Effects of different resistance mechanisms on antimicrobial resistance in Acinetobacter baumannii: a strategic system for screening and activity testing of new antibiotics

Current treatment strategies for targeting virulence factors and biofilm formation in Acinetobacter baumannii

A higher prevalence of Acinetobacter baumannii infections and mortality rate has been reported recently in hospital-acquired infections (HAI). The biofilm-forming capability of A. baumannii makes it an extremely dangerous pathogen, especially in device-associated hospital-acquired infections (DA-HAI), thereby it resists the penetration of antibiotics. Further, the transmission of the SARS-CoV-2 virus was exacerbated in DA-HAI during the epidemic. This review specifically examines the complex interconnections between several components and genes that play a role in the biofilm formation and the development of infections. The current review provides insights into innovative treatments and therapeutic approaches to combat A. baumannii biofilm-related infections, thereby ultimately improving patient outcomes and reducing the burden of HAI.

Epidemiology, resistance genomics and susceptibility of Acinetobacter species: results from the 2020 Spanish nationwide surveillance study

BackgroundAs increasing antibiotic resistance in Acinetobacter baumannii poses a global healthcare challenge, understanding its evolution is crucial for effective control strategies.AimWe aimed to evaluate the epidemiology, antimicrobial susceptibility and main resistance mechanisms of Acinetobacter spp. in Spain in 2020, and to explore temporal trends of A. baumannii.MethodsWe collected 199 single-patient Acinetobacter spp. clinical isolates in 2020 from 18 Spanish tertiary hospitals. Minimum inhibitory concentrations (MICs) for nine antimicrobials were determined. Short-read sequencing was performed for all isolates, and targeted long-read sequencing for A. baumannii. Resistance mechanisms, phylogenetics and clonality were assessed. Findings on resistance rates and infection types were compared with data from 2000 and 2010.ResultsCefiderocol and colistin exhibited the highest activity against A. baumannii, although colistin susceptibility has significantly declined over 2 decades. A. non-baumannii strains were highly susceptible to most tested antibiotics. Of the A. baumannii isolates, 47.5% (56/118) were multidrug-resistant (MDR). Phylogeny and clonal relationship analysis of A. baumannii revealed five prevalent international clones, notably IC2 (ST2, n = 52; ST745, n = 4) and IC1 (ST1, n = 14), and some episodes of clonal dissemination. Genes bla OXA-23, bla OXA-58 and bla OXA-24/40 were identified in 49 (41.5%), eight (6.8%) and one (0.8%) A. baumannii isolates, respectively. ISAba1 was found upstream of the gene (a bla OXA-51-like) in 10 isolates.ConclusionsThe emergence of OXA-23-producing ST1 and ST2, the predominant MDR lineages, shows a pivotal shift in carbapenem-resistant A. baumannii (CRAB) epidemiology in Spain. Coupled with increased colistin resistance, these changes underscore notable alterations in regional antimicrobial resistance dynamics.

First report of coexistence of blaKPC-2 and blaNDM-1 in carbapenem-resistant clinical isolates of Klebsiella aerogenes in Brazil

Klebsiella aerogenes is an important opportunistic pathogen with the potential to develop resistance against last-line antibiotics, such as carbapenems, limiting the treatment options. Here, we investigated the antibiotic resistance profiles of 10 K. aerogenes strains isolated from patient samples in the intensive-care unit of a Brazilian tertiary hospital using conventional PCR and a comprehensive genomic characterization of a specific K. aerogenes strain (CRK317) carrying both the blaKPC-2 and blaNDM-1 genes simultaneously. All isolates were completely resistant to β-lactam antibiotics, including ertapenem, imipenem, and meropenem with differencing levels of resistance to aminoglycosides, quinolones, and tigecycline also observed. Half of the strains studied were classified as multidrug-resistant. The carbapenemase-producing isolates carried many genes of interest including: β-lactams (blaNDM-1, blaKPC-2, blaTEM-1, blaCTX-M-1 group, blaOXA-1 group and blaSHVvariants in 20-80% of the strains), aminoglycoside resistance genes [aac(6')-Ib and aph(3')-VI, 70 and 80%], a fluoroquinolone resistance gene (qnrS, 80%), a sulfonamide resistance gene (sul-2, 80%) and a multidrug efflux system transporter (mdtK, 70%) while all strains carried the efflux pumps Acr (subunit A) and tolC. Moreover, we performed a comprehensive genomic characterization of a specific K. aerogenes strain (CRK317) carrying both the blaKPC-2 and blaNDM-1 genes simultaneously. The draft genome assembly of the CRK317 had a total length of 5,462,831 bp and a GC content of 54.8%. The chromosome was found to contain many essential genes. In silico analysis identified many genes associated with resistance phenotypes, including β-lactamases (blaOXA-9, blaTEM-1, blaNDM-1, blaCTX-M-15, blaAmpC-1, blaAmpC-2), the bleomycin resistance gene (bleMBL), an erythromycin resistance methylase (ermC), aminoglycoside-modifying enzymes [aac(6')-Ib, aadA/ant(3")-Ia, aph(3')-VI], a sulfonamide resistance enzyme (sul-2), a chloramphenicol acetyltransferase (catA-like), a plasmid-mediated quinolone resistance protein (qnrS1), a glutathione transferase (fosA), PEtN transferases (eptA, eptB) and a glycosyltransferase (arnT). We also detected 22 genomic islands, eight families of insertion sequences, two putative integrative and conjugative elements with a type IV secretion system, and eight prophage regions. This suggests the significant involvement of these genetic structures in the dissemination of antibiotic resistance. The results of our study show that the emergence of carbapenemase-producing K. aerogenes, co-harboring blaKPC-2 and blaNDM-1, is a worrying phenomenon which highlights the importance of developing strategies to detect, prevent, and control the spread of these microorganisms.

Molecular drivers of resistance to sulbactam-durlobactam in contemporary clinical isolates of Acinetobacter baumannii

Acinetobacter baumannii-calcoaceticus complex (ABC) causes severe infections that are difficult to treat due to pre-existing antibiotic resistance. Sulbactam-durlobactam (SUL-DUR) is a targeted β-lactam/β-lactamase inhibitor combination antibiotic designed to treat serious infections caused by Acinetobacter, including multidrug- and carbapenem-resistant strains. In a recent global surveillance study of 5,032 ABC clinical isolates collected from 2016 to 2021, less than 2% of ABC isolates had SUL-DUR MIC values >4 µg/mL. Molecular characterization of these isolates confirmed the primary drivers of resistance are metallo-β-lactamases or penicillin-binding protein 3 (PBP3) mutations, as previously described. In addition, this study shows that certain common PBP3 variants, such as A515V, are insufficient to confer sulbactam resistance and that the efflux of durlobactam by AdeIJK is likely to play a role in a subset of strains.

Global genomic epidemiology of chromosomally mediated non-enzymatic carbapenem resistance in Acinetobacter baumannii: on the way to predict and modify resistance

Introduction

Although carbapenemases are frequently reported in resistant A. baumannii clinical isolates, other chromosomally mediated elements of resistance that are considered essential are frequently underestimated. Having a wide substrate range, multidrug efflux pumps frequently underlie antibiotic treatment failure. Recognizing and exploiting variations in multidrug efflux pumps and penicillin-binding proteins (PBPs) is an essential approach in new antibiotic drug discovery and engineering to meet the growing challenge of multidrug-resistant Gram-negative bacteria.

Methods

A total of 980 whole genome sequences of A. baumannii were analyzed. Nucleotide sequences for the genes studied were queried against a custom database of FASTA sequences using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) system. The correlation between different variants and carbapenem Minimum Inhibitory Concentrations (MICs) was studied. PROVEAN and I-Mutant predictor suites were used to predict the effect of the studied amino acid substitutions on protein function and protein stability. Both PsiPred and FUpred were used for domain and secondary structure prediction. Phylogenetic reconstruction was performed using SANS serif and then visualized using iTOL and Phandango.

Results

Exhibiting the highest detection rate, AdeB codes for an important efflux-pump structural protein. T48V, T584I, and P660Q were important variants identified in the AdeB-predicted multidrug efflux transporter pore domains. These can act as probable targets for designing new efflux-pump inhibitors. Each of AdeC Q239L and AdeS D167N can also act as probable targets for restoring carbapenem susceptibility. Membrane proteins appear to have lower predictive potential than efflux pump-related changes. OprB and OprD changes show a greater effect than OmpA, OmpW, Omp33, and CarO changes on carbapenem susceptibility. Functional and statistical evidence make the variants T636A and S382N at PBP1a good markers for imipenem susceptibility and potential important drug targets that can modify imipenem resistance. In addition, PBP3_370, PBP1a_T636A, and PBP1a_S382N may act as potential drug targets that can be exploited to counteract imipenem resistance.

Conclusion

The study presents a comprehensive epidemiologic and statistical analysis of potential membrane proteins and efflux-pump variants related to carbapenem susceptibility in A. baumannii, shedding light on their clinical utility as diagnostic markers and treatment modification targets for more focused studies of candidate elements.

Outer Membrane Porins Contribute to Antimicrobial Resistance in Gram-Negative Bacteria

Gram-negative bacteria depend on their cell membranes for survival and environmental adaptation. They contain two membranes, one of which is the outer membrane (OM), which is home to several different outer membrane proteins (Omps). One class of important Omps is porins, which mediate the inflow of nutrients and several antimicrobial drugs. The microorganism's sensitivity to antibiotics, which are predominantly targeted at internal sites, is greatly influenced by the permeability characteristics of porins. In this review, the properties and interactions of five common porins, OmpA, OmpC, OmpF, OmpW, and OmpX, in connection to porin-mediated permeability are outlined. Meanwhile, this review also highlighted the discovered regulatory characteristics and identified molecular mechanisms in antibiotic penetration through porins. Taken together, uncovering porins' functional properties will pave the way to investigate effective agents or approaches that use porins as targets to get rid of resistant gram-negative bacteria.

Drug‑resistant Acinetobacter baumannii: From molecular mechanisms to potential therapeutics (Review)

Bacterial drug resistance is increasingly becoming an important problem that needs to be solved urgently in modern clinical practices. Infection caused by Acinetobacter baumannii is a serious threat to the life and health of patients. The drug resistance rate of Acinetobacter baumannii strains is increasing, thus research on the drug resistance of Acinetobacter baumannii has also seen an increase. When patients are infected with drug-resistant Acinetobacter baumannii, the availability of suitable antibiotics commonly used in clinical practices is becoming increasingly limited and the prognosis of patients is worsening. Studying the molecular mechanism of the drug resistance of Acinetobacter baumannii is fundamental to solving the problem of drug-resistant Acinetobacter baumannii and potentially other 'super bacteria'. Drug resistance mechanisms primarily include enzymes, membrane proteins, efflux pumps and beneficial mutations. Research on the underlying mechanisms provides a theoretical basis for the use and development of antibiotics and the development of novel treatment methods.

Loss of outer membrane protein A (OmpA) impairs the survival of Salmonella Typhimurium by inducing membrane damage in the presence of ceftazidime and meropenem

OBJECTIVES

Salmonella enterica serovar Typhimurium is one of the significant non-typhoidal Salmonella serovars that causes gastroenteritis. The rapid development of antimicrobial resistance necessitates studying new antimicrobials and their therapeutic targets in this pathogen. Our study aimed to investigate the role of four prominent outer membrane porins of S. Typhimurium, namely OmpA, OmpC, OmpD and OmpF, in developing resistance against ceftazidime and meropenem.

METHODS

The antibiotic-mediated inhibition of bacterial growth was determined by measuring the absorbance and the resazurin assay. DiBAC4 (Bis-(1,3-Dibutylbarbituric Acid)Trimethine Oxonol), 2,7-dichlorodihydrofluoroscein diacetate (DCFDA) and propidium iodide were used to determine the outer membrane depolarization, reactive oxygen species (ROS) generation and subsequent killing of Salmonella. The expression of oxidative stress-response and efflux pump genes was quantified by quantitative RT-qPCR. HPLC was done to determine the amount of antibiotics that entered the bacteria. The damage to the bacterial outer membrane was studied by confocal and atomic force microscopy. The in vivo efficacy of ceftazidime and meropenem were tested in the C57BL/6 mouse model.

RESULTS

Deleting ompA reduced the survival of Salmonella in the presence of ceftazidime and meropenem. Massive outer membrane depolarization and reduced expression of oxidative stress-response genes in S. Typhimurium ΔompA hampered its growth in the presence of antibiotics. The enhanced uptake of antibiotics and decreased expression of efflux pump genes in S. Typhimurium ΔompA resulted in damage to the bacterial outer membrane. The clearance of the S. Typhimurium ΔompA from C57BL/6 mice with ceftazidime treatment proved the role of OmpA in rendering protection against β-lactam antibiotics.

CONCLUSIONS

OmpA protects S. Typhimurium from two broad-spectrum β-lactam antibiotics, ceftazidime and meropenem, by maintaining the stability of the outer membrane.

Prevalence, genetic diversity, antibiotic resistance and biofilm formation of Acinetobacter baumannii isolated from urban environments

AIM

Acinetobacter baumannii is a well-known nosocomial pathogen that has been isolated from different clinical sources. This pathogen also causes community-acquired infections, with mortality rates as high as 64%. The exact natural habitat of this bacterium is still unknown. In this study, we investigated the prevalence of A. baumannii in diverse soil and high-touch surface samples collected from a university campus, malls, parks, hypermarkets and produce markets, roundabout playground slides, and bank ATMs.

METHODS AND RESULTS

All obtained isolates were characterized for their antibiotic susceptibility, biofilm formation capacities, and were typed by multi-locus sequence analysis. A total of 63 A. baumannii isolates were recovered, along with 46 A. pittii and 8 A. nosocomialis isolates. Sequence typing revealed that 25 A. baumannii isolates are novel strains. Toilets and sink washing basins were the most contaminated surfaces, accounting for almost 50% of the recovered isolates. A number of A. baumannii (n=10), A. pittii (n=19) and A. nosocomialis (n=5) isolates were recovered from handles of shopping carts and baskets. The majority of isolates were strong biofilm formers and 4 exhibited a multi-drug resistant (MDR) phenotype.

CONCLUSIONS

Our study is the first to highlight community restrooms and shopping carts as potential reservoirs for pathogenic Acinetobacter species. Further studies are required to identify the reasons associated with the occurrence of A. baumannii inside restrooms. Proper disinfection of community environmental surfaces and spreading awareness about the importance of hand hygiene may prevent the dissemination of pathogenic bacteria within the community.

SIGNIFICANCE AND IMPACT OF STUDY

Serious gaps remain in our knowledge of how A. baumannii spreads to cause disease. This study will advance our understanding of how this pathogen spreads between healthcare and community environments. In addition, our findings will help healthcare decision makers implement better measures to control and limit further transmission of A. baumannii.

Peptidoglycan Recycling Promotes Outer Membrane Integrity and Carbapenem Tolerance in Acinetobacter baumannii

β-Lactam antibiotics exploit the essentiality of the bacterial cell envelope by perturbing the peptidoglycan layer, typically resulting in rapid lysis and death. Many Gram-negative bacteria do not lyse but instead exhibit "tolerance," the ability to sustain viability in the presence of bactericidal antibiotics for extended periods. Antibiotic tolerance has been implicated in treatment failure and is a stepping-stone in the acquisition of true resistance, and the molecular factors that promote intrinsic tolerance are not well understood. Acinetobacter baumannii is a critical-threat nosocomial pathogen notorious for its ability to rapidly develop multidrug resistance. Carbapenem β-lactam antibiotics (i.e., meropenem) are first-line prescriptions to treat A. baumannii infections, but treatment failure is increasingly prevalent. Meropenem tolerance in Gram-negative pathogens is characterized by morphologically distinct populations of spheroplasts, but the impact of spheroplast formation is not fully understood. Here, we show that susceptible A. baumannii clinical isolates demonstrate tolerance to high-level meropenem treatment, form spheroplasts upon exposure to the antibiotic, and revert to normal growth after antibiotic removal. Using transcriptomics and genetic screens, we show that several genes associated with outer membrane integrity maintenance and efflux promote tolerance, likely by limiting entry into the periplasm. Genes associated with peptidoglycan homeostasis in the periplasm and cytoplasm also answered our screen, and their disruption compromised cell envelope barrier function. Finally, we defined the enzymatic activity of the tolerance determinants penicillin-binding protein 7 (PBP7) and ElsL (a cytoplasmic ld-carboxypeptidase). These data show that outer membrane integrity and peptidoglycan recycling are tightly linked in their contribution to A. baumannii meropenem tolerance. IMPORTANCE Carbapenem treatment failure associated with "superbug" infections has rapidly increased in prevalence, highlighting the urgent need to develop new therapeutic strategies. Antibiotic tolerance can directly lead to treatment failure but has also been shown to promote the acquisition of true resistance within a population. While some studies have addressed mechanisms that promote tolerance, factors that underlie Gram-negative bacterial survival during carbapenem treatment are not well understood. Here, we characterized the role of peptidoglycan recycling in outer membrane integrity maintenance and meropenem tolerance in A. baumannii. These studies suggest that the pathogen limits antibiotic concentrations in the periplasm and highlight physiological processes that could be targeted to improve antimicrobial treatment.

Auranofin promotes antibacterial effect of doripenem against carbapenem-resistant Acinetobacter baumannii

AIMS

This study was performed to identify the potential for repurposing auranofin as an antibiotic adjuvant against carbapenemase-producing A. baumannii.

METHODS AND RESULTS

The clinically isolated A. baumannii strains used in this study were all resistant to carbapenems and harbored the bla_OXA-23 gene. The synergistic effect of auranofin and doripenem against carbapenemase-producing A. baumannii was confirmed through checkerboard and growth kinetic analyses. This study also demonstrated the inhibitory effects of auranofin against A. baumannii biofilms. The anti-biofilm effects of auranofin were visualized by confocal laser scanning microscopy (CLSM). Furthermore, auranofin inhibited motility, one of the virulence factors. Additionally, the changes in the expression of carbapenemase-, biofilm- and efflux pump-related genes induced by auranofin were confirmed via quantitative polymerase chain reaction (qPCR).

CONCLUSIONS

Our results demonstrated that auranofin has an antibacterial effect with doripenem and an inhibitory effect on several factors related to carbapenem resistance.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study suggests that auranofin is a promising antibiotic adjuvant that can be used to prevent antibiotic resistance in carbapenem-resistant A. baumannii.

The distribution of mutations and hotspots in transcription regulators of resistance-nodulation-cell division efflux pumps in tigecycline non-susceptible Acinetobacter baumannii in China

OBJECTIVE

Acinetobacter baumannii has emerged as a problematic hospital pathogen and tigecycline is among the few remaining antibiotics retaining activity against multidrug-resistant A. baumannii. This study was aimed to elucidate the tigecycline resistance mechanisms in 28 unique clinical A. baumannii strains from nine provinces in China.

METHODS

Whole genome sequences were obtained via Illumina HiSeq sequencing and regulatory genes of efflux pumps were analyzed. Minimal inhibitory concentrations (MICs) were determined by agar/microbroth dilution according to the guidelines recommended by Clinical and Laboratory Standards Institute (CLSI). Tigecycline susceptibility data was interpreted using breakpoints for Enterobacterales recommended by EUCAST v8.1.

RESULTS

The majority of isolates belonged to the international clonal lineage IC2 (n = 27, 96.4%). Four isolates were considered tigecycline-intermediate (MIC = 2 mg/L), twenty-four isolates were tigecycline-resistant. The insertion of ISAba1 in adeS was found in six isolates and was the most prevalent insertion element (IS). In four isolates we observed an insertion of ISAba1 in adeN, and two of them had IS26 insertions. Two mutations in adeN (deletion and premature stop codon) were observed only in the MIC = 4 mg/L isolates. Other mutations in adeRS (amino acid insertion/substitutions and premature stop codons) were only detected in the MIC ≥ 8 group. The novel substitutions E219 K in adeR and A130 T in adeS were observed in five and four isolates respectively, suggesting a mutational hotspot.

CONCLUSIONS

This study demonstrates that changes in transcription regulators were important mechanisms in tigecycline resistance in A. baumannii. Also, we identified several chromosomal hotspots that can be used for prediction of tigecycline resistance.

The Outer Membrane Proteins OmpA, CarO, and OprD of Acinetobacter baumannii Confer a Two-Pronged Defense in Facilitating Its Success as a Potent Human Pathogen

Of all the ESKAPE pathogens, carbapenem-resistant and multidrug-resistant Acinetobacter baumannii is the leading cause of hospital-acquired and ventilator-associated pneumonia. A. baumannii infections are notoriously hard to eradicate due to its propensity to rapidly acquire multitude of resistance determinants and the virulence factor cornucopia elucidated by the bacterium that help it fend off a wide range of adverse conditions imposed upon by host and environment. One such weapon in the arsenal of A. baumannii is the outer membrane protein (OMP) compendium. OMPs in A. baumannii play distinctive roles in facilitating the bacterial acclimatization to antibiotic- and host-induced stresses, albeit following entirely different mechanisms. OMPs are major immunogenic proteins in bacteria conferring bacteria host-fitness advantages including immune evasion, stress tolerance, and resistance to antibiotics and antibacterials. In this review, we summarize the current knowledge of major A. baumannii OMPs and discuss their versatile role in antibiotic resistance and virulence. Specifically, we explore how OmpA, CarO, and OprD-like porins mediate antibiotic and amino acid shuttle and host virulence.