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Article

Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (OXA-23) and Klebsiella pneumoniae (KPC-2) Causing Hospital-Acquired Infections in Dogs

by
Isabela Pádua Zanon
1,
João Victor Ferreira Campos
1,
Yasmin Gonçalves de Castro
1,
Isadora Maria Soares de Melo
1,
Flávia Figueira Aburjaile
1,
Bertram Brenig
2,
Vasco Azevedo
3 and
Rodrigo Otávio Silveira Silva
1,*
1
Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30720440, Brazil
2
Institute of Veterinary Medicine, University of Göttingen, 37077 Göttingen, Germany
3
Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 30720440, Brazil
*
Author to whom correspondence should be addressed.
Antibiotics 2025, 14(6), 584; https://doi.org/10.3390/antibiotics14060584
Submission received: 1 May 2025 / Revised: 21 May 2025 / Accepted: 5 June 2025 / Published: 6 June 2025
(This article belongs to the Special Issue Antimicrobial Resistance: Epidemiology and Implications for Veterinary Medicine)
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Abstract

:
Background/Objectives: Antimicrobial resistance is a major global health threat. Among the most problematic pathogens are carbapenem-resistant Acinetobacter baumannii and Klebsiella pneumoniae, which are significant causes of mortality in humans, particularly in the context of nosocomial infections. In companion animals, these bacteria have been reported mainly as colonizers of healthy animals or, less frequently, in community-acquired infections. However, no confirmed cases of healthcare-associated infections caused by these species have been documented in this population. This study reports the first confirmed fatal cases of infection with carbapenem-resistant A. baumannii and KPC-producing K. pneumoniae in dogs. Methods: Three hospitalized dogs developed infections associated with distinct anatomical devices, including a venous catheter, an endotracheal tube, and a Penrose drain. Bacterial isolation followed by antimicrobial susceptibility testing identified carbapenem-resistant A. baumannii and K. pneumoniae. The isolates were subsequently subjected to additional antimicrobial resistance tests and whole-genome sequencing (WGS). Results: WGS confirmed the presence of the OXA-23 carbapenemase gene in both A. baumannii isolates and the KPC-2 carbapenemase gene was detected in the K. pneumoniae strain. All three strains exhibited resistance to multiple antimicrobial classes, including β-lactams (amoxicillin-clavulanic acid, ampicillin, cephalotin, piperacillin-tazobactam, cefoxitin, ceftiofur, cefotaxime, ertapenem, imipenem and meropenem), aminoglycosides (gentamicin, neomycin), tetracyclines (doxycycline, tetracycline and oxytetracycline), fluoroquinolones (ciprofloxacin, enrofloxacin), and folate pathway antagonists (trimethoprim-sulfamethoxazole). Multilocus sequence typing identified two high-risk clones: K. pneumoniae ST340 (CC258) and A. baumannii ST15 (CC15). Single nucleotide polymorphism analysis confirmed a high degree of genetic similarity between these isolates and strains previously associated with human infections in Brazil. Conclusions: These findings provide the first evidence of fatal, healthcare-associated infections caused by these multidrug-resistant pathogens in dogs and underscore the need to strengthen surveillance and infection control practices in veterinary hospitals. Furthermore, the results raise concerns about the potential of companion animals to act as reservoirs for multidrug-resistant organisms of public health relevance.

1. Introduction

Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic Gram-negative bacilli recognized as major etiological agents of healthcare-associated infections, particularly in immunocompromised and critically ill patients admitted to intensive care units [1,2,3]. In this context, the emergence of multidrug-resistant strains, particularly those resistant to carbapenems, poses a major clinical challenge, as it significantly limits therapeutic options and complicates clinical management [4,5]. Carbapenems are recognized as last-resort antimicrobials, primarily reserved for the treatment of infections caused by multidrug-resistant pathogens [6,7,8]. Moreover, the World Organization for Animal Health (WOAH) emphasizes that the use of this antimicrobial class should be restricted exclusively to human medicine in order to safeguard its efficacy [9]. Therefore, the detection of strains resistant to this class of antimicrobials in veterinary hospital settings is a cause for concern, as it underscores the dissemination of resistant isolates that pose a potential threat to public health [10].
Current studies have reported the presence of these pathogens in companion animals and veterinary environments, including mostly A. baumannii carrying blaOXA-23 and blaOXA-51 and Enterobacteriaceae KPC-producing isolates [11,12,13,14,15,16,17,18,19,20]. However, none have addressed the occurrence of carbapenem-resistant strains causing nosocomial infections in companion animals. Moreover, there is no available information regarding two clinically significant sequence types—K. pneumoniae ST340 and A. baumannii ST15—which are recognized as relevant epidemic clones circulating in several countries, including in Brazil [21,22,23,24]. Thus, the aim of this study was to describe three fatal cases of infection caused by carbapenemase-producing A. baumannii and K. pneumoniae in dogs, as well as to identify their antimicrobial resistance determinants and investigate their phylogenetic relationships with strains previously isolated from infected humans.

2. Results

2.1. Bacterial Isolation and Antimicrobial Susceptibility

In all three cases, the samples collected resulted in the growth of pure colonies on MacConkey agar and Blood agar after 24 h of incubation. Species identification confirmed K. pneumoniae in Case 1 (B145) and A. baumannii in Cases 2 and 3 (B146 and BR250, respectively). In Case 1, the K. pneumoniae isolate exhibited resistance to penicillins (amoxicillin-clavulanic acid and ampicillin), third-generation cephalosporins (ceftiofur and cefotaxime), fluoroquinolones (ciprofloxacin and enrofloxacin), tetracyclines (doxycycline and oxytetracycline), aminoglycosides (gentamicin and neomycin), nitrofurans (nitrofurantoin), and carbapenems (ertapenem). It remained susceptible only to phenicols (florfenicol) and folate pathway antagonists (trimethoprim-sulfamethoxazole). Additionally, the isolate showed a minimum inhibitory concentration (MIC) of 12 µg/mL for ertapenem and 0.125 µg/mL for colistin, being categorized as resistant and intermediate, respectively.
A. baumannii isolate B146 (Case 2) exhibited resistance to penicillins (piperacillin-tazobactam), fluoroquinolones (ciprofloxacin), carbapenems (imipenem and meropenem), aminoglycosides (gentamicin), folate pathway antagonists (trimethoprim-sulfamethoxazole), and tetracyclines (tetracycline) in the disk diffusion method, displaying susceptibility only to third-generation cephalosporins (ceftazidime). This isolate presented a MIC of 4 µg/mL for meropenem and 0.125 µg/mL for colistin, both falling within the intermediate range. Conversely, isolate BR250 (Case 3) was resistant to penicillins (piperacillin-tazobactam), third-generation cephalosporins (ceftazidime), fluoroquinolones (ciprofloxacin), carbapenems (imipenem), folate pathway antagonists (trimethoprim-sulfamethoxazole), and tetracyclines (tetracycline). It remained susceptible only to aminoglycosides (gentamicin). The isolate showed a MIC of >32 µg/mL for meropenem and 0.047 µg/mL for colistin, being classified as resistant and intermediate, respectively. The three isolates obtained in this study were all classified as multidrug resistant [5].

2.2. Comparative Genomics

2.2.1. Presence and Type of Carbapenemase Genes

The K. pneumoniae isolate harbored the blaKPC-2 gene, which encodes a class A carbapenemase commonly found in Enterobacteriaceae [6]. Additionally, this isolate exhibited point mutations in the genes encoding the OmpK36 and OmpK37 porins (ompK36 and ompK37). These mutations likely reduce the permeability of the outer membrane to carbapenem antibiotics, thereby contributing to resistance to these compounds. Both A. baumannii isolates harbored the blaOXA-23 gene, which encodes a class D carbapenem-hydrolyzing β-lactamase (Figure 1). Additionally, the A. baumannii BR250 also carried the blaOXA-51 gene, another relevant carbapenemase.

2.2.2. Other Determinants of Antimicrobial Resistance

K. pneumoniae isolate B145 (Case 1) carried resistance genes for multiple antimicrobial classes (Figure 1). Notably, it harbored several bla and SHV genes encoding β-lactamases, which confer resistance to non-carbapenem β-lactams, including SHV-158 and SHV-159 (Figure 1), which are Extended-Spectrum Beta-Lactamases (ESBL) [25,26]. Additionally, the isolate possessed oqxA and oqxB, encoding a multidrug efflux pump that contributes to resistance against quinolones, folate pathway antagonists, and phenicols. Furthermore, multiple determinants of fluoroquinolone resistance were identified, including point mutations in the acrR gene, the presence of plasmid-mediated quinolone resistance (PMQR) gene (qnrB19), and the aac(6′)-Ib-cr gene, which encodes an aminoglycoside acetyltransferase that also reduces fluoroquinolone susceptibility in clinical bacterial isolates [27].
Both A. baumannii isolates carried resistance determinants associated with tetracyclines (tet(39)), folate pathway antagonists (sul2), and macrolides (msr(E) and mph(E)). In isolate B146, a particularly high number of aminoglycoside resistance genes was also observed (Figure 1).

2.2.3. Mobile Genetic Elements

Six plasmid replicons were detected in the sequenced K. pneumoniae strain, and two of them carried antimicrobial resistance determinants (Supplementary File S2). Additionally, this isolate also harbored the insertion sequence (IS) ISCfr1, which carries the aac(3)-IId gene associated with aminoglycoside resistance. In the two A. baumannii isolates, no plasmids were identified. On the other hand, relevant ISs were detected, including ISVsa3, which harbors the sul2 gene associated with resistance to folate pathway antagonists (Supplementary File S2).

2.2.4. MLST, KL-Typing, OCL-Typing and SNP Analysis

MLST analysis revealed that the K. pneumoniae isolate belonged to sequence type (ST) 340, which is part of clonal complex (CC) 258. Meanwhile, the A. baumannii isolates B146 and BR250 were assigned to ST15 (CC15Pas/CC103Ox) and ST1632, respectively. The K and O loci of the K. pneumoniae isolate were identified as KL15 and O4, respectively. The SNP analysis of the K. pneumoniae isolate revealed high similarity to strains previously isolated from infected humans in Brazil, with differences ranging from 59 up to 2228 SNPs (Supplementary File S3) (Figure 2).
Additionally, SNP analysis of the A. baumannii isolate BR250 (Case 3) revealed high genetic similarity to strains previously isolated from infected humans in Brazil, with differences ranging from 13 to 968 SNPs among strains belonging to ST15. In contrast, SNP analysis of the B146 A. baumannii (Case 2) isolate showed greater diversity, with differences ranging from at least 14,023 SNPs (Supplementary File S3) (Figure 3).

3. Discussion

Carbapenem-resistant A. baumannii and K. pneumoniae are globally distributed and are associated with human infections, particularly in intensive care units [1,29]. According to the World Health Organization (WHO), carbapenem-resistant Enterobacterales are listed in the critical priority category due to the urgent need for the development of new antibiotics [30]. The multidrug-resistant profile of these isolates limits treatment options and can lead to fatal outcomes [31,32]. Data on antimicrobial resistance and phylogenetic relationships between A. baumannii and K. pneumoniae isolates from animals are scarce and most are limited to studies of colonized animals or veterinary environments [11,17,33,34]. Furthermore, to the best of our knowledge, no cases have yet been reported of infections caused by A. baumannii ST15 and K. pneumoniae ST340 in companion animals—two globally disseminated STs responsible for human infections [21,22,23,24,35,36].
In this study, we describe three cases—two of them fatal—caused by carbapenem-resistant A. baumannii and K. pneumoniae in dogs hospitalized at a veterinary hospital. Both A. baumannii isolates harbored the acquired carbapenemase gene blaOXA-23, which encodes a class D β-lactamase (oxacillinase) commonly associated with carbapenem resistance and widely reported in human clinical isolates across multiple geographic regions [37]. In addition, the A. baumannii isolates carried the insertion sequence ISAba1, which is known to enhance the expression of blaOXA-23 and the intrinsic gene blaOXA-51 (another relevant carbapenemase) by providing a strong promoter upstream of both genes [38,39]. Conversely, the K. pneumoniae isolate harbored the blaKPC-2 gene, which is globally disseminated and associated with high-risk multidrug-resistant clones [40,41,42,43]. In addition, this isolate also carried the blaCTX-M-15 gene and SHV-type β-lactamase genes, such as blaSHV-158 and blaSHV-159. As previously mentioned, carbapenems are considered the first-line therapy for infections caused by ESBL-producing Enterobacteriaceae [44,45]. In this context, the detection of such findings in veterinary clinical settings is particularly alarming, as the presence of carbapenemase-producing organisms significantly compromises therapeutic efficacy, often leading to prolonged treatment courses and an increased risk of therapeutic failure [6,46,47].
Two clinically significant sequence types (STs) were identified in the K. pneumoniae and A. baumannii isolates, ST340 and ST15, respectively. K. pneumoniae ST340 belongs to clonal complex 258 (CC258), one of the most globally disseminated lineages, highly adapted to human populations and frequently associated with nosocomial infections [48,49]. Moreover, ST340 has previously been reported as the causative agent of hospital outbreaks in Brazil [24,50,51]. Interestingly, previous works documented the presence of K. pneumoniae from CC258 in animals [18,52,53], but the present report seems to be the first report of K. pneumoniae ST340 in animals.
One of the A. baumannii isolates (from Case 3) was assigned to ST15 (CC15), a clonal complex that, although less prevalent than the epidemic clonal complexes (CC1 and CC2), is frequently reported in South America, including Brazil [21,22,35,54,55,56,57,58,59,60]. These findings highlight the spread of globally significant high-risk clones among companion animals, underscoring their potential role in the transmission of antimicrobial-resistant strains to humans. In contrast, the A. baumannii B146 (Case 2) isolate was assigned to ST1632, a poorly characterized sequence type that has not yet been reported as a cause of infection in either humans or animals.
SNP analysis revealed a high genetic similarity between the K. pneumoniae isolate and clinical strains recovered from infected human patients, with a minimum difference of only 59 SNPs. This finding suggests that strains from this clonal complex—already known to be endemic in the human population in Brazil and previously detected in veterinary hospital environments [23,61]—can be shared with and also infect companion animals. A study conducted in Portugal has already provided evidence of strain sharing of K. pneumoniae between healthy humans and their cohabiting companion animals [62]. In a hospital environment, this scenario becomes even more concerning, as it often involves multidrug-resistant and hypervirulent isolates, such as the one described in the present study. Similarly, SNP analysis of the A. baumannii isolate belonging to ST15 revealed high genomic similarity to strains of the same ST previously isolated from infected humans in Brazil, with a minimum difference of only 13 SNPs. This sequence type, already recognized as endemic among A. baumannii isolates in Latin America, including Brazil [21,63,64], poses a public health concern due to its detection in a veterinary hospital and its close genetic relatedness to strains previously isolated from infected humans.
Antimicrobial resistance is already a reality in human medicine, representing a global concern due to its economic and social impact [65,66,67]. The detection of resistant strains is closely associated with worse patient outcomes and, consequently, higher mortality rates [68,69,70]. Since 2017, WHO has categorized various bacterial pathogens into different priority levels [71]. In veterinary medicine, the occurrence of these pathogens, including multidrug-resistant strains, is increasingly observed and warrants attention [72]. Interestingly, food animals are well-recognized reservoirs of antimicrobial-resistant microorganisms, and consequently, most public policies and research efforts have traditionally focused on these species [73,74]. However, the present study highlights the need for increased attention to companion animals. Although cats and dogs are generally less likely to receive antimicrobials compared to food animals, they are occasionally treated with critically important drugs, such as vancomycin and carbapenems. Additionally, they may be hospitalized, including in intensive care units, conditions that substantially increase the risk of colonization or infection with multidrug-resistant organisms such as KPC-producing bacteria and carbapenem-resistant A. baumannii. Anyway, for both companion and food animals, it is clear that antimicrobial resistance in animals must be addressed within the One Health approach, as epidemiology in animals is closely linked to that in humans [75,76].
Beyond surveillance approaches, reassessing clinical practices is imperative, including the stepwise use of antimicrobials for each clinical case, in accordance with established international guidelines [77,78,79,80,81]. Considering these concerns, a Hospital Infection Control Committee was established at the veterinary facility where these cases occurred, with the primary responsibility of monitoring all cases of nosocomial infections caused by multidrug-resistant pathogens, particularly those resistant to carbapenems.
This study has some limitations. Although it highlights the occurrence of nosocomial infections caused by carbapenem-resistant strains and raises awareness of this emerging threat, it is based on only three cases. Therefore, broader investigations are needed to better assess the frequency of such infections and to identify potential risk factors. In addition, necropsies were not performed because the owners did not authorize the procedures. This limited our ability to fully characterize the pathological findings, which would have strengthened the clinical interpretation of the cases.

4. Materials and Methods

4.1. Case 1

An eleven-year-old neutered male Lhasa Apso dog (B145), positive for leishmaniasis and living with five other dogs, was presented to the veterinary hospital with suspected chronic pancreatitis. The patient was immediately admitted to the hospital, where he received antimicrobial therapy with clindamycin, doxycycline, and ceftriaxone. Vasoactive therapy and exogenous oxygen administration were also initiated. Two days after admission, purulent secretion was observed in the endotracheal tube. The animal showed signs of sepsis and died three days after admission. A swab of endotracheal tube secretion was aseptically collected for bacteriological analysis. Informed consent was obtained from the owner for this case report but not for a necropsy.

4.2. Case 2

A thirteen-year-old intact male Golden Retriever (B146), diagnosed with chronic kidney disease and hip dysplasia, was admitted to the veterinary hospital with a history of lethargy, polyuria, dyschezia and scrotal sac lesion. On clinical examination, facial edema and submandibular abscess were noted. Ultrasonographic examination revealed lymphadenomegaly and acute hepatitis, as well as testicular asymmetry due to a possible neoplastic process in the left testicle. The patient was hospitalized in the intensive care unit and antimicrobial therapy was initiated. Initial treatment consisted of ampicillin with sulbactam (22 mg/kg, TID, IV). Three days after hospitalization, the patient developed hyperthermia and leukocytosis, and a marked edema in the left pelvic limb accompanied by hematoma formation was observed at the venous access site. The venous access was removed and sent to bacterial culture. Antimicrobial therapy was adjusted to clindamycin (11 mg/kg, TID, IV) and enrofloxacin (10 mg/kg, SID, IV) and escalated to include amikacin and ampicillin-sulbactam on the eleventh day. Due to the progressive clinical deterioration, the owner elected to proceed with euthanasia. Informed consent was obtained from the owner for this case report but not for a necropsy.

4.3. Case 3

A three-month-old mixed-breed female dog (BR250) was admitted to the emergency sector of the veterinary hospital with a history of vehicular trauma. The patient presented with open fractures in the hind limbs and underwent bilateral hind limb amputation due to extensive tissue devitalization and signs of contamination near the surgical sites. A Penrose drain was placed, and wound dressings were applied. For the first four days post-surgery, the dog was treated with amoxicillin with clavulanic acid (0.6 mL, BID, IV) and metronidazole 5 mg/mL (8.4 mL, BID, IV). On the fourth day of hospitalization, purulent secretion was observed at the site of the Penrose drain. The antimicrobial therapy was adjusted to ceftriaxone 1 g diluted in 10 mL (1.10 mL, BID, IV) and a swab of the secretion was surgically collected and submitted for bacterial culture. The dog remained hospitalized in the ICU for 18 days, receiving pain management, antimicrobial therapy, and local treatment of the surgical site, being released after a total of 35 days of hospitalization.

4.4. Bacterial Culture, Identification and Antimicrobial Resistance Tests

Samples collected from the three cases (swab of endotracheal tube secretion, swab from the venous access site on the left pelvic limb, and Penrose drain secretion swab from the left pelvic limb) were plated onto Brain Heart Infusion agar (BHI, Oxoid, Hampshire, UK) supplemented with equine blood and MacConkey agar (Kasvi, Pinhais, Brazil). Species identification was performed using MALDI-ToF as previously described [82] and antimicrobial susceptibility testing was performed using the disk diffusion method following the M100-Ed31 guidelines [83], with Escherichia coli ATCC® 25922 used as the control. Isolates resistant to three or more antimicrobial classes were classified as multidrug-resistant [5].
For the isolate in Case 1 (B145), the following antimicrobials were tested: amoxicillin/clavulanic acid (30 μg), ampicillin (10 μg), cefoxitin (30 μg), ceftiofur (30 μg), cefotaxime (30 μg), cephalothin (30 μg), ciprofloxacin (5 μg), doxycycline (10 μg), enrofloxacin (5 μg), neomycin (30 μg), gentamicin (30 μg), nitrofurantoin (300 μg), trimethoprim-sulfamethoxazole (25 μg), ertapenem (10 μg), florfenicol (30 μg), and oxytetracycline (30 μg). Furthermore, an Etest (bioMérieux, Marcy l’Étoile, France) for ertapenem and colistin was performed in accordance with the manufacturer’s instructions. The MIC was determined as the lowest concentration showing complete inhibition of bacterial growth, as described by the Clinical and Laboratory Standards Institute (CLSI) [83].
For Cases 2 and 3 (B146 and BR250, respectively), seven antimicrobials were tested, each representing seven distinct classes: ciprofloxacin (5 μg), tetracycline (30 μg), gentamicin (10 μg), trimethoprim-sulfamethoxazole (25 μg), imipenem (10 μg), piperacillin-tazobactam (100/10 μg), and ceftazidime (30 μg). Similar to Case 1, an Etest (bioMérieux, Marcy l’Étoile, France) for meropenem and colistin was performed and interpreted according to the CLSI.

4.5. Whole Genome Sequencing and Comparative Genomics

The strains were incubated on Mueller–Hinton agar (Kasvi, Pinhais, Brazil) at 37 °C for 24 h. Genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega, EUA, Madison, WI, USA). Genome sequencing was performed using the Illumina MiSeq platform (mid-out 2 × 150 bp cycles). The raw data were analyzed using FastQC (Babraham Bioinformatics, Cambridge, UK), retaining only paired reads with a phred quality of 30 or higher.
The assembly was performed using SPAdes 3.5.0 in the careful mode [84,85]. GAP filling and polishing were performed using Pilon 1.24 [86]. The genomes have been deposited in the National Center for Biotechnology Information (NCBI) under BioProject accession number PRJNA1255613.
ResFinder 4.6 [87,88] was used to identify acquired antimicrobial resistance determinants and MobileElementFinder v1.0.3 [89] was used to identify mobile genetic elements. Kaptive 2.0 was used to type the capsule (K) and outer lipopolysaccharide (O) loci of K. pneumoniae [90]. Multilocus sequence typing (MLST) was performed using the Pasteur scheme, with sequence type (ST) determined through the PubMLST database [91].
The Singles nucleotide polymorphism (SNP) analysis was performed in CSIPhylogeny [92,93] with a minimal Z-score of 1.96 and a minimal depth at a SNP position of 10x. A. baumannii from ST15 (BioSample accession number SAMN14420901) and K. pneumoniae from ST340 (BioSample accession number SAMN05193406) were used as references [21,94]. Brazilian A. baumannii strains from human clinical isolates, including major carbapenemase-producing clones prevalent in Brazil (ST15 and ST79) as well as globally disseminated clones circulating in the country (ST1 and ST2), were obtained from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC, available at https://www.bv-brc.org/) database [63,95] and used for comparative analysis with the isolates described in this study. Additionally, Brazilian human K. pneumoniae strains of ST340 (CC258) were obtained from the same database and included in the comparison with our K. pneumoniae isolate (Supplementary File S1). The phylogenetic tree was generated using iTOL v.6 online, applying midpoint rooting [28].

5. Conclusions

In this study, we report the occurrence of carbapenemase-producing K. pneumoniae and A. baumannii in three dogs hospitalized at a veterinary facility. This is the first description of K. pneumoniae ST340 and A. baumannii ST15 in animals. The detection of the major carbapenemase genes blaKPC-2 and blaOXA-23 highlights the potential role of companion animals in the dissemination of critical antimicrobial resistance determinants. Moreover, the close phylogenetic relationship between our isolates and clinical human strains underscores the need for One Health-focused studies to further investigate the epidemiology of globally relevant pathogens.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/antibiotics14060584/s1, Supplementary File S1; Supplementary File S2; Supplementary File S3.

Author Contributions

Conceptualization, V.A. and R.O.S.S.; methodology, I.P.Z., F.F.A., B.B., V.A. and R.O.S.S.; formal analysis, I.P.Z., J.V.F.C., Y.G.d.C. and I.M.S.d.M.; investigation, I.P.Z., J.V.F.C., Y.G.d.C. and I.M.S.d.M.; writing—original draft preparation, I.P.Z. and R.O.S.S.; writing—review and editing, I.P.Z., B.B. and R.O.S.S.; project administration, F.F.A.; funding acquisition, F.F.A., B.B., V.A. and R.O.S.S. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), by Fundação de Amparo à Pesquisa de Minas Gerais (FAPEMIG, RED-00132-16 and RED 00131-23), and by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).

Institutional Review Board Statement

This study was approved by the Ethics Committee on Animal Use (CEUA) of the Federal University of Minas Gerais under protocols 277/2020 and 184/2022.

Informed Consent Statement

Not applicable.

Data Availability Statement

Part of the data presented in this study are openly available in GenBank under BioProject accession number PRJNA1255613. The remaining data are provided in the three supplementary files accompanying this article.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Jiang, Y.; Ding, Y.; Wei, Y.; Jian, C.; Liu, J.; Zeng, Z. Carbapenem-Resistant Acinetobacter baumannii: A Challenge in the Intensive Care Unit. Front. Microbiol. 2022, 13, 1045206. [Google Scholar] [CrossRef] [PubMed]
  2. Čiginskienė, A.; Dambrauskienė, A.; Rello, J.; Adukauskienė, D. Ventilator-Associated Pneumonia Due to Drug-Resistant Acinetobacter baumannii: Risk Factors and Mortality Relation with Resistance Profiles, and Independent Predictors of In-Hospital Mortality. Medicina 2019, 55, 49. [Google Scholar] [CrossRef] [PubMed]
  3. Martin, R.M.; Cao, J.; Brisse, S.; Passet, V.; Wu, W.; Zhao, L.; Malani, P.N.; Rao, K.; Bachman, M.A. Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae. mSphere 2016, 1, e00261-16. [Google Scholar] [CrossRef] [PubMed]
  4. Pachanon, R.; Khine, N.O.; Phumthanakorn, N.; Wongsurawat, T.; Niyomtham, W.; Chatsuwan, T.; Hampson, D.J.; Prapasarakul, N. Genomic Characterization of Carbapenem and Colistin-Resistant Klebsiella pneumoniae Isolates from Humans and Dogs. Front. Vet. Sci. 2024, 11, 1386496. [Google Scholar] [CrossRef]
  5. Magiorakos, A.-P.; Srinivasan, A.; Carey, R.B.; Carmeli, Y.; Falagas, M.E.; Giske, C.G.; Harbarth, S.; Hindler, J.F.; Kahlmeter, G.; Olsson-Liljequist, B.; et al. Multidrug-Resistant, Extensively Drug-Resistant and Pandrug-Resistant Bacteria: An International Expert Proposal for Interim Standard Definitions for Acquired Resistance. Clin. Microbiol. Infect. 2012, 18, 268–281. [Google Scholar] [CrossRef]
  6. Doi, Y.; Paterson, D. Carbapenemase-Producing Enterobacteriaceae. Semin. Respir. Crit. Care Med. 2015, 36, 074–084. [Google Scholar] [CrossRef]
  7. Bouza, E. The Role of New Carbapenem Combinations in the Treatment of Multidrug-Resistant Gram-Negative Infections. J. Antimicrob. Chemother. 2021, 76, iv38–iv45. [Google Scholar] [CrossRef]
  8. Paul, M.; Carrara, E.; Retamar, P.; Tängdén, T.; Bitterman, R.; Bonomo, R.A.; De Waele, J.; Daikos, G.L.; Akova, M.; Harbarth, S.; et al. European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Guidelines for the Treatment of Infections Caused by Multidrug-Resistant Gram-Negative Bacilli (Endorsed by European Society of Intensive Care Medicine). Clin. Microbiol. Infect. 2022, 28, 521–547. [Google Scholar] [CrossRef]
  9. WOAH. WOAH List of Antimicrobial Agents of Veterinary Importance 2025; WOAH: Paris, France, 2025. [Google Scholar]
  10. Gentilini, F.; Turba, M.E.; Pasquali, F.; Mion, D.; Romagnoli, N.; Zambon, E.; Terni, D.; Peirano, G.; Pitout, J.D.D.; Parisi, A.; et al. Hospitalized Pets as a Source of Carbapenem-Resistance. Front. Microbiol. 2018, 9, 2872. [Google Scholar] [CrossRef]
  11. Lupo, A.; Châtre, P.; Ponsin, C.; Saras, E.; Boulouis, H.-J.; Keck, N.; Haenni, M.; Madec, J.-Y. Clonal Spread of Acinetobacter baumannii Sequence Type 25 Carrying BlaOXA-23 in Companion Animals in France. Antimicrob. Agents Chemother. 2017, 61, e01881-16. [Google Scholar] [CrossRef]
  12. Ewers, C.; Klotz, P.; Leidner, U.; Stamm, I.; Prenger-Berninghoff, E.; Göttig, S.; Semmler, T.; Scheufen, S. OXA-23 and ISAba1-OXA-66 Class D β-Lactamases in Acinetobacter baumannii Isolates from Companion Animals. Int. J. Antimicrob. Agents 2017, 49, 37–44. [Google Scholar] [CrossRef] [PubMed]
  13. Jacobmeyer, L.; Semmler, T.; Stamm, I.; Ewers, C. Genomic Analysis of Acinetobacter baumannii Isolates Carrying OXA-23 and OXA-58 Genes from Animals Reveals ST1 and ST25 as Major Clonal Lineages. Antibiotics 2022, 11, 1045. [Google Scholar] [CrossRef]
  14. Dietrich, J.; LeCuyer, T.E.; Hendrix, G.K.; Burbick, C.R.; Jacob, M.E.; Byrne, B.A.; Olsen, K.; Mitchell, M.; Ceric, O.; Lin, R.; et al. Prevalence and Molecular Epidemiology of Carbapenemase-producing Enterobacterales Isolated from Dog and Cat Faeces Submitted to Veterinary Laboratories in the USA. Zoonoses Public Health 2024, 71, 538–548. [Google Scholar] [CrossRef] [PubMed]
  15. Moreira Da Silva, J.; Menezes, J.; Fernandes, L.; Marques, C.; Costa, S.S.; Timofte, D.; Amaral, A.; Pomba, C. Dynamics of blaOXA-23 Gene Transmission in Acinetobacter Spp. from Contaminated Veterinary Environmental Surfaces: An Emerging One Health Threat? J. Hosp. Infect. 2024, 146, 116–124. [Google Scholar] [CrossRef]
  16. Tartor, Y.H.; Ammar, A.M.; Abdelkhalek, A.; Hassan, K.A.; Shaker, A.; Elnahriry, S.S.; Nekouei, O.; Elsohaby, I. Emergence of Pandrug-Resistant Carbapenemase-Producing Enterobacterales in Dogs and Cats: A Cross-Sectional Study in Egypt. Front. Cell. Infect. Microbiol. 2024, 14, 1318585. [Google Scholar] [CrossRef]
  17. Moreira Da Silva, J.; Menezes, J.; Mendes, G.; Santos Costa, S.; Caneiras, C.; Poirel, L.; Amaral, A.J.; Pomba, C. KPC-3-Producing Klebsiella pneumoniae Sequence Type 392 from a Dog’s Clinical Isolate in Portugal. Microbiol. Spectr. 2022, 10, e00893-22. [Google Scholar] [CrossRef] [PubMed]
  18. Sellera, F.P.; Fuga, B.; Fontana, H.; Esposito, F.; Cardoso, B.; Konno, S.; Berl, C.; Cappellanes, M.H.; Cortez, M.; Ikeda, M.; et al. Detection of IncN-pST15 One-health Plasmid Harbouring BlaKPC-2 in a Hypermucoviscous Klebsiella pneumoniae CG258 Isolated from an Infected Dog, Brazil. Transbound. Emerg. Dis. 2021, 68, 3083–3088. [Google Scholar] [CrossRef]
  19. Ortiz-Díez, G.; Mengíbar, R.L.; Turrientes, M.-C.; Artigao, M.-R.B.; Gallifa, R.L.; Tello, A.M.; Pérez, C.F.; Santiago, T.A. Prevalence, Incidence and Risk Factors for Acquisition and Colonization of Extended-Spectrum Beta-Lactamase- and Carbapenemase-Producing Enterobacteriaceae from Dogs Attended at a Veterinary Hospital in Spain. Comp. Immunol. Microbiol. Infect. Dis. 2023, 92, 101922. [Google Scholar] [CrossRef]
  20. Köck, R.; Daniels-Haardt, I.; Becker, K.; Mellmann, A.; Friedrich, A.W.; Mevius, D.; Schwarz, S.; Jurke, A. Carbapenem-Resistant Enterobacteriaceae in Wildlife, Food-Producing, and Companion Animals: A Systematic Review. Clin. Microbiol. Infect. 2018, 24, 1241–1250. [Google Scholar] [CrossRef]
  21. Bueno, M.S.; Freire, M.P.; Cunha, M.P.V.; De Barcellos, T.A.F.; Bertani, A.M.D.J.; Dos Santos, C.A.; Chimara, E.; Nagamori, F.O.; Takagi, E.H.; Costa, S.F.; et al. Detection of Pandrug-Resistant ST15 Acinetobacter baumannii Causing Bloodstream Infection in an HSCT Patient in Brazil. J. Antimicrob. Chemother. 2020, 75, 2691–2693. [Google Scholar] [CrossRef]
  22. Chagas, T.P.G.; Carvalho, K.R.; De Oliveira Santos, I.C.; Carvalho-Assef, A.P.D.; Asensi, M.D. Characterization of Carbapenem-Resistant Acinetobacter baumannii in Brazil (2008–2011): Countrywide Spread of OXA-23–Producing Clones (CC15 and CC79). Diagn. Microbiol. Infect. Dis. 2014, 79, 468–472. [Google Scholar] [CrossRef] [PubMed]
  23. Tolentino, F.M.; Bueno, M.F.C.; Franscisco, G.R.; Barcelos, D.D.D.P.; Lobo, S.M.; Tomaz, F.M.M.B.; Da Silva, N.S.; De Andrade, L.N.; Casella, T.; Darini, A.L.D.C.; et al. Endemicity of the High-Risk Clone Klebsiella pneumoniae ST340 Coproducing QnrB, CTX-M-15, and KPC-2 in a Brazilian Hospital. Microb. Drug Resist. 2019, 25, 528–537. [Google Scholar] [CrossRef] [PubMed]
  24. Camargo, C.H.; Yamada, A.Y.; Souza, A.R.D.; Reis, A.D.; Santos, M.B.N.; Assis, D.B.D.; Carvalho, E.D.; Takagi, E.H.; Cunha, M.P.V.; Tiba-Casas, M.R. Genomic Diversity of NDM-Producing Klebsiella Species from Brazil, 2013–2022. Antibiotics 2022, 11, 1395. [Google Scholar] [CrossRef] [PubMed]
  25. Tsang, K.K.; Lam, M.M.C.; Wick, R.R.; Wyres, K.L.; Bachman, M.; Baker, S.; Barry, K.; Brisse, S.; Campino, S.; Chiaverini, A.; et al. Diversity, Functional Classification and Genotyping of SHV β-Lactamases in Klebsiella pneumoniae. Microb. Genom. 2024, 10, 001294. [Google Scholar] [CrossRef]
  26. Bush, K.; Jacoby, G.A. Updated Functional Classification of β-Lactamases. Antimicrob. Agents Chemother. 2010, 54, 969–976. [Google Scholar] [CrossRef]
  27. Robicsek, A.; Strahilevitz, J.; Jacoby, G.A.; Macielag, M.; Abbanat, D.; Hye Park, C.; Bush, K.; Hooper, D.C. Fluoroquinolone-Modifying Enzyme: A New Adaptation of a Common Aminoglycoside Acetyltransferase. Nat. Med. 2006, 12, 83–88. [Google Scholar] [CrossRef]
  28. Letunic, I.; Bork, P. Interactive Tree Of Life (iTOL) v4: Recent Updates and New Developments. Nucleic Acids Res. 2019, 47, W256–W259. [Google Scholar] [CrossRef]
  29. Palacios-Baena, Z.R.; Giannella, M.; Manissero, D.; Rodríguez-Baño, J.; Viale, P.; Lopes, S.; Wilson, K.; McCool, R.; Longshaw, C. Risk Factors for Carbapenem-Resistant Gram-Negative Bacterial Infections: A Systematic Review. Clin. Microbiol. Infect. 2021, 27, 228–235. [Google Scholar] [CrossRef]
  30. Jesudason, T. WHO Publishes Updated List of Bacterial Priority Pathogens. Lancet Microbe 2024, 5, 100940. [Google Scholar] [CrossRef]
  31. De Oliveira, D.M.P.; Forde, B.M.; Kidd, T.J.; Harris, P.N.A.; Schembri, M.A.; Beatson, S.A.; Paterson, D.L.; Walker, M.J. Antimicrobial Resistance in ESKAPE Pathogens. Clin. Microbiol. Rev. 2020, 33, e00181-19. [Google Scholar] [CrossRef]
  32. Miller, W.R.; Arias, C.A. ESKAPE Pathogens: Antimicrobial Resistance, Epidemiology, Clinical Impact and Therapeutics. Nat. Rev. Microbiol. 2024, 22, 598–616. [Google Scholar] [CrossRef] [PubMed]
  33. Pomba, C.; Endimiani, A.; Rossano, A.; Saial, D.; Couto, N.; Perreten, V. First Report of OXA-23-Mediated Carbapenem Resistance in Sequence Type 2 Multidrug-Resistant Acinetobacter baumannii Associated with Urinary Tract Infection in a Cat. Antimicrob. Agents Chemother. 2014, 58, 1267–1268. [Google Scholar] [CrossRef] [PubMed]
  34. Sebola, D.C.; Oguttu, J.W.; Kock, M.M.; Qekwana, D.N. Antimicrobial Resistance Patterns of Acinetobacter baumannii and Klebsiella pneumoniae Isolated from Dogs Presented at a Veterinary Academic Hospital in South Africa. Vet. World 2023, 16, 1880–1888. [Google Scholar] [CrossRef]
  35. Cifuentes, S.; Moura, Q.; Cardoso, B.; Esposito, F.; Cerdeira, L.; Álvarez, E.; Barrera, E.; Opazo-Capurro, A.; Gonzalez-Rocha, G.; Lincopan, N. Genomic Features of a Carbapenem-Resistant OXA-219-Positive Acinetobacter baumannii of International ST15 (CC15) from a Patient with Community-Onset Urinary Tract Infection in Chilean Patagonia. J. Glob. Antimicrob. Resist. 2020, 22, 756–758. [Google Scholar] [CrossRef] [PubMed]
  36. Bialek-Davenet, S.; Criscuolo, A.; Ailloud, F.; Passet, V.; Jones, L.; Delannoy-Vieillard, A.-S.; Garin, B.; Le Hello, S.; Arlet, G.; Nicolas-Chanoine, M.-H.; et al. Genomic Definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups. Emerg. Infect. Dis. 2014, 20, 1812–1820. [Google Scholar] [CrossRef]
  37. Lee, Y.-L.; Ko, W.-C.; Hsueh, P.-R. Geographic Patterns of Acinetobacter baumannii and Carbapenem Resistance in the Asia-Pacific Region: Results from the Antimicrobial Testing Leadership and Surveillance (ATLAS) Program, 2012–2019. Int. J. Infect. Dis. 2023, 127, 48–55. [Google Scholar] [CrossRef] [PubMed]
  38. Turton, J.F.; Ward, M.E.; Woodford, N.; Kaufmann, M.E.; Pike, R.; Livermore, D.M.; Pitt, T.L. The Role of ISAba1 in Expression of OXA Carbapenemase Genes in Acinetobacter baumannii. FEMS Microbiol. Lett. 2006, 258, 72–77. [Google Scholar] [CrossRef]
  39. Nigro, S.J.; Hall, R.M. Does the Intrinsic oxaAb (blaOXA-51-like) Gene of Acinetobacter baumannii Confer Resistance to Carbapenems When Activated by ISAba1? J. Antimicrob. Chemother. 2018, 73, 3518–3520. [Google Scholar] [CrossRef]
  40. Hobson, C.A.; Pierrat, G.; Tenaillon, O.; Bonacorsi, S.; Bercot, B.; Jaouen, E.; Jacquier, H.; Birgy, A. Klebsiella pneumoniae Carbapenemase Variants Resistant to Ceftazidime-Avibactam: An Evolutionary Overview. Antimicrob. Agents Chemother. 2022, 66, e00447-22. [Google Scholar] [CrossRef]
  41. Hansen, G.T. Continuous Evolution: Perspective on the Epidemiology of Carbapenemase Resistance Among Enterobacterales and Other Gram-Negative Bacteria. Infect. Dis. Ther. 2021, 10, 75–92. [Google Scholar] [CrossRef]
  42. Nordmann, P.; Naas, T.; Poirel, L. Global Spread of Carbapenemase-Producing Enterobacteriaceae. Emerg. Infect. Dis. 2011, 17, 1791–1798. [Google Scholar] [CrossRef] [PubMed]
  43. Budia-Silva, M.; Kostyanev, T.; Ayala-Montaño, S.; Bravo-Ferrer Acosta, J.; Garcia-Castillo, M.; Cantón, R.; Goossens, H.; Rodriguez-Baño, J.; Grundmann, H.; Reuter, S. International and Regional Spread of Carbapenem-Resistant Klebsiella pneumoniae in Europe. Nat. Commun. 2024, 15, 5092. [Google Scholar] [CrossRef] [PubMed]
  44. Carvalho, I.; Chenouf, N.S.; Carvalho, J.A.; Castro, A.P.; Silva, V.; Capita, R.; Alonso-Calleja, C.; Enes Dapkevicius, M.D.L.N.; Igrejas, G.; Torres, C.; et al. Multidrug-Resistant Klebsiella pneumoniae Harboring Extended Spectrum β-Lactamase Encoding Genes Isolated from Human Septicemias. PLoS ONE 2021, 16, e0250525. [Google Scholar] [CrossRef]
  45. Poulou, A.; Voulgari, E.; Vrioni, G.; Xidopoulos, G.; Pliagkos, A.; Chatzipantazi, V.; Markou, F.; Tsakris, A. Imported Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Clones in a Greek Hospital: Impact of Infection Control Measures for Restraining Their Dissemination. J. Clin. Microbiol. 2012, 50, 2618–2623. [Google Scholar] [CrossRef]
  46. Durante-Mangoni, E.; Andini, R.; Zampino, R. Management of Carbapenem-Resistant Enterobacteriaceae Infections. Clin. Microbiol. Infect. 2019, 25, 943–950. [Google Scholar] [CrossRef] [PubMed]
  47. Zhang, X.; Chen, D.; Xu, G.; Huang, W.; Wang, X. Molecular Epidemiology and Drug Resistant Mechanism in Carbapenem-Resistant Klebsiella pneumoniae Isolated from Pediatric Patients in Shanghai, China. PLoS ONE 2018, 13, e0194000. [Google Scholar] [CrossRef]
  48. Castanheira, M.; Costello, A.J.; Deshpande, L.M.; Jones, R.N. Expansion of Clonal Complex 258 KPC-2-Producing Klebsiella pneumoniae in Latin American Hospitals: Report of the SENTRY Antimicrobial Surveillance Program. Antimicrob. Agents Chemother. 2012, 56, 1668–1669. [Google Scholar] [CrossRef]
  49. Wyres, K.L.; Holt, K.E. Klebsiella pneumoniae as a Key Trafficker of Drug Resistance Genes from Environmental to Clinically Important Bacteria. Curr. Opin. Microbiol. 2018, 45, 131–139. [Google Scholar] [CrossRef]
  50. Monteiro, J.; Inoue, F.M.; Lobo, A.P.T.; Ibanes, A.S.; Tufik, S.; Kiffer, C.R.V. A Major Monoclonal Hospital Outbreak of NDM-1–Producing Klebsiella Pneumoniae ST340 and the First Report of ST2570 in Brazil. Infect. Control Hosp. Epidemiol. 2019, 40, 492–494. [Google Scholar] [CrossRef]
  51. Aires, C.A.M.; Pereira, P.S.; De Araujo, C.F.M.; Chagas, T.P.G.; Oliveira, J.C.R.; Buonora, S.N.; Albano, R.M.; Carvalho-Assef, A.P.D.; Asensi, M.D. Multiclonal Expansion of Klebsiella pneumoniae Isolates Producing NDM-1 in Rio de Janeiro, Brazil. Antimicrob. Agents Chemother. 2017, 61, e01048-16. [Google Scholar] [CrossRef]
  52. Haenni, M.; Métayer, V.; Lupo, A.; Drapeau, A.; Madec, J.-Y. Spread of the BlaOXA-48/IncL Plasmid within and between Dogs in City Parks, France. Microbiol. Spectr. 2022, 10, e00403-22. [Google Scholar] [CrossRef] [PubMed]
  53. Haenni, M.; Boulouis, H.J.; Lagrée, A.C.; Drapeau, A.; Va, F.; Billet, M.; Châtre, P.; Madec, J.Y. Enterobacterales High-Risk Clones and Plasmids Spreading Bla ESBL/AmpC and Bla OXA-48 Genes within and between Hospitalized Dogs and Their Environment. J. Antimicrob. Chemother. 2022, 77, 2754–2762. [Google Scholar] [CrossRef] [PubMed]
  54. Brito, B.P.; Koong, J.; Wozniak, A.; Opazo-Capurro, A.; To, J.; Garcia, P.; Hamidian, M. Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Strains Recovered from Chilean Hospitals Reveals Lineages Specific to South America and Multiple Routes for Acquisition of Antibiotic Resistance Genes. Microbiol. Spectr. 2022, 10, e02463-22. [Google Scholar] [CrossRef] [PubMed]
  55. Nodari, C.S.; Cayô, R.; Streling, A.P.; Lei, F.; Wille, J.; Almeida, M.S.; De Paula, A.I.; Pignatari, A.C.C.; Seifert, H.; Higgins, P.G.; et al. Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates Belonging to Major Endemic Clones in South America. Front. Microbiol. 2020, 11, 584603. [Google Scholar] [CrossRef]
  56. Opazo-Capurro, A.; San Martín, I.; Quezada-Aguiluz, M.; Morales-León, F.; Domínguez-Yévenes, M.; Lima, C.A.; Esposito, F.; Cerdeira, L.; Bello-Toledo, H.; Lincopan, N.; et al. Evolutionary Dynamics of Carbapenem-Resistant Acinetobacter baumannii Circulating in Chilean Hospitals. Infect. Genet. Evol. 2019, 73, 93–97. [Google Scholar] [CrossRef]
  57. Camargo, C.H.; Cunha, M.P.V.; De Barcellos, T.A.F.; Bueno, M.S.; Bertani, A.M.D.J.; Dos Santos, C.A.; Nagamori, F.O.; Takagi, E.H.; Chimara, E.; De Carvalho, E.; et al. Genomic and Phenotypic Characterisation of Antimicrobial Resistance in Carbapenem-Resistant Acinetobacter baumannii Hyperendemic Clones CC1, CC15, CC79 and CC25. Int. J. Antimicrob. Agents 2020, 56, 106195. [Google Scholar] [CrossRef]
  58. Cameranesi, M.M.; Paganini, J.; Limansky, A.S.; Moran-Barrio, J.; Salcedo, S.P.; Viale, A.M.; Repizo, G.D. Acquisition of Plasmids Conferring Carbapenem and Aminoglycoside Resistance and Loss of Surface-Exposed Macromolecule Structures as Strategies for the Adaptation of Acinetobacter baumannii CC104O/CC15P Strains to the Clinical Setting. Microb. Genom. 2020, 6, mgen000360. [Google Scholar] [CrossRef]
  59. De Azevedo, F.K.S.F.; Dutra, V.; Nakazato, L.; Mello, C.M.; Pepato, M.A.; De Sousa, A.T.H.I.; Takahara, D.T.; Hahn, R.C.; Souto, F.J.D. Molecular Epidemiology of Multidrug-Resistant Acinetobacter baumannii Infection in Two Hospitals in Central Brazil: The Role of ST730 and ST162 in Clinical Outcomes. J. Med. Microbiol. 2019, 68, 31–40. [Google Scholar] [CrossRef]
  60. Leal, N.C.; Campos, T.L.; Rezende, A.M.; Docena, C.; Mendes-Marques, C.L.; De Sá Cavalcanti, F.L.; Wallau, G.L.; Rocha, I.V.; Cavalcanti, C.L.B.; Veras, D.L.; et al. Comparative Genomics of Acinetobacter baumannii Clinical Strains from Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated with Resistance Genes. Front. Microbiol. 2020, 11, 1176. [Google Scholar] [CrossRef]
  61. Pereira, P.S.; De Araujo, C.F.M.; Seki, L.M.; Zahner, V.; Carvalho-Assef, A.P.D.; Asensi, M.D. Update of the Molecular Epidemiology of KPC-2-Producing Klebsiella pneumoniae in Brazil: Spread of Clonal Complex 11 (ST11, ST437 and ST340). J. Antimicrob. Chemother. 2013, 68, 312–316. [Google Scholar] [CrossRef]
  62. Marques, C.; Belas, A.; Aboim, C.; Cavaco-Silva, P.; Trigueiro, G.; Gama, L.T.; Pomba, C. Evidence of Sharing of Klebsiella pneumoniae Strains between Healthy Companion Animals and Cohabiting Humans. J. Clin. Microbiol. 2019, 57, e01537-18. [Google Scholar] [CrossRef] [PubMed]
  63. Rodríguez, C.H.; Nastro, M.; Famiglietti, A. Carbapenemases in Acinetobacter baumannii. Review of Their Dissemination in Latin America. Rev. Argent. Microbiol. 2018, 50, 327–333. [Google Scholar] [CrossRef] [PubMed]
  64. Pagano, M.; Rocha, L.; Sampaio, J.L.M.; Martins, A.F.; Barth, A.L. Emergence of OXA-72-Producing Acinetobacter Baumannii Belonging to High-Risk Clones (CC15 and CC79) in Different Brazilian States. Infect. Control Hosp. Epidemiol. 2017, 38, 252–254. [Google Scholar] [CrossRef] [PubMed]
  65. Lewnard, J.A.; Charani, E.; Gleason, A.; Hsu, L.Y.; Khan, W.A.; Karkey, A.; Chandler, C.I.R.; Mashe, T.; Khan, E.A.; Bulabula, A.N.H.; et al. Burden of Bacterial Antimicrobial Resistance in Low-Income and Middle-Income Countries Avertible by Existing Interventions: An Evidence Review and Modelling Analysis. Lancet 2024, 403, 2439–2454. [Google Scholar] [CrossRef]
  66. The Lancet. Antimicrobial Resistance: An Agenda for All. Lancet 2024, 403, 2349. [Google Scholar] [CrossRef]
  67. Murray, C.J.L.; Ikuta, K.S.; Sharara, F.; Swetschinski, L.; Robles Aguilar, G.; Gray, A.; Han, C.; Bisignano, C.; Rao, P.; Wool, E.; et al. Global Burden of Bacterial Antimicrobial Resistance in 2019: A Systematic Analysis. Lancet 2022, 399, 629–655. [Google Scholar] [CrossRef]
  68. Naghavi, M.; Vollset, S.E.; Ikuta, K.S.; Swetschinski, L.R.; Gray, A.P.; Wool, E.E.; Robles Aguilar, G.; Mestrovic, T.; Smith, G.; Han, C.; et al. Global Burden of Bacterial Antimicrobial Resistance 1990–2021: A Systematic Analysis with Forecasts to 2050. Lancet 2024, 404, 1199–1226. [Google Scholar] [CrossRef]
  69. Walsh, T.R.; Gales, A.C.; Laxminarayan, R.; Dodd, P.C. Antimicrobial Resistance: Addressing a Global Threat to Humanity. PLoS Med. 2023, 20, e1004264. [Google Scholar] [CrossRef] [PubMed]
  70. Koukoubani, T.; Makris, D.; Daniil, Z.; Paraforou, T.; Tsolaki, V.; Zakynthinos, E.; Papanikolaou, J. The Role of Antimicrobial Resistance on Long-Term Mortality and Quality of Life in Critically Ill Patients: A Prospective Longitudinal 2-Year Study. Health Qual. Life Outcomes 2021, 19, 72. [Google Scholar] [CrossRef]
  71. WHO. WHO Bacterial Priority Pathogens List 2024: Bacterial Pathogens of Public Health Importance, to Guide Research, Development, and Strategies to Prevent and Control Antimicrobial Resistance, 1st ed.; World Health Organization: Geneva, Switzerland, 2024; ISBN 978-92-4-009346-1. [Google Scholar]
  72. Zendri, F.; Isgren, C.M.; Devaney, J.; Schmidt, V.; Rankin, R.; Timofte, D. Resistome-Based Surveillance Identifies ESKAPE Pathogens as the Predominant Gram-Negative Organisms Circulating in Veterinary Hospitals. Front. Microbiol. 2023, 14, 1252216. [Google Scholar] [CrossRef]
  73. Njoga, E.O.; Nwanta, J.A.; Chah, K.F. Detection of Multidrug-Resistant Campylobacter species from Food-Producing Animals and Humans in Nigeria: Public Health Implications and One Health Control Measures. Comp. Immunol. Microbiol. Infect. Dis. 2023, 103, 102083. [Google Scholar] [CrossRef]
  74. Onwumere-Idolor, O.S.; Kperegbeyi, J.I.; Imonikebe, U.G.; Okoli, C.E.; Ajibo, F.E.; Njoga, E.O. Epidemiology of Multidrug-Resistant Zoonotic E. coli from Beef Processing and Retail Points in Delta State, Nigeria: Public Health Implications. Prev. Vet. Med. 2024, 224, 106132. [Google Scholar] [CrossRef]
  75. White, A.; Hughes, J.M. Critical Importance of a One Health Approach to Antimicrobial Resistance. EcoHealth 2019, 16, 404–409. [Google Scholar] [CrossRef] [PubMed]
  76. Djordjevic, S.P.; Jarocki, V.M.; Seemann, T.; Cummins, M.L.; Watt, A.E.; Drigo, B.; Wyrsch, E.R.; Reid, C.J.; Donner, E.; Howden, B.P. Genomic Surveillance for Antimicrobial Resistance—A One Health Perspective. Nat. Rev. Genet. 2024, 25, 142–157. [Google Scholar] [CrossRef] [PubMed]
  77. Jessen, L.R.; Damborg, P.; Spohr, A.; Goericke-Pesch, S.; Langhorn, R.; Houser, G.; Willesen, J.; Schjærff, M.; Eriksen, T.; Møller Sørensen, T.; et al. Antibiotic Use Guidelines for Companion Animal Practice, 2nd ed.; The Danish Veterinary Association: Frederiksberg, Denmark, 2019. [Google Scholar]
  78. Weese, J.S.; Blondeau, J.; Boothe, D.; Guardabassi, L.G.; Gumley, N.; Papich, M.; Jessen, L.R.; Lappin, M.; Rankin, S.; Westropp, J.L.; et al. International Society for Companion Animal Infectious Diseases (ISCAID) Guidelines for the Diagnosis and Management of Bacterial Urinary Tract Infections in Dogs and Cats. Vet. J. 2019, 247, 8–25. [Google Scholar] [CrossRef] [PubMed]
  79. Allerton, F.; Prior, C.; Bagcigil, A.; Broens, E.; Callens, B.; Damborg, P.; Dewulf, J.; Filippitzi, M.-E.; Carmo, L.; Gómez-Raja, J.; et al. Overview and Evaluation of Existing Guidelines for Rational Antimicrobial Use in Small-Animal Veterinary Practice in Europe. Antibiotics 2021, 10, 409. [Google Scholar] [CrossRef]
  80. UMN. Educational Resource Review: Handbook of Antimicrobial Stewardship in Companion Animal Veterinary Settings. JAC Antimicrob. Resist. 2021, 3, dlab132. [Google Scholar] [CrossRef]
  81. Hardefeldt, L.; Browning, G.; Bailey, K. Australian Veterinary Prescribing Guidelines 2017; Asia Pacific Centre for Animal Health and National Centre for Antimicrobial Stewardship: Parkville, VIC, Australia, 2017. [Google Scholar]
  82. Assis, G.B.N.; Pereira, F.L.; Zegarra, A.U.; Tavares, G.C.; Leal, C.A.; Figueiredo, H.C.P. Use of MALDI-TOF Mass Spectrometry for the Fast Identification of Gram-Positive Fish Pathogens. Front. Microbiol. 2017, 8, 1492. [Google Scholar] [CrossRef]
  83. CLSI. Clinical and Laboratory Standards Institute (CLSI). Performance Standards for Antimicrobial Susceptibility Testing, 31st ed.; CLSI Supplement M100; Clinical and Laboratory Standards Institute: Berwyn, PA, USA, 2021; ISBN 978-1-68440-104-8 [Print]/978-1-68440-105-5 [Electronic]. [Google Scholar]
  84. Bankevich, A.; Nurk, S.; Antipov, D.; Gurevich, A.A.; Dvorkin, M.; Kulikov, A.S.; Lesin, V.M.; Nikolenko, S.I.; Pham, S.; Prjibelski, A.D.; et al. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. J. Comput. Biol. 2012, 19, 455–477. [Google Scholar] [CrossRef]
  85. Nurk, S.; Bankevich, A.; Antipov, D.; Gurevich, A.A.; Korobeynikov, A.; Lapidus, A.; Prjibelski, A.D.; Pyshkin, A.; Sirotkin, A.; Sirotkin, Y.; et al. Assembling Single-Cell Genomes and Mini-Metagenomes from Chimeric MDA Products. J. Comput. Biol. 2013, 20, 714–737. [Google Scholar] [CrossRef]
  86. Walker, B.J.; Abeel, T.; Shea, T.; Priest, M.; Abouelliel, A.; Sakthikumar, S.; Cuomo, C.A.; Zeng, Q.; Wortman, J.; Young, S.K.; et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 2014, 9, e112963. [Google Scholar] [CrossRef]
  87. Bortolaia, V.; Kaas, R.S.; Ruppe, E.; Roberts, M.C.; Schwarz, S.; Cattoir, V.; Philippon, A.; Allesoe, R.L.; Rebelo, A.R.; Florensa, A.F.; et al. ResFinder 4.0 for Predictions of Phenotypes from Genotypes. J. Antimicrob. Chemother. 2020, 75, 3491–3500. [Google Scholar] [CrossRef]
  88. Zankari, E.; Allesøe, R.; Joensen, K.G.; Cavaco, L.M.; Lund, O.; Aarestrup, F.M. PointFinder: A Novel Web Tool for WGS-Based Detection of Antimicrobial Resistance Associated with Chromosomal Point Mutations in Bacterial Pathogens. J. Antimicrob. Chemother. 2017, 72, 2764–2768. [Google Scholar] [CrossRef] [PubMed]
  89. Johansson, M.H.K.; Bortolaia, V.; Tansirichaiya, S.; Aarestrup, F.M.; Roberts, A.P.; Petersen, T.N. Detection of Mobile Genetic Elements Associated with Antibiotic Resistance in Salmonella enterica Using a Newly Developed Web Tool: MobileElementFinder. J. Antimicrob. Chemother. 2021, 76, 101–109. [Google Scholar] [CrossRef] [PubMed]
  90. Lam, M.M.C.; Wick, R.R.; Judd, L.M.; Holt, K.E.; Wyres, K.L. Kaptive 2.0: Updated Capsule and Lipopolysaccharide Locus Typing for the Klebsiella pneumoniae Species Complex. Microb. Genom. 2022, 8, 000800. [Google Scholar] [CrossRef]
  91. Jolley, K.A.; Bray, J.E.; Maiden, M.C.J. Open-Access Bacterial Population Genomics: BIGSdb Software, the PubMLST.Org Website and Their Applications. Wellcome Open Res. 2018, 3, 124. [Google Scholar] [CrossRef] [PubMed]
  92. Kaas, R.S.; Leekitcharoenphon, P.; Aarestrup, F.M.; Lund, O. Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms. PLoS ONE 2014, 9, e104984. [Google Scholar] [CrossRef]
  93. Price, M.N.; Dehal, P.S.; Arkin, A.P. FastTree 2—Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE 2010, 5, e9490. [Google Scholar] [CrossRef]
  94. Cerdeira, L.; Fernandes, M.R.; Francisco, G.R.; Bueno, M.F.C.; Ienne, S.; Souza, T.A.; De Oliveira Garcia, D.; Lincopan, N. Draft Genome Sequence of a Hospital-Associated Clone of Klebsiella pneumoniae ST340/CC258 Coproducing RmtG and KPC-2 Isolated from a Pediatric Patient. Genome Announc. 2016, 4, e01130-16. [Google Scholar] [CrossRef]
  95. Olson, R.D.; Assaf, R.; Brettin, T.; Conrad, N.; Cucinell, C.; Davis, J.J.; Dempsey, D.M.; Dickerman, A.; Dietrich, E.M.; Kenyon, R.W.; et al. Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): A Resource Combining PATRIC, IRD and ViPR. Nucleic Acids Res. 2023, 51, D678–D689. [Google Scholar] [CrossRef]
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Figure 1. Multilocus sequence typing (MLST) and antimicrobial resistance determinant genes detected in clinical isolates of K. pneumoniae and A. baumannii.
Figure 1. Multilocus sequence typing (MLST) and antimicrobial resistance determinant genes detected in clinical isolates of K. pneumoniae and A. baumannii.
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Antibiotics 14 00584 g002
Figure 2. Single nucleotide polymorphism (SNP) analysis showing the genetic relationship between the B145 K. pneumoniae isolate and human isolates belonging to ST340 from Brazil. The phylogenetic tree was generated online using iTOL [28] with midpoint rooting.
Figure 2. Single nucleotide polymorphism (SNP) analysis showing the genetic relationship between the B145 K. pneumoniae isolate and human isolates belonging to ST340 from Brazil. The phylogenetic tree was generated online using iTOL [28] with midpoint rooting.
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Antibiotics 14 00584 g003
Figure 3. Single nucleotide polymorphism (SNP) analysis illustrating the genetic relationships between A. baumannii isolates B146 (Case 2) and BR250 (Case 3) and human ST15, ST79, ST1, and ST2 strains from Brazil. The phylogenetic tree was generated online using iTOL [28] with midpoint rooting.
Figure 3. Single nucleotide polymorphism (SNP) analysis illustrating the genetic relationships between A. baumannii isolates B146 (Case 2) and BR250 (Case 3) and human ST15, ST79, ST1, and ST2 strains from Brazil. The phylogenetic tree was generated online using iTOL [28] with midpoint rooting.
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MDPI and ACS Style

Zanon, I.P.; Campos, J.V.F.; Castro, Y.G.d.; Melo, I.M.S.d.; Aburjaile, F.F.; Brenig, B.; Azevedo, V.; Silva, R.O.S. Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (OXA-23) and Klebsiella pneumoniae (KPC-2) Causing Hospital-Acquired Infections in Dogs. Antibiotics 2025, 14, 584. https://doi.org/10.3390/antibiotics14060584

AMA Style

Zanon IP, Campos JVF, Castro YGd, Melo IMSd, Aburjaile FF, Brenig B, Azevedo V, Silva ROS. Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (OXA-23) and Klebsiella pneumoniae (KPC-2) Causing Hospital-Acquired Infections in Dogs. Antibiotics. 2025; 14(6):584. https://doi.org/10.3390/antibiotics14060584

Chicago/Turabian Style

Zanon, Isabela Pádua, João Victor Ferreira Campos, Yasmin Gonçalves de Castro, Isadora Maria Soares de Melo, Flávia Figueira Aburjaile, Bertram Brenig, Vasco Azevedo, and Rodrigo Otávio Silveira Silva. 2025. "Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (OXA-23) and Klebsiella pneumoniae (KPC-2) Causing Hospital-Acquired Infections in Dogs" Antibiotics 14, no. 6: 584. https://doi.org/10.3390/antibiotics14060584

APA Style

Zanon, I. P., Campos, J. V. F., Castro, Y. G. d., Melo, I. M. S. d., Aburjaile, F. F., Brenig, B., Azevedo, V., & Silva, R. O. S. (2025). Genomic Characterization of Carbapenem-Resistant Acinetobacter baumannii (OXA-23) and Klebsiella pneumoniae (KPC-2) Causing Hospital-Acquired Infections in Dogs. Antibiotics, 14(6), 584. https://doi.org/10.3390/antibiotics14060584

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