Regional distribution of carbapenemase‑producing Acinetobacter baumannii isolates in southern Spain (Andalusia)

Vol.:(0123456789) European Journal of Clinical Microbiology & Infectious Diseases https://doi.org/10.1007/s10096-025-05047-2 RESEARCH Regional distribution ofcarbapenemase‑producing Acinetobacter baumannii isolates insouthern Spain (Andalusia) FelipeFernández‑Cuenca1,2,4· SaludRodríguez‑Pallares5· LorenaLópez‑Cerero1,2,3,4· JoséGutiérrez‑Fernández6· MaríaFeBautista7· JuanAntonioSánchezGómez8· WaldoSánchez‑YebraRomera8· MercedesDelgado1,2,3,4· EstherRecacha1,2,4· AlvaroPascual1,2,3,4 Received: 10 October 2024 / Accepted: 16 January 2025 © The Author(s) 2025 Abstract Objectives This is the first study conducted in southern Spain to determine i) the population structure (PS) of carbapenemresistant (CR) Acinetobacter baumannii isolates by multilocus sequencing typing (MLST) and core genome MLST (cgMLST) and ii) the association between the sequence type ST and the blaOXA-51 variant, capsule polysaccharide locus (KL) and lipooligosaccharide outer core locus (OCL) types. Methods Of 336 isolates submitted to the Andalusian reference laboratory (PIRASOA; December 2017–2020), 73 were subjected to WGS (MiSeq). The following analyses were performed: bacterial identification (ribosomal MLST), carbapenemase gene detection (Resfinder 4.0), PS delineation (MLST by MLSTfinder 2.0 and cgMLST by Ridom SeqSphere+), and KL types and OCL types (Kaptive tool). Results The carbapenemases detected were blaOXA-23 (n = 41), blaOXA-58 (n = 26), blaOXA-24 (n = 5), blaOXA-72 (n = 1) and blaNDM-1 (n = 2). The PS revealed one major ST2 clone (n = 54) and seven minor ST clones by MLST, and 41 lineages by cgMLST. Thirty-five lineages were detected only in a single hospital whereas five lineages were observed in several hospitals and provinces. blaOXA-66 was the most frequent blaOXA-51 variant and was mainly associated with the ST2 clone. Eleven KL types and 3 OCL types were assigned, with KL2 (n = 27), KL7 (n = 16) and OCL1 being the most frequent. Conclusions The PS of CR A. baumannii in Andalusia is characterized by a dominant ST2/blaOXA-23 clone and several lineages, showing local spread of lineages in most hospitals, and intercenter or interregional spread of a few lineages. Singlelocus blaOXA-51-like typing and KL typing may be useful as complementary preliminary typing tool. Keywords Acinetobacter baumannii· Southern of Spain· KL type· Interregional spread Introduction Carbapenem-resistant A. baumannii (CR-Ab) is one of the most important nosocomial pathogens worldwide [1]. The main carbapenem resistance mechanism described in CR-Ab is the acquisition of OXA-type carbapenemase genes [2]. The most frequently reported carbapenemase genes worldwide are blaOXA-23, blaOXA-24/40 and blaOXA-58 [3, 4]. It has been observed that the naturally occurring blaOXA-51 of A. baumannii is a useful target for preliminary identification of some Acinetobacter spp. and for differentiation of some international clones (IC) of CR-Ab [4, 5]. From an epidemiological point of view, CR-Ab isolates represent a serious global health problem due to their ability to cause outbreaks [1–3]. This applies particularly to isolates belonging to certain IC lineages, such as IC-2 [5]. The * Lorena López-Cerero [email protected] 1 University Hospital Virgen Macarena, Seville, Spain 2 Institute ofBiomedicine ofSeville, Seville, Spain 3 University ofSeville, Seville, Spain 4 CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain 5 Servicio de Microbiología e Instituto de Investigación Biomédica ACoruña (INIBIC), Complexo Hospitalario Universitario ACoruña, ACoruña, Spain 6 University Hospital Virgen de Las Nieves, Granada, Spain 7 La-Inmaculada Hospital, Almería, Spain 8 UGC Biotechnology, Unit ofMicrobiology, University Hospital Torrecárdenas, Almería, Spain European Journal of Clinical Microbiology & Infectious Diseases introduction of typing methods based on large-scale whole genome sequencing (WGS) has been a major advance in molecular epidemiological research [6]. WGS is currently regarded as the gold standard for bacterial genotyping, offering greater discriminatory power than pulsed-field gel electrophoresis (PFGE), previously considered as the gold standard, and multilocus sequencing typing (MLST), which are widely used for delineating the population structures of bacteria [6–8]. Core genome (cgMLST) and whole genome (wgMLST) schemes, as well as genotyping methods based on sequencing the capsular polysaccharide locus (KL) and the oligosaccharide locus (OCL) have been developed for A. baumannii [7–11]. While these genotyping techniques have the potential to be useful for characterizing the population structure of CP-Ab at a regional level, the available experience is still limited and results inconclusive. The primary objective of this study was to describe by MLST and cgMLST the population structure and clonal distribution of clinical and environmental CR-Ab isolates detected in Andalusia over a 4-year period. The association between the ST and the blaOXA-51-like variant, KL type and OCL type was also investigated. Material andmethods Bacterial isolates andidentification Three hundred and thirty-six CR-Ab isolates, collected from surveillance (51%), clinical (48%) and environmental samples (1%) of patients attended in 16 hospitals in Andalusia (Spain) between December 2017 and 2020 were submitted to the Andalusian reference laboratory for antimicrobial reference laboratory for antimicrobial resistance and molecular epidemiology typing (PIRASOA). Submission of isolates was voluntary and not all hospitals submitted all isolates that were detected during this period. The mean annual incidence density of CR-Ab during this period was < 0.01 for 14 out of 16 hospitals (TableS1). In the remaining two hospitals, it was 0.64 for HHO, the Hospital La Inmaculada, in Almeria) and 0.24 for HIE (Hospital Infanta Elena, in Huelva). The preliminary identification of isolates was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, (MALDI-TOF MS) (MALDI Biotyper CA system; Bruker Daltonics, Madrid, Spain) and detection of blaOXA-51 by PCR amplification [12]. Carbapenem susceptibility testing anddetection ofcarbapenemase production Susceptibility to three carbapenems (ertapenem, imipenem and meropenem) was performed using MicroScan NMDRM1 panels (Beckman Coulter, Inc, Madrid, Spain). Susceptibility testing for imipenem and meropenem was also performed using gradient strips (Etest®, Biomérieux). For phenotypic detection of carbapenemase production, the combined disc test was performed on imipenem with carbapenemase inhibitors (Rosco, Madrid, Spain) and the β CARBA test (BioRad, Madrid, Spain). Initial detection of carbapenemase-encoding genes was performed by end-point PCR, using primers specific for blaOXA-23-like, blaOXA-24/40-like and blaOXA-58-like [12]. Whole genome DNA sequencing (WGS) The Nextera XT DNA Library Preparation Kit (Illumina GmbH, Germany) and the MiSeq Reagent Kit V3 (600 cycles) were used to prepare DNA libraries for sequencing on the Illumina MiSeq sequencer (2 × 300 paired end reads). Reads were quality filtered and de novo assembled using the CLC Genomics Workbench v10 (Qiagen). TableS2 shows the results of the QC analysis and the percentage of cgMLST good targets of Acinetobacter Ridom scheme. Annotation of resistance determinants in the assemblies, including blaOXA-51-like detection and characterization, was performed using the ResFinder tool, version 4.0 (https:// cge. food. dtu. dk/ servi ces/ ResFi nder/) and the Comprehensive Antibiotic Resistance Database (CARD; https:// card. mcmas ter. ca/) were used. Final bacterial identification was performed using the ribosomal MLST database (https:// pubml st. org/ speci esid) and blaOXA-51-like gene typing [4]. Molecular typing For all isolates, the initial clonal relationship was determined by PFGE with ApaI [13]. PFGE patterns were analyzed using Bionumerics version 8.1.1 software and the Dice coefficient. Isolates differing by 1 band or more were selected for NGS (Fig.S1). Assemblies were used for further MLST typing using MLSTfinder version 2.0 (https:// cge. food. dtu. dk/ servi ces/ MLST/). The core genome sequence type (cgST) was determined using Ridom SeqSphere+ software based on the scheme of 2390 alleles for the core genome and 1083 alleles for the accessory genome. A. baumannii ACICU was included as the reference genome to characterize the allelic profile of isolates on a gene-by-gene basis. To investigate the relatedness of isolates, a minimum spanning tree was constructed based on differences in cgMLST allelic profiles, and including missing values in the UPGMA algorithm. According to RIdom SeqSphere scheme, isolates showing ≤ 9 allelic differences were considered highly related. KL and OCL typing were performed using the Kaptive tool (https:// kapti veweb. erc. monash. edu/). Phylogenetic trees were visualized using the Interactive Tree Of Life (iTOL) (http:// itol. embl. de). Additionally, Andalusian genomes were compared European Journal of Clinical Microbiology & Infectious Diseases with those of a recent Portuguese collection of A. baumannii isolates detected between 2005–2019 [14]. Results Bacterial identification anddetection ofcarbapenemase production Of the 336 isolates tested, 335 were identified as A. baumannii and one was identified as Acinetobacter pittii by Maldi TOF and rMLST. All A. baumannii isolates were PCR-positive for blaOXA-51-like whereas the A. pittii isolate was PCR-negative for blaOXA-51-like. The most frequently detected carbapenemase gene was blaOXA-23-like (60%; n = 203 isolates, found in 9 hospitals), followed by blaOXA-58-like (37%; n = 124 isolates, found in 8 hospitals), and blaOXA-24/40-like (5%; n = 18 isolates, found in 2 hospitals). Two isolates (0.6%) were only PCR-positive for blaNDM-like. Co-detection of different carbapenemase genes was observed only in isolates carrying blaOXA-24/40-like and blaOXA-58-like (n = 10, 3%) or blaOXA-23-like (n = 1, 0.3%). As shown in Fig.1, the majority of the 336 isolates were collected in 4 provinces and 6 hospitals: 82% of blaOXA-23-like isolates in HVN, HVM, HIE and HT, 88% of blaOXA-58-like in HHO, HVN, HPE and HT, and 94% of blaOXA-24/40-like isolates in HHO and HT. A subset of 73 isolates (72 A. baumannii and one A. pittii) representing 73 ApaI-PFGE types were selected and subjected to WGS with further identification of carbapenemase-encoding allelic variants, molecular genotyping by MLST and cgMLST, blaOXA-51-like typing, KL typing and OCL typing. The carbapenemase allelic variants were distributed as follows: blaOXA-23 (n = 41, 56%), blaXA-58 (n = 26, 36%), blaOXA-24 (n = 5, 7%), blaNDM-1 (n = 2, 3%) and blaOXA-72 (n = 1, 1%) and. Co-detection of two carbapenemase genes was observed in only two blaOXA-58 and blaOXA-24carrying isolate and one blaOXA-23 and blaOXA-72carrying isolate. A. baumannii isolates were assigned by MLST to one of the following eight sequence types or clones: ST2, ST745, ST32, ST1474, ST1363, ST1, ST208 or ST85 (Fig.1). Two sequence types accounted for 90% of the 73 sequenced isolates: ST2 (n = 54, 75%) and ST745 (n = 11, 15%). Isolates belonging to the ST2 clone were detected in 13 (66%) of Fig. 1 Dendrogram generated from the scheme that combines 1083 accessory genes and 2390 cgMLST genes (Ridom SeqSphere +). A box with dotted lines indicates isolates with the same cgMLST detected in different hospitals in different provinces European Journal of Clinical Microbiology & Infectious Diseases 16 hospitals, and most of these isolates harbored blaOXA-23 (n = 40, 74%) or blaOXA-58 (n = 13, 24%). In contrast, isolates of the ST745 clone were found in only two hospitals, and carried blaOXA-58. A percentage of 95.0–99.6% of good targets were obtained using cgMLST Ridom scheme. As shown in Fig.1 and 2, the population structure determined by cgMLST revealed 41 different cgMLSTs or lineages. Twenty-six lineages were identified in 100% of blaOXA-23-bearing isolates, whereas only 9 lineages were observed in 46% of blaOXA-58-carrying isolates. The 26 lineages assigned to blaOXA-23-bearing isolates were identified in 10 hospitals and 6 provinces (Fig.1 and 2). During the 3-year period, 21 lineages were observed only once, while 5 lineages were observed in more than one hospital and/or province. In terms of the number of allele differences in the core genome of the lineages, fewer than 10 allele differences were observed in 2 lineages in hospitals in two different provinces each. The same lineage was detected in two hospitals in the city of Seville (10 allele differences in the core genome) and another lineage in two hospitals in the city of Granada (13 allele differences in the core genome). The 9 lineages assigned to blaOXA-58-bearing isolates were identified in 8 hospitals and 5 provinces (Fig.1 and 2). Eight lineages were observed only once, and one lineage was observed in five hospitals. Less than 10 alleles of difference in the core genome between lineages were detected in isolates from 4 hospitals in 3 different provinces. Six strains belonged to the ST2 clone and the other 2 to single locus variants of the ST2 clone (ST208 and ST1474). There was a poor correlation between cgMLST and PFGE, especially for cgMLST 2985, 3001, and 1694 which were assigned to 10, 8 and 5 different pulsotypes, respectively. When comparing the Andalusian genomes with the collection of Portuguese isolates, none of the latter shared a cgMLST with those from our region (Fig.S2). Seven different allelic variants of blaOXA-51-like were identified among A. baumannii isolates (blaOXA-66, blaOXA-67, blaOXA-69, blaOXA-94, blaOXA-100, blaOXA-109, and blaOXA-508). Of these variants, blaOXA-66 was by far the most frequently detected (n = 62; 87%), and was carried by all ST2 isolates harboring blaOXA-23 or blaOXA-58, as well as by ST208 and ST745 isolates harboring blaOXA-58. The remaining five minor blaOXA-51-like variants were associated with unique STs (Fig.1). blaOXA-421 was detected in the A. pittii isolate. A total of eleven KL types were observed (Fig.1). A low level of discrimination in the KL typing was observed due to the presence of 6 KL types that contained more than 1 cgMLST. The majority (83%) of the KL types observed were classified as either KL2, KL151 or KL7. The KL2 type was the most frequent (n = 27, 38%) and ubiquitous, being observed in 96% of isolates harboring blaOXA-58. The KL2 type was observed in isolates from 4 provinces and belonged to 4 STs and 11 cgMLSTs. All 11 isolates assigned to ST745 were of the KL2 type (Fig.1). All 17 isolates with the KL151 type were found in two eastern provinces, carried blaOXA-23 (41% of blaOXA-23 isolates), belonged to the ST2 clone, and were represented by 11 different cgMLSTs. The 16 isolates with the KL7 type were from two western provinces of Andalusia and also carried blaOXA-23 (39% of blaOXA-23 isolates). They were assigned to the ST2 clone and were represented by 10 cgMLSTs. Four OCL types were observed, the most frequent being OCL1, which was identified in 69 (96%) isolates. Discussion This study presents the findings of a recent population structure analysis of CR-Ab performed in the region of Andalusia (surface area 87,600 Km2), southern Spain. In our study, the population structure of CR-Ab isolates defined by MLST and using the Pasteur scheme revealed the presence of a dominant high-risk clone, composed mainly of blaOXA-23 isolates belonging to ST2, included in the clonal complex 2 (CC2), which were disseminated in most Andalusian hospitals and provinces. These results agree with previous studies performed in Spain, other countries of Europe, Asia and the USA [3, 15, 16], revealing the significant potential of ST2/blaOXA-23 isolates for global dissemination in the nosocomial environment [2, 3, 16, 17]. Also worth highlighting is the presence of additional minor clones within CC2, especially ST32 and ST1474, which are single-locus variants of the rpoB allele. To the best of our knowledge, this is the first study to evaluate the ability of cgMLST to define and characterize the population structure of CR-Ab in all the hospitals in our region, as well as its practical value in investigating the regional and interregional spread of CR-Ab in Andalusia. The application of this genotyping method showed that most CR-Ab isolates at each hospital were of local origin, but that this was in parallel with the spread of a single lineage between hospitals. On the other hand, we did not find any genetic relationship between Portuguese and Andalusian isolates, despite the geographical proximity. The epidemiological situation of CR-Ab in Andalusia is consistent with the findings of the international multicenter study performed by Lötsch etal. in nine European countries, which reported regional or inter-regional spread as well as endemicity in seven countries [18]. However, in our study there were some discrepancies between MLST sequence types and the Ridom cgMLST scheme. In the case of the 8 genomes of the cgMLST2985 lineage, six genomes belonged to sequence type ST2 and the other 2 genomes belonged to two single locus variants of ST2. To avoid these discrepancies, the algorithm for new cgMLST assignment could consider the European Journal of Clinical Microbiology & Infectious Diseases cgMLST cgMLST A B Fig. 2 Minimum spanning tree for blaOXA-23 isolates (panel A) and blaOXA-58 (panel B) isolates based on cgMLST using the `pairwise ignore missing values´ during distance calculations. The numbers on the connecting lines illustrate the numbers of target genes with different alleles. Different colors of isolates indicate the assigned cgMLST European Journal of Clinical Microbiology & Infectious Diseases changes in the MLST scheme loci. On the other hand, there was a poor correlation between cgMLST and PFGE pulsotypes, suggesting that the cgMLST scheme used has a lower discriminatory power than that of PFGE. Our results corroborate those of previous studies, which indicate that blaOXA-23 and, to a lesser extent, blaOXA-58 were widely distributed in most Andalusian hospitals and provinces [2, 3, 5, 16]. Part of its capacity for dissemination may be attributed in part to the association of blaOXA-23 with various mobile genetic platforms containing ISAbatype insertion sequences and/or transposons, as described previously [3, 19]. It is noteworthy that, in the four hospitals that accounted for more than 70% of isolates, isolates carrying different blaOXA were found simultaneously. This event is not common in CR-Ab. In one of these 4 hospitals, in the same year, blaOXA-58, blaOXA-23 and blaOXA-72 genes were detected and could explain the co-detection of both blaOXA-23 with blaOXA-72 and blaOXA-58 with blaOXA-24 in some isolates, probably due to the mobilization by horizontal transfer of plasmids carrying genes encoding OXA-type carbapenemases [20]. In line with previous studies, the intrinsic blaOXA-66 allelic variant was associated with the dominant ST2 clone, whereas the minor variants blaOXA-100, blaOXA-69 and blaOXA-94 were associated with the ST32, ST1 and ST85 clones, respectively [5]. This finding is in agreement with previous studies, which have suggested that single-locus blaOXA-51-like sequence-based typing is a useful preliminary typing method, particularly for local epidemiological investigations, as it is able to discriminate between unrelated ST clones [4]. However, it is recommended that blaOXA-51-like sequencing be employed in conjunction with other typing methods, as some plasmid-encoded blaOXA-51-like gene variants may be carried by certain Acinetobacter non-baumannii species [21]. Capsular polysaccharides and lipopolysaccharides have been associated with carbapenem resistance, virulence, disease severity, and mortality inA. baumannii [22]. However, there is very little information on the usefulness of capsular typing in CR-Ab, particularly in the context of sequencebased K and O locus typing. In our study, capsular type KL2 was the most frequent KL type, which is in line with previous studies where KL2 was the dominant KL type [23], which suggests that this capsule may confer some kind of advantage to CR-Ab compared to other less frequent capsular types, as has been previously reported [23, 24]. Furthermore, KL typing showed much greater discriminatory power than OCL typing, which is also in agreement with previous studies, indicating that KL typing could be a valuable tool for CR-Ab typing [11, 22, 23]. However, our results show that KL typing correlates weakly with ST when using the Pasteur scheme or the cgST scheme of Higgins etal. are employed. The limited correlation between KL type and ST using the Pasteur scheme differs from the results of Luo YC etal. obtained using the Oxford scheme on isolates from Taiwan, where the major KL types were associated with ST and suggesting that KL typing could be a useful tool for studying the population structure of A. baumannii, especially when used in conjunction with other genotyping assays [25]. The lack of association between KL type and ST could be explained by the greater discriminatory power of the Oxford scheme compared to the Pasteur scheme [25, 26]. Therefore, we are unable to exclude the possibility that KL type is associated with the ST clone of our isolates according to the Oxford scheme. The main value of KL typing may be to distinguish ST2/blaOXA-23 isolates from ST2/blaOXA-58, as well as from isolates with an ST other than ST2. The main strength of our study is its use of a wellcharacterized collection of CR-Ab isolates from Andalusia (87,600Km2), one of the largest regions of Spain. However, the present study has some limitations. The most important is that it was not mandatory to send samples to our reference laboratory. Therefore, it is possible that the real prevalence of isolates, blaOXA-type carbapenemase genes, ST clones and cgST lineages may differ from those observed in the present study. However, the majority of isolates came from the two hospitals with the highest prevalence. Another important limitation is the lack of epidemiological data, which would be very useful in interpreting the results and conclusions of this study. In conclusion, the results of our study show that ST2 is the dominant clone and blaOXA-23 the most prevalent carbapenemase in Andalusia. The population structure of A. baumannii determined by cgMLST shows that most CR-Ab isolates were disseminated locally, whereas a few lineages were involved in interhospital and/or interregional spread. While single-locus blaOXA-51-like typing and capsular KL typing are much less discriminant than ST and cgMLST, they may serve as useful complementary typing tools in the preliminary characterization of the population structure of A. baumannii. Supplementary Information The online version contains supplementary material available at https:// doi. org/ 10. 1007/ s1009602505047-2. Acknowledgements We thank the participating hospitals that submitted isolates to the Andalusian Reference Laboratory, Program for the Prevention and Control of Healthcare-Associated Infections and Antimicrobial Stewardship (PIRASOA, Servicio Andaluz de Salud). Author contribution FFC: manuscript writing, Supplementary Table2, Fig.2. SRP: manuscript writing and Fig.2 LLC: Supplementary Table1 and Fig.1. Manuscript revision. PG, MFB, JASG, WSYR: preliminary identification of Acinetobacter species and antimicrobial susceptibility testing. MD: Detection of carbapenemase production (phenotypic assays) and PFGE ER. Detection of carbapenemase genes and PFGE APH: Supervision and revision. European Journal of Clinical Microbiology & Infectious Diseases Funding Funding for open access publishing: Universidad de Sevilla/ CBUA. Data availability No datasets were generated or analysed during the current study. Declarations Competing Interests The authors declare no competing interests. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. References 1. Miller WR, Arias CA (2024) ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 22(10):598–616 2. Müller C, Reuter S, Wille J, Xanthopoulou K, Stefanik D, Grundmann H, Higgins PG, Seifert H (2023) A global view on carbapenem-resistant Acinetobacter baumannii. mBio 14(6):e0226023 3. Castanheira M, Mendes RE, Gales AC (2023) Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis 76(Suppl 2):S166–S178 4. Pournaras S, Gogou V, Giannouli M, Dimitroulia E, Dafopoulou K, Tsakris A, Zarrilli R (2014) Single-locus-sequence-based typing of blaOXA-51-like genes for rapid assignment of Acinetobacter baumannii clinical isolates to international clonal lineages. J Clin Microbiol 52(5):1653–1657 5. Li J, Li Y, Cao X, Zheng J, Zhang Y, Xie H, Li C, Liu C, Shen H (2023) Genome-wide identification and oxacillinase OXA distribution characteristics of Acinetobacter spp. based on a global database. Front Microbiol 1(14):1174200 6. Simar SR, Hanson BM, Arias CA (2021) Techniques in bacterial strain typing: past, present, and future. Curr Opin Infect Dis 34(4):339–345 7. Forde BM, Bergh H, Cuddihy T, Hajkowicz K, Hurst T, Playford EG, Henderson BC, Runnegar N, Clark J, Jennison AV, Moss S, Hume A, Leroux H, Beatson SA, Paterson DL, Harris PNA (2023) Clinical Implementation of Routine Whole-genome Sequencing for Hospital Infection Control of Multi-drug Resistant Pathogens. Clin Infect Dis 76(3):e1277–e1284 8. Dekker JP, Frank KM (2016) Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy. J Clin Microbiol 54(12):2850–2853 9. Higgins PG, Prior K, Harmsen D, Seifert H (2017) Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii. PLoS ONE 12(6):e0179228 10. Venditti C, Vulcano A, D’Arezzo S, Gruber CEM, Selleri M, Antonini M, Lanini S, Marani A, Puro V, Nisii C, Di Caro A (2019) Epidemiological investigation of an Acinetobacter baumannii outbreak using core genome multilocus sequence typing. J Glob Antimicrob Resist 17:245–249 11. Wyres KL, Cahill SM, Holt KE, Hall RM, Kenyon JJ (2020) Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. Microb Genom 6(3):e000339 12. Woodford N, Ellington MJ, Coelho JM, Turton JF, Ward ME, Brown S, Amyes SG, Livermore DM (2006) Multiplex PCR for genes encoding prevalent OXA carbapenemases in Acinetobacter spp. Int J Antimicrob Agents 27(4):351–353 13. Seifert H, Dolzani L, Bressan R, van der Reijden T, van Strijen B, Stefanik D, Heersma H, Dijkshoorn L (2005) Standardization and interlaboratory reproducibility assessment of pulsed-field gel electrophoresis-generated fingerprints of Acinetobacter baumannii. J Clin Microbiol 43(9):4328–4335 14. Domingues R, Oliveira R, Silva S, Araújo D, Almeida C, Cho GS, Franz CMAP, Saavedra MJ, Azeredo J, Oliveira H (2024) Molecular Detection of Carbapenemases in Acinetobacter baumannii Strains of Portugal and Association With Sequence Types, Capsular Types, and Virulence. Clin Ther 46(12):e9–e15 15. Villalón P, Valdezate S, Medina-Pascual MJ, Rubio V, Vindel A, Saez-Nieto JA (2011) Clonal diversity of nosocomial epidemic Acinetobacter baumannii strains isolated in Spain. J Clin Microbiol 49(3):875–882 16. Lasarte-Monterrubio C, Guijarro-Sánchez P, Alonso-Garcia I, Outeda M, Maceiras R, González-Pinto L, Martínez-Guitián M, Fernández-Lozano C, Vázquez-Ucha JC, Bou G, ArcaSuárez J, Beceiro A (2024) Epidemiology, resistance genomics and susceptibility of Acinetobacter species: results from the 2020 Spanish nationwide surveillance study. Euro Surveill 29(15):2300352 17. Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S (2010) The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS ONE 5(4):e10034 18. Lötsch F, Albiger B, Monnet DL, Struelens MJ, Seifert H, Kohlenberg A, European Antimicrobial Resistance Genes Surveillance Network (EURGen-Net) carbapenem-resistant Acinetobacter baumannii capacity survey group; EURGen-Net carbapenem-resistant Acinetobacter baumannii capacity survey group (2020) Epidemiological situation, laboratory capacity and preparedness for carbapenem-resistant Acinetobacter baumannii in Europe, 2019. Euro Surveill 25(45):2001735 19. Poirel L, Nordmann P (2006) Genetic structures at the origin of acquisition and expression of the carbapenem-hydrolyzing oxacillinase gene blaOXA-58 in Acinetobacter baumannii. Antimicrob Agents Chemother 50(4):1442–1448 20. Salgado-Camargo AD, Castro-Jaimes S, Gutierrez-Rios RM, Lozano LF, Altamirano-Pacheco L, Silva-Sanchez J, PérezOseguera Á, Volkow P, Castillo-Ramírez S, Cevallos MA (2020) Structure and Evolution of Acinetobacter baumannii Plasmids. Front Microbiol 11:1283 21. Lee YT, Kuo SC, Chiang MC, Yang SP, Chen CP, Chen TL, Fung CP (2012) Emergence of carbapenem-resistant nonbaumannii species of Acinetobacter harboring a blaOXA-51like gene that is intrinsic to A. baumannii. Antimicrob Agents Chemother 56(2):1124–1127 European Journal of Clinical Microbiology & Infectious Diseases 22. Hsieh YC, Wang SH, Chen YY, Lin TL, Shie SS, Huang CT, Lee CH, Chen YC, Quyen TLT, Pan YJ (2020) Association of capsular types with carbapenem resistance, disease severity, and mortality in Acinetobacter baumannii. Emerg Microbes Infect 9(1):2094–2104 23. Kostyanev T, Xavier BB, García-Castillo M, Lammens C, Bravo-Ferrer Acosta J, Rodríguez-Baño J, Cantón R, Glupczynski Y, Goossens H, EURECA/WP1B Group (2021) Phenotypic and molecular characterizations of carbapenem-resistant Acinetobacter baumannii isolates collected within the EURECA study. Int J Antimicrob Agents 57(6):106345 24. Oliveira H, Mendes A, Fraga AG, Ferreira A, Pimenta AI, MilHomens D, Fialho AM, Pedrosa J, Azeredo J (2019) K2 Capsule Depolymerase Is Highly Stable, Is Refractory to Resistance, and Protects Larvae and Mice from Acinetobacter baumannii Sepsis. Appl Environ Microbiol 85(17):e00934-e1019 25. Luo YC, Hsieh YC, Wu JW, Quyen TLT, Chen YY, Liao WC, Li SW, Wang SH, Pan YJ (2022) Exploring the association between capsular types, sequence types, and carbapenemase genes in Acinetobacter baumannii. Int J Antimicrob Agents 59(1):106470 26. Gaiarsa S, BatistiBiffignandi G, Esposito EP, Castelli M, Jolley KA, Brisse S, Sassera D, Zarrilli R (2019) Comparative Analysis of the Two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes. Front Microbiol 10:930 Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.