Genomic analysis of carbapenem-resistant non-baumannii Acinetobacter harboring chromosomal blaOXA-23 or plasmid-mediated blaNDM-1, blaIMP-14, and blaOXA-58
The results suggest that the dissemination of CP-NBA isolates should be handled carefully in terms of transmission between bacterial strains in the clinical setting, and that the blaIMP-14 gene was first identified in South Korea.
Abstract
Introduction Carbapenem-resistant Acinetobacter species are among the top priority pathogens, posing a threat to public health in both hospital- and community-acquired settings. Notably, the prevalence of carbapenemase-producing non-baumanniiAcinetobacter (CP-NBA) has recently increased worldwide. Methods This study aimed to describe the molecular characteristics of non-baumannii Acinetobacter isolates with two or more carbapenemases in South Korea. Among 590 nonduplicated carbapenem-resistant Acinetobacter species collected from community hospitals in South Korea between 2022 and 2023, a total of 13 CP-NBA isolates were used in this study. Whole-genome sequencing and in silico molecular analysis were performed to characterize their genomic features. Results Of the thirteen CP-NBA isolates, nine (four A. nosocomialis, two A. pittii, two A. seifertii, and one A. bereziniae) carried chromosomal blaOXA-23 integrated within Tn2006 in AbaRs. In addition, two A. bereziniae isolates with Rep3-T25 plasmids carrying blaVIM-2 and blaOXA-58 and one A. bereziniae isolate with the Rep3-T25 plasmid carrying blaNDM-1 and blaOXA-58 were identified. Finally, one A. pittii isolate with a putative 289 kb plasmid carrying three carbapenemase genes, blaNDM-1, blaOXA-58, and blaIMP-14, lacking a replication origin gene was detected. Conclusion In conclusion, our study described the genomic structure of carbapenemase genes and related mobile genetic elements in 13 CP-NBA isolates. Although the carbapenemase genotypes are diverse, CP-NBA strains are still relatively rare in local clinics in South Korea. In particular, the blaIMP-14 gene was first identified in South Korea. These results suggest that the dissemination of CP-NBA isolates should be handled carefully in terms of transmission between bacterial strains in the clinical setting.
Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of hospital-acquired bloodstream infections in Thailand, with limited treatment options and a strong association with high morbidity and mortality. We performed nationwide genomic surveillance of 41 CRAB isolates from bloodstream infections collected across Thailand between 2020 and 2024 to characterize the population structure, antimicrobial resistance determinants, and the genomic context of blaNDM-harboring mobile genetic elements (MGEs). Whole-genome sequencing and core genome SNP-based phylogenetic analysis of the Thai samples revealed the dominance of international clone II (Pasteur ST2), which was widely distributed across geographic regions. Carbapenem resistance was primarily mediated by blaOXA-23, together with intrinsic blaOXA-66 and resistance-associated mutations in a penicillin-binding protein gene. In addition to OXA-type carbapenemase genes, blaNDM-5 and blaNDM-1 were detected in a subset of isolates. In particular, blaNDM-5 was located within a highly conserved MGE associated with a class 1 integron, IS91 family transposase and ISAba125 and was detected across multiple ST2 sublineages. This MGE was distributed across multiple geographic regions and phylogenetic lineages in Thailand, with evidence suggesting widespread horizontal dissemination followed by local clonal expansion. By contrast, blaNDM-1 was detected less frequently but was consistently associated with a canonical Tn125 transposon in both ST2 and ST16 isolates, highlighting its continued epidemiological relevance. Collectively, our findings demonstrate that CRAB bloodstream infections in Thailand are driven by a combination of endemic high-risk lineages and the sustained circulation of blaNDM-harboring MGEs. Overall, our results confirm the importance of continued genomic surveillance for monitoring the emergence and dissemination of blaNDM-producing CRAB and for strengthening infection prevention and antimicrobial resistance control efforts in hospital settings.
Aekkawat Unahalekhaka, Kulsumpun Krobanan, W. Kamjumphol et al.· PLoS ONE· 0 citations
INTRODUCTION AND AIMS
Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a serious global threat, prioritized by the WHO for new antibiotic development. The ECDC proposed the integration of genomic sequencing into surveillance. This study characterizes phenotypic and genotypic features of nationwide-collected CRAB isolates from Spanish hospitals (2016-2020).
MATERIALS AND METHODS
A total of 822 CRAB isolates sent to the Spanish reference laboratory were analyzed, and 108 representative isolates were selected from 48 hospitals in 25 Spanish provinces. Antibiotic susceptibility was determined according to EUCAST guidelines, and WGS was performed by Illumina. Resistome, virulome, phylogeny (cgMLST; 2390 genes), insertion sequences and plasmids were analyzed.
RESULTS
Of the 108 representative isolates, 68.5% produced OXA-23, 10.2% OXA-24, 7.4% OXA-58, 1.9% NDM-1 and 2.7% others. 3.7% co-produced two acquired carbapenemases, and six that did not have them showed the ISAba1 upstream of the blaOXA-51 like. The predominant STs were ST2pas (82.4%) and ST218Oxf (61.1%). blaOXA-66 chromosomal carbapenemase allele was present in 75% of the 108 isolates, armA 16s rRNA methyltransferase gene in 61.1% and the kL-7/OCL-18 was present in 59.3% of the isolates. The most active antibiotic was colistin. 65.4% of invasive cases were caused by isolates harboring all 38 virulence genes tested. In the 64.8% of isolates a plasmid type was detected, mainly pS32-1-like (54.6%).
CONCLUSIONS
In Spain, CRAB dissemination is driven by interregional spread of isolates belonging to the ST218Oxf/ST2Pas clones, characterized by the blaOXA-23/blaOXA-66 genotype, the presence of armA, the KL7/OCL18 capsular profile and the presence of pS32-1 plasmid.
Jared Sotelo, B. Aracil, J. Arca-Suárez et al.· International Journal of Ant...· 0 citations
Carbapenem-resistant Enterobacterales (CRE) are a major public health concern, yet genomic data from Bulgaria remain limited. We investigated the genomic epidemiology and genomic characteristics of clinically significant CRE recovered at University Hospital “Lozenetz”, Sofia, between 2022 and 2025. Antimicrobial susceptibility testing, phenotypic carbapenemase characterization, and PCR were combined with whole-genome sequencing of 23 purposively selected isolates chosen to capture temporal, species, carbapenemase, specimen, ward, and resistance-phenotype diversity. The proportion of CRE among all Enterobacterales remained broadly stable over the study period, and Klebsiella pneumoniae was the predominant species throughout. NDM-type carbapenemases were the most frequent overall, although VIM-, KPC-, and OXA-48-like enzymes were also detected. Among the sequenced isolates K. pneumoniae ST6260 (n = 16) was predominant. The remaining isolates included single K. pneumoniae isolates belonging to ST11, ST101, and ST258; two Enterobacter hormaechei ST114; one Proteus mirabilis ST93; and one Providencia stuartii ST46. All ST6260 isolates carried chromosomal blaNDM-5 within a conserved multidrug-resistance module with variable downstream regions, whereas blaOXA-232 was situated on a small ColKP3 plasmid within a defined subcluster. Overall, the data indicate that ST6260 is an emerging hospital-associated multidrug-resistant lineage.
Emma Keuleyan, I. Stoikov, Theodor Todorov et al.· Acta Microbiologica Hellenic...· 0 citations
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.
Yue Zhang, Yanru Liang, Yuanping Wang et al.· Frontiers in Cellular and In...· 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
ABSTRACT The aim of this study was to perform molecular characterization of the carbapenem-resistant Enterobacter cloacae complex (ECC) isolates from colonized patients in a hospital using whole-genome sequencing (WGS) technology. As part of routine surveillance for multidrug-resistant bacterial colonization, 21 ECC isolates were recovered from patients at San Carlos Hospital in Madrid (Spain) between December 2020 and November 2024. WGS was used to determine their genetic relatedness. Furthermore, species identification, sequence type (ST), resistome, plasmid content, and flanking mobile genetic elements (MGEs) of the carbapenemase genes were derived from the WGS data. The most prevalent carbapenemase gene identified was blaVIM-1 (n = 18, 85.7%), with other notable genes including blaKPC-2 (n = 1, 4.8%), blaKPC-3 (n = 1, 4.8%), and blaOXA-48 (n = 1, 4.8%). Several blaACT and blaESBL variants were also found among the carbapenem-resistant ECC isolates. All of them carried at least one blaACT gene, with blaACT-7 (11/21) and blaTEM-type (14/21) genes being the most common AmpC and ESBL-encoding genes, respectively. Additionally, two isolates exhibited the presence of the mcr-9 gene. Overall, E. hormaechei subsp. steigerwaltii (ST93), followed by E. hormaechei subsp. hoffmanii (ST78 and ST50), were the predominant species and STs circulating among the carbapenem-resistant ECC strains. The blaVIM-1 gene was part of class 1 integrons located within a Tn3-family transposon, Tn6292. blaKPC and blaOXA-48 were linked to Tn4401 and Tn1999 transposons, respectively. In conclusion, the presence of the blaVIM within a transposon Tn6292 enhances its mobility across bacterial genomes, underscoring the value of high-throughput sequencing in monitoring the spread of carbapenem-resistant ECC isolates. IMPORTANCE This study highlights why monitoring the spread of antibiotic-resistant bacteria in hospitals is critical. By analyzing the complete DNA of carbapenem-resistant bacteria, antibiotics were considered a last line of treatment. We found that the resistance genes are not isolated. Instead, they are embedded within mobile elements called transposons. This means that they can “jump” between different bacteria, accelerating the spread of resistance. These findings emphasize the importance of high-resolution genomic technologies to track and control the spread of these dangerous bacteria in clinical settings, helping preserve the effectiveness of life-saving treatments. This study highlights why monitoring the spread of antibiotic-resistant bacteria in hospitals is critical. By analyzing the complete DNA of carbapenem-resistant bacteria, antibiotics were considered a last line of treatment. We found that the resistance genes are not isolated. Instead, they are embedded within mobile elements called transposons. This means that they can “jump” between different bacteria, accelerating the spread of resistance. These findings emphasize the importance of high-resolution genomic technologies to track and control the spread of these dangerous bacteria in clinical settings, helping preserve the effectiveness of life-saving treatments.
E. Ríos, Iciar Rodríguez-Avial, Rodrigo López et al.· Microbiology spectrum· 0 citations