72.2% for meropenem. High resistance rates were also detected for fluoroquinolones and aminoglycosides, whereas colistin and tigecycline retained comparatively greater activity. PCR screening revealed prevalence rates of 100% for blaOXA-51, 86.1% for blaOXA-23, 69.4% for blaOXA-24, and 47.2% for blaOXA-58. Multiple blaOXA genes were detected in more than half of the isolates, suggesting horizontal gene transfer and local clonal expansion. Phylogenetic analysis demonstrated high similarity between local isolates and international reference strains, supporting the widespread dissemination of resistance determinants. Several nucleotide substitutions were identified within the blaOXA-23 and blaOXA-24 genes.
CONCLUSION
The findings indicate that blaOXA-23 is the predominant contributor to carbapenem resistance among A. baumannii isolates in Baghdad, while blaOXA-24 and blaOXA-58 are also increasingly prevalent. The observed resistance patterns and phylogenetic relationships underscore the importance of continuous molecular surveillance, antimicrobial stewardship, and effective infection control measures to limit the spread of multidrug-resistant A. baumannii. These data contribute valuable regional information to the global understanding of antimicrobial resistance epidemiology.
A. A. Abdulhassan, Hiba Hazim Hamid, Sara Mahdi Al-Lami et al.· Cellular Physiology and Bioc...· 0 citations
