Antimicrobial resistance in Acinetobacter baumannii: From bench to bedside

Exploring imidazo[4,5-g]quinoline-4,9-dione derivatives as Acinetobacter baumannii efflux pump inhibitor: an in silico approach

Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. World Health Organization (WHO) statistics show that globally 0.7 million people are dying yearly due to the emergence of AMR. By 2050, the expected number of lives lost will be 10 million per year. Acinetobacter baumannii is a dreadful nosocomial pathogen that has developed multidrug resistance (MDR) to several currently prescribed antibiotics worldwide. Overexpression of drug efflux transporters (DETs) is one of the mechanisms of multidrug resistance (MDR) in Acinetobacter baumannii. Therefore, blocking the DET can raise the efficacy of the existing antibiotics by increasing their residence time inside the bacteria. In silico screening of five synthetic compounds against three drug efflux pump from A. baumannii has identified KSA5, a novel imidazo[4,5-g]quinoline-4,9-dione derivative, to block the efflux of antibiotics. Molecular docking and simulation results showed that KSA5 could bind to adeB, adeG, and adeJ by consistently interacting with ligand-binding site residues. KSA5 has a higher binding free energy and a lower HOMO-LUMO energy gap than PAβN, suggesting a better ability to interact and inhibit DETs. Further analysis showed that KSA5 is a drug-like molecule with optimal physicochemical and ADME properties. Hence, KSA5 could be combined with antibiotics to overcome antimicrobial resistance.Communicated by Ramaswamy H. Sarma.

In silico design and assessment of a multi-epitope peptide vaccine against multidrug-resistant Acinetobacter baumannii

Acinetobacter baumannii, an opportunistic and notorious nosocomial pathogen, is responsible for many infections affecting soft tissues, skin, lungs, bloodstream, and urinary tract, accounting for more than 722,000 cases annually. Despite the numerous advancements in therapeutic options, no approved vaccine is currently available for this particular bacterium. Consequently, this study focused on creating a rational vaccine design using bioinformatics tools. Three outer membrane proteins with immunogenic potential and properties of good vaccine candidates were used to select epitopes based on good antigenic properties, non-allergenicity, high binding scores, and a low IC50 value. A multi-epitope peptide (MEP) construct was created by sequentially linking the epitopes using suitable linkers. ClusPro 2.0 and C-ImmSim web servers were used for docking analysis with TLR2/TLR4 and immune response respectively. The Ramachandran plot showed an accurate model of the MEP with 100% residue in the most favored and allowed regions. The construct was highly antigenic, stable, non-allergenic, non-toxic, and soluble, and showed maximum population coverage. Additionally, molecular docking demonstrated strong binding between the designed MEP vaccine and TLR2/TLR4. In silico immunological simulations showed significant increases in T-cell and B-cell populations. Finally, codon optimization and in silico cloning were conducted using the pET-28a (+) plasmid vector to evaluate the efficiency of the expression of vaccine peptide in the host organism (Escherichia coli). This designed MEP vaccine would support and accelerate the laboratory work to develop a potent vaccine targeting MDR Acinetobacter baumannii.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00292-3.

Copper induced augmentation of antibiotic resistance in Acinetobacter baumannii MCC 3114

Increasing antibiotic resistance among the common nosocomial pathogen i.e. Acinetobacter baumannii poses life threat to the health care workers as well as to the society. The dissemination of antibiotic resistance in this pathogen at an alarming rate could be not only due to the overuse of antibiotics but also due to the stress caused by exposure of bacterium to several environmental contaminants in their niches. In the present study, effect of copper stress on augmentation in the antibiotic resistance of A. baumannii MCC 3114 against three clinically used antibiotics was investigated along with the phenotypic and genotypic alterations in the cell. It induced 8, 44 and 22-fold increase in resistance against colistin, ciprofloxacin and levofloxacin, respectively. Moreover, the biofilm formation of adapted culture was significantly enhanced due to a dense EPS around the cell (as revealed by SEM images). The structural changes in EPS were demonstrated by FTIR spectroscopy. The adequate growth of adapted MCC 3114 despite increased level of ROS indicates its persistence in copper and ROS stress. The physiological alterations in cell viz., increased efflux pump activity and decreased membrane permeability was observed. Molecular analysis revealed increased expression of efflux pump related genes, oxidative stress genes, integron and antibiotic resistance genes. In sum, our study revealed that the exposure of the critical pathogen, A. baunmannii to copper in hospital settings and environmental reservoirs can impose adaptive pressure which may lead to genotypic as well phenotypic changes in cell resulting into the augmentation of antibiotic resistance.

Analysis of Acinetobacter P-type type IV secretion system-encoding plasmid diversity uncovers extensive secretion system conservation and diverse antibiotic resistance determinants

Acinetobacter baumannii is globally recognized as a multi-drug-resistant pathogen of critical concern due to its capacity for horizontal gene transfer and resistance to antibiotics. Phylogenetically diverse Acinetobacter species mediate human infection, including many considered as important emerging pathogens. While globally recognized as a pathogen of concern, pathogenesis mechanisms are poorly understood. P-type type IV secretion systems (T4SSs) represent important drivers of pathogen evolution, responsible for horizontal gene transfer and secretion of proteins that mediate host-pathogen interactions, contributing to pathogen survival, antibiotic resistance, virulence, and biofilm formation. Genes encoding a P-type T4SS were previously identified on plasmids harboring the carbapenemase gene blaNDM-1 in several clinically problematic Acinetobacter; however, their prevalence among the genus, geographical distribution, the conservation of T4SS proteins, and full capacity for resistance genes remain unclear. Using systematic analyses, we show that these plasmids belong to a group of 53 P-type T4SS-encoding plasmids in 20 established Acinetobacter species, the majority of clinical relevance, including diverse A. baumannii sequence types and one strain of Providencia rettgeri. The strains were globally distributed in 14 countries spanning five continents, and the conjugative operon's T4SS proteins were highly conserved in most plasmids. A high proportion of plasmids harbored resistance genes, with 17 different genes spanning seven drug classes. Collectively, this demonstrates that P-type T4SS-encoding plasmids are more widespread among the Acinetobacter genus than previously anticipated, including strains of both clinical and environmental importance. This research provides insight into the spread of resistance genes among Acinetobacter and highlights a group of plasmids of importance for future surveillance.

Epidemiological and Clinical Insights into Acinetobacter baumannii: A Six-Year Study on Age, Antibiotics, and Specimens

Background

This six-year retrospective study provides an in-depth analysis of the epidemiological and clinical patterns associated with Acinetobacter baumannii (A. baumannii) infections, focusing on age distribution, antibiotic resistance profiles, and specimen types.

Aim

The research examines the incidence and characteristics of both non-Multi-Drug Resistant (non-MDR) and Multi-Drug Resistant (MDR) A. baumannii strains by reviewing patient records from January 2016 to December 2022.

Methods

Through a statistical analysis, the study highlights the incidence rates across diverse age groups and explores the impact of antibiotic treatment regimens on infection outcomes. Additionally, it identifies the primary clinical specimen types for each strain, noting an association between non-MDR A. baumannii and midstream urine samples, while MDR A. baumannii strains were more frequently found in respiratory, wound, peripheral, and central line swaps/specimens.

Results

The results indicate that in 2016, non-MDR A. baumannii infections were notably more frequent compared to MDR A. baumannii cases. However, a significant shift occurred in 2021 and 2022, with a marked decrease in non-MDR A. baumannii cases and an increase in MDR A. baumannii infections. Antibiotic susceptibility testing revealed that non-MDR strains were commonly tested against cefazolin, ceftazidime, ciprofloxacin, gentamicin, nitrofurantoin, oxacillin, piperacillin/tazobactam, and trimethoprim/sulfamethoxazole. In contrast, MDR strains were frequently tested against amikacin, cefepime, colistin, meropenem, imipenem, and tigecycline.

Conclusion

This study enhances the understanding of A. baumannii clinical behaviour and resistance patterns, offering valuable insights to support future research and inform strategies for infectious disease management and control.

Inside-out, antimicrobial resistance mediated by efflux pumps in clinical strains of Acinetobacter baumannii isolated from burn wound infections

Acinetobacter baumannii belongs to the ESKAPE group. It is classified as a critical priority group by the World Health Organization and a global concern on account of its capacity to acquire and develop resistance mechanisms to multiple antibiotics. Data from the United States indicates 500 deaths annually. Resistance mechanisms of this bacterium include enzymatic pathways such as ß-lactamases, carbapenemases, and aminoglycoside-modifying enzymes, decreased permeability, and overexpression of efflux pumps. A. baumannii has been demonstrated to possess efflux pumps, which are classified as members of the MATE family, RND and MFS superfamilies, and SMR transporters. The aim of our work was to assess the distribution of efflux pumps and their regulatory gene expression in clinical strains of A. baumannii isolated from burned patients. METHODS: From the Clinical Microbiology Laboratory at the Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra collection in Mexico, 199 strains were selected. Antibiotics susceptibilities were performed by broth microdilutions to determine minimal inhibitory concentrations. Phenotypic assays with efflux pump inhibitors were conducted using carbonyl cyanide 3-chlorophenylhydrazone (CCCP) and phenylalanine-arginine ß-naphthylamide (PAßN) in conjunction with amikacin, ceftazidime, imipenem, meropenem and levofloxacin. A search was conducted for structural genes that are linked to efflux pumps, and the relative expression of the adeR, adeS, and adeL genes was analyzed. RESULTS: Among a total of 199 strains, 186 exhibited multidrug resistance (MDR). Fluoroquinolones demonstrated the highest resistance rates, while minocycline and amikacin displayed comparatively reduced resistance rates (1.5 and 28.1, respectively). The efflux activity of fluorquinolones exhibited the highest phenotypic detection (from 85 to 100%), while IMP demonstrated the lowest activity of 27% with PAßN and 43.3% with CCCP. Overexpression was observed in adeS and adeL, with adeR exhibiting overexpression. Concluding that clinical strains of A. baumannii from our institution exhibited efflux pumps as one of the resistance mechanisms.

Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter

The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.

A comprehensive investigation of the anion inhibition profile of a β-carbonic anhydrase from Acinetobacter baumannii for crafting innovative antimicrobial treatments

This study refers to the intricate world of Acinetobacter baumannii, a resilient pathogenic bacterium notorious for its propensity at antibiotic resistance in nosocomial infections. Expanding upon previous findings that emphasised the bifunctional enzyme PaaY, revealing unexpected γ-carbonic anhydrase (CA) activity, our research focuses on a different class of CA identified within the A. baumannii genome, the β-CA, designated as 𝛽-AbauCA (also indicated as CanB), which plays a crucial role in the resistance mechanism mediated by AmpC beta-lactamase. Here, we cloned, expressed, and purified the recombinant 𝛽-AbauCA, unveiling its distinctive kinetic properties and inhibition profile with inorganic anions (classical CA inhibitors). The exploration of 𝛽-AbauCA not only enhances our understanding of the CA repertoire of A. baumannii but also establishes a foundation for targeted therapeutic interventions against this resilient pathogen, promising advancements in combating its adaptability and antibiotic resistance.

Drug resistance of Acinetobacter ssp. in patients with pneumonia in a Brazilian Pre-Amazon region during the pre-pandemic and pandemic periods of COVID-19

Antimicrobial resistance is a global public health threat that has been impacted by the COVID-19 pandemic. The aim of this study was to evaluate the resistance of Acinetobacter spp. isolated from patients with pneumonia in a Brazilian Pre-Amazon region during the pre-pandemic and pandemic periods of COVID-19. Bacterial strains were obtained from tracheal aspiration, sputum and bronchoalveolar lavage for diagnosis and phenotypic characterization. MALD-TOF was used to identify strains. The automated Phoenix and VITEK® 2 Compact system and the disc diffusion method were performed to determine the antimicrobial susceptibility profile. Were analyzed a total of 41,590 samples from patients admitted to hospitals of a Brazilian Pre-Amazon region, from January 2019 to December 2021. Of these, 162 isolates of Acinetobacter spp. were from the pre-pandemic period and 308 from the pandemic COVID-19. A. baumannii was the most prevalent species. Among the samples, 52% were male patients, aged over 60 years, hospitalized in intensive care units. Acinetobacter spp. showed higher rates of resistance to cefepime (79.1%), levofloxacin (77.8%), and ceftazidime (77%) in the pre-pandemic period and during the pandemic to piperacillin (72.4%), imipenem (71.6%) and ciprofloxacin (71.8%). Taken together, the data showed that A. baumannii was the most prevalent species among Acinetobacter spp., being more frequent among elderly patients admitted to the ICU. The strains presented high resistance to most antibiotics tested, mainly carbapenems. In addition, there was an increase in resistance to polymyxin B, which raises an alert since this is a therapeutic choice to treat infections caused by Acinetobacter spp. multidrug resistant.

Sulfonamide-Based Inhibition of the β-Carbonic Anhydrase from A. baumannii, a Multidrug-Resistant Bacterium

Acinetobacter baumannii is a Gram-negative opportunistic pathogen responsible for severe hospital-associated infections. Owing to its ability to develop resistance to a wide range of antibiotics, novel therapeutic strategies are urgently needed. One promising approach is to target bacterial carbonic anhydrases (CAs; EC 4.2.1.1), which are enzymes critical for various metabolic processes. The genome of A. baumannii encodes a β-CA (βAbauCA), which is essential for producing bicarbonate ions required in the early stages of uridine triphosphate (UTP) synthesis, a precursor for the synthesis of peptidoglycans, which are vital components of the bacterial cell wall. This study aimed to inhibit βAbauCA in vitro, with the potential to impair the vitality of the pathogen in vivo. We conducted sequence and structural analyses of βAbauCA to explore its differences from those of human CAs. Additionally, kinetic and inhibition studies were performed to investigate the catalytic efficiency of βAbauCAβ and its interactions with sulfonamides and their bioisosteres, classical CA inhibitors. Our results showed that βAbauCA has a turnover rate higher than that of hCA I but lower than that of hCA II and displays distinct inhibition profiles compared to human α-CAs. Based on the obtained data, there are notable differences between the inhibition profiles of the human isoforms CA I and CA II and bacterial βAbauCA. This could open the door to designing inhibitors that selectively target bacterial β-CAs without affecting human α-CAs, as well as offer a novel strategy to weaken A. baumannii and other multidrug-resistant pathogens.

Novel chiral phthalimides: Antimicrobial evaluation and docking study against Acinetobacter baumannii's OmpA protein

Antibiotics have been a vital component in the fight against microbial diseases for over 75 years, saving countless lives. However, the global rise of multi-drug-resistance (MDR) bacterial infections is pushing us closer to a post-antibiotic era where common infections may once again become lethal. To combat MDR Acinetobacter baumannii, we investigated chiral phthalimides and used molecular docking to identify potential targets. Outer membrane protein A (OmpA) is crucial for A. baumannii resistant to antibiotics, making it a pathogen of great concern due to its high mortality rate and limited treatment options. In this study, we evaluated three distinct compounds against the OmpA protein: FIA (2-(1,3-dioxoindolin-2yl)-3-phenylpropanoic acid), FIC (2-(1,3-dioxoindolin-2yl)-4-(methylthio) butanoic acid), and FII (3-(1,3-dioxoindolin-2yl)-3-phenylpropanoic acid). Molecular docking results showed that these three compounds exhibited strong interactions with the OmpA protein. Molecular dynamics (MD) simulation analysis further confirmed the stability and binding efficacy of these compounds with OmpA. Their antimicrobial activities were assessed using the agar well diffusion method, revealing that FIA had an optimal zone of inhibition of 24 mm. Additionally, the minimum inhibitory concentrations (MIC) of these compounds were determined, demonstrating their bactericidal properties against A. baumannii, with MICs of 11 μg/μL for FIA, 46 μg/μL for FIC, and 375 μg/μL for FII. In vitro cytotoxicity data indicated that none of the three compounds were hemolytic when exposed to human red blood cells. This finding is particularly significant as it highlights the superior efficacy of FIA against A. baumannii compared to the other compounds. With thorough pharmacokinetic validations, these chiral phthalimides are promising alternative therapeutic options for treating infections caused by A. baumannii, offering new hope in the face of rising antibiotic resistance.

Insertion Sequences within Oxacillinases Genes as Molecular Determinants of Acinetobacter baumannii Resistance to Carbapenems-A Pilot Study

Carbapenem-resistant Acinetobacter baumannii is one of the major problems among hospitalized patients. The presence of multiple virulence factors results in bacteria persistence in the hospital environment. It facilitates bacterial transmission between patients, causing various types of infections, mostly ventilator-associated pneumonia and wound and bloodstream infections. A. baumannii has a variable number of resistance mechanisms, but the most commonly produced are carbapenem-hydrolyzing class D β-lactamases (CHDLs). In our study, the presence of blaOXA-23, blaOXA-40 and blaOXA-51 genes was investigated among 88 clinical isolates of A. baumannii, including 53 (60.2%) strains resistant to both carbapenems (meropenem and imipenem) and 35 (39.8%) strains susceptible to at least meropenem. Among these bacteria, all the isolates carried the blaOXA-51 gene. The blaOXA-23 and blaOXA-40 genes were detected in two (5.7%) and three (8.6%) strains, respectively. Among the OXA-23 carbapenemase-producing A. baumannii strains (n = 55), insertion sequences (ISAba1) were detected upstream of the blaOXA-23 gene in fifty-two (94.5%) carbapenem-resistant and two (3.6%) meropenem-susceptible isolates. A. baumannii clinical strains from Poland have a similar antimicrobial resistance profile as those worldwide, with the presence of ISAba1 among blaOXA-23-positive isolates also being quite common. Carbapenem resistance among A. baumannii strains is associated with the presence of CHDLs, especially when insertion sequences are present.

Carbapenem-resistant Klebsiella pneumoniae strains isolated from clinical specimens in Siirt, Türkiye; molecular characterization and antimicrobial resistance genes detection

This study aimed to molecularly identify carbapenem-resistant Klebsiella pneumoniae (CRKP) strains isolated from clinical samples and to determine antibiotic resistance genes. Only carbapenem-resistant strains were included in our study. Of the 35 CRKP strains, 18 (51.4%) were extensive drug, 11 (31.4%) were multi-drug, and 6 (17.1%) were pan-drug resistances. PCR amplification revealed that 25% of the strains carried the OXA-51, 20% the OXA-48, and %5 the OXA23 genes. Multilocus sequence typing (MLST) analysis based on seven house-keeping genes revealed sequence type 39. The capsule and O-antigen types were determined as KL103 and O2a, respectively. WGS analysis revealed the existence of β-lactamase, aminoglycoside, sulfonamide, Phenicol, and Fosfomycin-resistant genes. While the K. pneumoniae OmpK37 gene was detected in all 3 strains, the OmpK36 gene was detected only in the CRSU20 strain. This study is important as it is the first study to perform molecular analysis of CRKP strains from Siirt, Türkiye.

The Combinatory Effects of Essential Oil from Lippia macrophylla on Multidrug Resistant Acinetobacter baumannii Clinical Isolates

To assess the antibacterial effectiveness of Lippia macrophylla essential oil (LMEO) against multidrug-resistant Acinetobacter baumannii isolates, both as a standalone treatment and in combination with conventional antibiotics. LMEO demonstrated a significant inhibitory effect on the growth of A. baumannii, with a minimum inhibitory concentration (MIC) below 500 μg/mL. Notably, LMEO was capable of reversing the antibiotic resistance of clinical isolates or reducing their MIC values when used in combination with antibiotics, showing synergistic (FICI≤0.5) or additive effects. The combination of LMEO and imipenem was particularly effective, displaying synergistic interactions for most isolates. Ultrastructural analyses supported these findings, revealing that the combination of LMEO+ceftazidime compromised the membrane integrity of the Acb35 isolate, leading to cytoplasmic leakage and increased formation of Outer Membrane Vesicles (OMVs). Taken together our results point for the use of LMEO alone or in combination as an antibacterial agent against A. baumannii. These findings offer promising avenues for utilizing LMEO as a novel antibacterial strategy against drug-resistant infections in healthcare settings, underscoring the potential of essential oils in enhancing antibiotic efficacy.

Whole-genome sequencing of two multidrug-resistant acinetobacter baumannii strains isolated from a neonatal intensive care unit in Egypt: a prospective cross-sectional study

BACKGROUND

Acinetobacter baumannii (A. baumannii) is a life-threatening and challenging pathogen. In addition, it accounts for numerous serious infections, particularly among immunocompromised patients. Resistance to nearly all clinically used antibiotics and their ability to spread this resistance is one of the most important concerns related to this bacterium.

OBJECTIVES

This study describes different molecular mechanisms of two multidrug-resistant A. baumannii isolates obtained from endotracheal aspirates collected from the neonatal intensive care unit (NICU), Ain Shams University Hospital, Egypt.

METHODS

Following the identification of two isolates, they were examined for susceptibility to antimicrobial agents. This was followed by multilocus sequence typing as well as whole-genome sequence (WGS). Additionally, a Pathosystems Resources Integration Center (PATRIC) analysis was performed.

RESULTS

Two isolates, Ab119 and Ab123, exhibited resistance to all tested antibiotics except for tigecycline and colistin. The WGS analysis of antimicrobial resistance genes (AMR) indicated that both isolates shared beta-lactam, aminoglycoside, macrolides, and sulfonamide resistance genes. Furthermore, each strain revealed different resistance genes such as blaNDM-1, blaNDM-10, OXA-64, aph (3')-VI, Tet-B in Ab119 strain and blaOXA-68, blaPER-1, blaPER-7, Tet-39 in Ab123 strain. Multiple efflux pump genes were detected. Multilocus sequence typing indicated that both isolates belong to the same sequence type (ST931), which belongs to international clone (IC3). Both isolates exhibited the presence of multiple mobile genetic elements (MGEs), but no plasmid was detected in either of them.

CONCLUSIONS

A low prevalence of the IC3 sequence type was identified among two A. baumannii isolates obtained from the NICU in Egypt, exhibiting a high resistance level. Healthcare workers must have knowledge regarding the prevalence of A. baumannii among different populations in order to administer suitable treatment, improve patient outcomes, and apply effective infection control practices.