Acquisition of resistance to carbapenems in multidrug-resistant clinical strains of Acinetobacter baumannii: natural insertional inactivation of a gene encoding a member of a novel family of beta-barrel outer membrane proteins

Molecular sequence typing of carbapenem-resistant Acinetobacter baumannii clinical isolates: A comprehensive global update

The emergence and spread of antimicrobial resistance (AMR) pose significant challenges to public health worldwide. Understanding the dynamics of AMR within bacterial populations is crucial for devising effective strategies to mitigate its impact. Clonal lineages, representing genetically related group of bacteria, play a vital role in shaping the landscape of AMR dissemination. This review endeavors to provide a comprehensive update on the molecular sequence typing of carbapenem-resistant Acinetobacter baumannii (CRAB) clinical isolates across various geographical regions, with particular emphasis on the application of multilocus sequence typing (MLST). CRAB poses a silent threat in healthcare settings, emerging as a public health concern globally corporate with limited treatment options due to the resistance to carbapenems, the last-line antibiotics, leading to increased mortality rates. This review will serve as invaluable resources, offering in-depth analysis and interpretation of epidemiological data related to CRAB. Through meticulous examination of this data, healthcare professionals will be equipped with a nuanced understanding of the spread and prevalence of this pathogen across diverse geographic regions. Additionally, by incorporating evidence-based strategies informed by epidemiological insights, stakeholders can enhance their ability to effectively combat this formidable pathogen, thereby safeguarding public health and promoting optimal patient outcomes.

Antibiotic conjugates: Using molecular Trojan Horses to overcome drug resistance

Antimicrobial resistance (AMR) has become a global health crisis due to the rapid emergence of multi-drug-resistant bacteria. The paucity of novel antibiotics in the clinical pipeline has exacerbated this issue, thereby warranting the development of new antibacterial therapies. The 'Trojan Horse' strategy entails conjugating antibiotics with bioactive components that not only facilitate the entry of antibiotic molecules into bacterial cells by circumventing the membrane barriers, but also augment the effects of conventional antibiotics against recalcitrant pathogens. These Trojan Horse elements can also serve as a promising tool for repurposing drugs with hitherto unexamined antimicrobial activity, or drugs with limited clinical utility due to considerable toxic side effects. In this review, we have discussed the current state of research on antibiotic conjugates with monoclonal antibodies (mAbs), antimicrobial peptides (AMPs) and the iron-chelating siderophores. The rationale and mechanisms of different antibiotic conjugates have been summarized, and the preclinical and clinical evidence pertaining to the activity of these conjugates against drug-resistant pathogens have been reviewed. Furthermore, the challenges associated with the clinical translation of these novel antimicrobials, and the future research directions have also been discussed. While antibiotic conjugates offer an attractive alternative to conventional antimicrobials, there are several obstacles to their clinical translation. A greater understanding of the mechanisms underlying AMR, and continuing advances in genetic engineering, synthetic biology, and bioinformatics will be crucial in designing more selective, potent, and safe antibiotic conjugates for tackling multi-drug resistant (MDR) infections.

Antibiotic resistance genes in Escherichia coli - literature review

Antimicrobial resistance threatens humans and animals worldwide and is recognized as one of the leading global public health issues. Escherichia coli (E. coli) has an unquestionable role in carrying and transmitting antibiotic resistance genes (ARGs), which in many cases are encoded on plasmids or phage, thus creating the potential for horizontal gene transfer. In this literature review, the authors summarize the major antibiotic resistance genes occurring in E. coli bacteria, through the major antibiotic classes. The aim was not only listing the resistance genes against the clinically relevant antibiotics, used in the treatment of E. coli infections, but also to cover the entire resistance gene carriage in E. coli, providing a more complete picture. We started with the long-standing antibiotic groups (beta-lactams, aminoglycosides, tetracyclines, sulfonamides and diaminopyrimidines), then moved toward the newer groups (phenicols, peptides, fluoroquinolones, nitrofurans and nitroimidazoles), and in every group we summarized the resistance genes grouped by the mechanism of their action (enzymatic inactivation, antibiotic efflux, reduced permeability, etc.). We observed that the frequency of antibiotic resistance mechanisms changes in the different groups.

Phenotypic and Molecular Characterization of Pyomelanin-Producing Acinetobacter baumannii ST2Pas;ST1816/ST195Oxf Causing the First European Nosocomial Outbreak

Acinetobacter baumannii is one of the most successful and feared nosocomial pathogens. A. baumannii is considered a global threat in the healthcare setting, mainly owing to its ability to acquire multidrug resistance phenotypes. The A. baumannii pathogenesis is guided by its environmental persistence, as well as the production of numerous virulence factors. In several bacteria, the production of pigments, such as melanin, has indeed been linked with virulence and pathogenicity. Melanin is a brownish pigment, rarely observed in A. baumannii, that potentially reduces the susceptibility of the bacteria to host defense mechanisms and environmental insults. This study reports the first outbreak in Europe by pyomelanin-producing A. baumannii strains, in a tertiary-care university hospital in Pisa, Italy. Phenotypic and molecular analyses were performed.

Increasing Burden of Antibiotic Resistance in India Due to Co-existence of Multiple Classes of Carbapenem and Different Aminoglycoside Resistance Genes in Clinical Isolates of Acinetobacter baumannii

Acinetobacter baumannii is a significant pathogen responsible for resistant recalcitrant infections and outbreaks in hospitals worldwide, which is of much concern. The main goal of the present study is to determine the levels of antibiotic resistance in recent clinical isolates of Acinetobacter baumannii and to investigate the presence of diverse resistance determinants among these isolates and also to correlate these findings. A total of 133 A. baumannii clinical isolates from hospitalized patients were investigated for antibiotic resistance levels by determining their MIC by microbroth dilution method. The presence of β-lactamase-encoding genes (blaPER-1, blaNDM-1, blaIMP-1, blaADC, blaOXA51, blaOXA23, blaOXA58 and blaOXA24), aminoglycoside resistance-related genes (armA, aph3(III), aac3(I), aac6, ant3, and aph3(I) and genes associated with biofilm formation were checked by amplifying them by PCR using gene specific primers. The genotyping of isolates was carried out by REP-PCR. Coexistence of diverse intrinsic and acquired carbapenem-hydrolyzing β-lactamases (CHDLs) genes was observed in the isolates: Ambler class A: blaPER-1 (50.37%), Class B: blaNDM-1 (63.90%), blaIMP-1 (76%), Class C: blaADC (75.93) and class D: blaOXA-23 (91.7%), blaOXA-51 (97.74%). A significant difference (P < 0.05) was observed in the prevalence of blaOXA-23 among the isolates obtained from ICU (n = 52) patients and with that of non-ICU (n = 81) patients. MIC results revealed 105 (79%) isolates were extremely drug-resistant (XDR) while 28 (21%) isolates were multi-drug-resistant. All the isolates were susceptible only to colistin. Rampant emergence of XDR isolates and co-existence of multiple CHDLs and different aminoglycoside-modifying enzymes genes in A. baumannii isolates in this study points out the increasing burden of antibiotic resistance in our region.

Unraveling sulbactam-durlobactam: insights into its role in combating infections caused by Acinetobacter baumannii

INTRODUCTION

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a critical priority pathogen posing a substantial threat to our public health due to its virulence and resistance to broad-spectrum antimicrobials. Sulbactam-durlobactam (Xacduro) is a newly approved β-lactam-β-lactamase inhibitor combination agent with potent in vitro and in vivo activity against CRAB. The phase III randomized trial (ATTACK) demonstrated the safety and efficacy of sulbactam-durlobactam in combination with imipenem-cilastatin as background therapy in treating adult patients with hospital-acquired bacterial pneumonia and ventilator-associated bacterial pneumonia caused by CRAB.

AREAS COVERED

This review will discuss pharmacology, antimicrobial activity, pharmacokinetics/pharmacodynamics, clinical efficacy, safety, and therapeutic role of sulbactam-durlobactam. To gather relevant information, a literature search was performed using PubMed and Google Scholar electronic databases. Search terms used include sulbactam, sulbactam-durlobactam, ETX2514, Acinetobacter baumannii, Acinetobacter baumannii-calcoaceticus complex, CRAB, OXA-24, and OmpA. Additional information was obtained from the sulbactam-durlobactam FDA package insert and infectious diseases conference abstracts.

EXPERT OPINION

Sulbactam-durlobactam is a well-tolerated β-lactam-β-lactamase inhibitor combination agent with efficacy against CRAB. Given the limitations of alternative treatment options, sulbactam-durlobactam may also be considered as a treatment option for non-respiratory infections caused by CRAB, however further clinical studies are warranted.

Green synthesis of silver nanoparticles using Acroptilon repens aqueous extract and their antibacterial efficacy against multidrug-resistant Acinetobacter baumannii

BACKGROUND

Acinetobacter baumannii is a critical pathogen associated with hospital-acquired infections, particularly in burn and intensive care unit (ICU) patients, and is notorious for its high level of antibiotic resistance. This study aims to evaluate the antibacterial potential of silver nanoparticles (AgNPs) synthesized using Acroptilon repens extract as a promising alternative treatment for combating multidrug-resistant A. baumannii.

METHODS AND RESULTS

Twelve clinical isolates of A. baumannii were identified through biochemical testing. Antibiotic susceptibility testing using the Kirby-Bauer disk diffusion method revealed universal resistance to ceftazidime, amikacin, imipenem, gentamicin, ciprofloxacin, and piperacillin-tazobactam, while all isolates remained sensitive to colistin (p ≤ 0.05). AgNPs were synthesized using A. repens extract and characterized through transmission electron microscopy (TEM), scanning electron microscopy (SEM), particle size analysis (PSA), UV-Vis spectroscopy, X-ray diffraction (XRD), and Fourier-transform infrared spectroscopy (FT-IR). TEM analysis showed that the AgNPs had a spherical morphology with an average particle size of approximately 30 nm, while SEM confirmed their spherical shape and size distribution, ranging from 10 to 130 nm, with a mean size of 38.89 nm. UV-Vis spectroscopy confirmed the successful formation of AgNPs, indicated by a distinct broad absorption peak between 400 and 480 nm. XRD analysis validated the crystalline nature of the nanoparticles, with characteristic peaks at 2θ values of 38.21°, 46.28°, 64.57°, and 77.49°, corresponding to the (111), (200), (220), and (311) planes of face-centered cubic (fcc) silver. Antibacterial activity was evaluated by determining the minimum inhibitory concentration (MIC), which ranged from 50 to 400 µg/mL. The highest inhibitory activity was observed at 400 µg/mL. Gene expression analysis using quantitative real-time PCR (qRT-PCR) demonstrated downregulation of the oprD and carO porin genes following AgNP treatment. However, these reductions were not statistically significant (p = 0.302 and p = 0.198, respectively).

CONCLUSIONS

AgNPs synthesized from A. repens demonstrated strong antibacterial activity against multidrug-resistant A. baumannii. While downregulation of porin genes was observed, further investigation is required to elucidate the underlying mechanisms of action and assess their potential clinical applications. These findings support the potential of AgNPs as an alternative therapeutic strategy for addressing A. baumannii infections resistant to conventional antibiotics.

Tissue damage alleviation and mucin inhibition by P5 in a respiratory infection mouse model with multidrug-resistant Acinetobacter baumannii

Although the discovery of antibiotics has made significant positive contributions to public health and medicine, it now poses a serious threat due to the increasing antibiotic resistance in various bacteria. Carbapenem-resistant and multidrug-resistant (MDR) Acinetobacter baumannii is spreading globally, exacerbating respiratory diseases such as chronic obstructive pulmonary disease and cystic fibrosis. Antimicrobial peptides (AMPs), with broad antibacterial activity, have emerged as promising alternatives for treating MDR A. baumannii infections. The AMP P5 exhibits strong antibacterial and anti-biofilm activities against MDR A. baumannii strains isolated from patients. Compared to colistin, a commonly used antibiotic for MDR A. baumannii infections, P5 has a lower potential for inducing drug resistance. Additionally, P5 displays stability in human serum and minimal cytotoxicity in human cell lines. P5 not only suppressed the overexpression of pro-inflammatory cytokines and inflammatory transcription factors in lung epithelial cells (A549) and in a mouse model of respiratory infection but also alleviated lung tissue damage caused by infection. Moreover, P5 effectively alleviated excessive mucin secretion in vitro and in vivo by inhibiting inflammatory transcription factors, epidermal growth factor receptor, and signal transducer and activator of transcription 3-key regulators of mucin expression, a hallmark of inflammatory respiratory diseases. These findings highlight the therapeutic potential of P5 in treating MDR A. baumannii infections and associated inflammatory respiratory conditions.

Comprehensive Approaches to Combatting Acinetobacter baumannii Biofilms: From Biofilm Structure to Phage-Based Therapies

Acinetobacter baumannii-a multidrug-resistant (MDR) pathogen that causes, for example, skin and soft tissue wounds; urinary tract infections; pneumonia; bacteremia; and endocarditis, particularly due to its ability to form robust biofilms-poses a significant challenge in clinical settings. This structure protects the bacteria from immune responses and antibiotic treatments, making infections difficult to eradicate. Given the rise in antibiotic resistance, alternative therapeutic approaches are urgently needed. Bacteriophage-based strategies have emerged as a promising solution for combating A. baumannii biofilms. Phages, which are viruses that specifically infect bacteria, offer a targeted and effective means of disrupting biofilm and lysing bacterial cells. This review explores the current advancements in bacteriophage therapy, focusing on its potential for treating A. baumannii biofilm-related infections. We described the mechanisms by which phages interact with biofilms, the challenges in phage therapy implementation, and the strategies being developed to enhance its efficacy (phage cocktails, engineered phages, combination therapies with antibiotics). Understanding the role of bacteriophages in both biofilm disruption and in inhibition of its forming could pave the way for innovative treatments in combating MDR A. baumannii infections as well as the prevention of their development.

Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO

Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies. Critical to adaptation to changing environments in bacteria are small regulatory RNAs (sRNAs), however, the role that sRNAs play in the biology of A. baumannii is poorly understood. To assess the regulatory function of sRNAs and to uncover their RNA interaction partners, we employed an RNA proximity ligation and sequencing method (Hi-GRIL-seq) in three different environmental conditions. Forty sRNAs were ligated to sRNA-RNA chimeric sequencing reads, suggesting that sRNA-mediated gene regulation is pervasive in A. baumannii. In-depth characterization uncovered the sRNA Aar to be a post-transcriptional regulator of four mRNA targets including the transcript encoding outer membrane protein CarO. Aar initiates base-pairing with these mRNAs using a conserved seed region of nine nucleotides, sequestering the ribosome binding sites and inhibiting translation. Aar is differentially expressed in multiple stress conditions suggesting a role in fine-tuning translation of the Aar-target molecules. Our study provides mechanistic insights into sRNA-mediated gene regulation in A. baumannii and represents a valuable resource for future RNA-centric research endeavours.

Exploring quinoxaline derivatives: An overview of a new approach to combat antimicrobial resistance

Antimicrobial resistance (AMR) has emerged as a long-standing global issue ever since the introduction of penicillin, the first antibiotic. Scientists are constantly working to develop innovative antibiotics that are more effective and superior. Unfortunately, the misuse of antibiotics has resulted in their declining effectiveness over the years. By 2050, it is projected that approximately 10 million lives could be lost annually due to antibiotic resistance. Gaining insight into the mechanisms behind the development and transmission of AMR in well-known bacteria including Escherichia coli, Bacillus pumilus, Enterobacter aerogenes, Salmonella typhimurium, and the gut microbiota is crucial for researchers. Environmental contamination in third world and developing countries also plays a significant role in the increase of AMR. Despite the availability of numerous recognized antibiotics to combat bacterial infections, their effectiveness is diminishing due to the growing problem of AMR. The overuse of antibiotics has led to an increase in resistance rates and negative impacts on global health. This highlights the importance of implementing strong antimicrobial stewardship and improving global monitoring, as emphasized by the World Health Organization (WHO) and other organizations. In the face of these obstacles, quinoxaline derivatives have emerged as promising candidates. They are characterized by their remarkable efficacy against a broad spectrum of harmful bacteria, including strains that are resistant to multiple drugs. These compounds are known for their strong structural stability and adaptability, making them a promising and creative solution to the AMR crisis. This review aims to assess the effectiveness of quinoxaline derivatives in treating drug-resistant infections, with the goal of making a meaningful contribution to the global fight against AMR.

Acinetobacter baumannii OmpA-like porins: functional characterization of bacterial physiology, antibiotic-resistance, and virulence

Acinetobacter baumannii is a critical opportunistic pathogen associated with nosocomial infections. The high rates of antibiotic-resistance acquisition make most antibiotics ineffective. Thus, new medical countermeasures are urgently needed. Outer membrane proteins (OMPs) are prime candidates for developing novel drug targets and antibacterial strategies. However, there are substantial gaps in our knowledge of A. baumannii OMPs. This study reports the impact of OmpA-like protein on bacterial physiology and virulence in A. baumannii strain AB5075. We found that PsaB (ABUW_0505) negatively correlates to stress tolerance, while ArfA (ABUW_2730) significantly affects bacterial stiffness, cell shape, and cell envelope thickness. Furthermore, we expand our knowledge on YiaD (ABUW_3045), demonstrating structural and virulence roles of this porin, in addition to meropenem resistance. This study provides solid foundations for understanding how uncharacterized OMPs contribute to A. baumannii's physiological and pathological processes, aiding the development of innovative therapeutic strategies against A. baumannii infections.

Exposure to imipenem at sub-minimum inhibitory concentration leads to altered expression of major outer membrane proteins in Acinetobacter baumannii

AIMS

Acinetobacter baumannii is a nosocomial pathogen known to be multidrug-resistant (MDR), especially to drugs of the carbapenem class. Several factors contribute to resistance, including efflux pumps, β-lactamases, alteration of target sites, and permeability defects. In addition, outer membrane proteins (OMPs), like porins are involved in the passage of antibiotics, and their alteration could lead to resistance development. This study aimed to explore the possible involvement of porins and OMPs in developing carbapenem resistance due to differential expression.

METHODS AND RESULTS

The antibiotic-susceptible and MDR isolates of A. baumannii were first studied for differences in their transcriptional levels of OMP expression and OMP profiles. The antibiotic-susceptible isolates were further treated with imipenem, and it was found that the omp genes were differentially expressed. Six of the nine genes studied were upregulated at 1 h of exposure to imipenem. Their expression gradually decreased with time, further confirmed by their OMP profile and two-dimensional gel electrophoresis.

CONCLUSIONS

This study could identify OMPs that were differentially expressed on exposure to imipenem. Hence, this study provides insights into the role of specific OMPs in antibiotic resistance in A. baumannii.

Role of β-Lactamase Inhibitors as Potentiators in Antimicrobial Chemotherapy Targeting Gram-Negative Bacteria

Since the discovery of penicillin, β-lactam antibiotics have commonly been used to treat bacterial infections. Unfortunately, at the same time, pathogens can develop resistance to β-lactam antibiotics such as penicillins, cephalosporins, monobactams, and carbapenems by producing β-lactamases. Therefore, a combination of β-lactam antibiotics with β-lactamase inhibitors has been a promising approach to controlling β-lactam-resistant bacteria. The discovery of novel β-lactamase inhibitors (BLIs) is essential for effectively treating antibiotic-resistant bacterial infections. Therefore, this review discusses the development of innovative inhibitors meant to enhance the activity of β-lactam antibiotics. Specifically, this review describes the classification and characteristics of different classes of β-lactamases and the synergistic mechanisms of β-lactams and BLIs. In addition, we introduce potential sources of compounds for use as novel BLIs. This provides insights into overcoming current challenges in β-lactamase-producing bacteria and designing effective treatment options in combination with BLIs.

Sulbactam-durlobactam: a β-lactam/β-lactamase inhibitor combination targeting Acinetobacter baumannii

Sulbactam-durlobactam is a pathogen-targeted β-lactam/β-lactamase inhibitor combination that has been approved by the US FDA for the treatment of hospital-acquired and ventilator-associated bacterial pneumonia caused by susceptible isolates of Acinetobacter baumannii-calcoaceticus complex (ABC) in patients 18 years of age and older. Sulbactam is a penicillin derivative with antibacterial activity against Acinetobacter but is prone to hydrolysis by β-lactamases encoded by contemporary isolates. Durlobactam is a diazabicyclooctane β-lactamase inhibitor with activity against Ambler classes A, C and D serine β-lactamases that restores sulbactam activity both in vitro and in vivo against multidrug-resistant ABC. Sulbactam-durlobactam is a promising alternative therapy for the treatment of serious Acinetobacter infections, which can have high rates of mortality.

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.

Induced Heteroresistance in Carbapenem-Resistant Acinetobacter baumannii (CRAB) via Exposure to Human Pleural Fluid (HPF) and Its Impact on Cefiderocol Susceptibility

Infections caused by Carbapenem-resistant Acinetobacter baumannii (CRAB) isolates, such as hospital-acquired pneumonia (HAP), bacteremia, and skin and soft tissue infections, among others, are particularly challenging to treat. Cefiderocol, a chlorocatechol-substituted siderophore antibiotic, was approved by the U.S. Food and Drug Administration (FDA) in 2019 and prescribed for the treatment of CRAB infections. Despite the initial positive treatment outcomes with this antimicrobial, recent studies reported a higher-than-average all-cause mortality rate in patients treated with cefiderocol compared to the best available therapy. The cause(s) behind these outcomes remains unconfirmed. A plausible hypothesis is heteroresistance, a phenotype characterized by the survival of a small proportion of cells in a population that is seemingly isogenic. Recent results have demonstrated that the addition of human fluids to CRAB cultures leads to cefiderocol heteroresistance. Here, we describe the molecular and phenotypic analyses of CRAB heteroresistant bacterial subpopulations to better understand the nature of the less-than-expected successful outcomes after cefiderocol treatment. Isolation of heteroresistant variants of the CRAB strain AMA40 was carried out in cultures supplemented with cefiderocol and human pleural fluid (HPF). Two AMA40 variants, AMA40 IHC1 and IHC2, were resistant to cefiderocol. To identify mutations and gene expression changes associated with cefiderocol heteroresistance, we subjected these variants to whole genome sequencing and global transcriptional analysis. We then assessed the impact of these mutations on the pharmacodynamic activity of cefiderocol via susceptibility testing, EDTA and boronic acid inhibition analysis, biofilm formation, and static time-kill assays. Heteroresistant variants AMA40 IHC1 and AMA40 IHC2 have 53 chromosomal mutations, of which 40 are common to both strains. None of the mutations occurred in genes associated with high affinity iron-uptake systems or β-lactam resistance. However, transcriptional analyses demonstrated significant modifications in levels of expression of genes associated with iron-uptake systems or β-lactam resistance. The blaNDM-1 and blaADC-2, as well as various iron-uptake system genes, were expressed at higher levels than the parental strain. On the other hand, the carO and ompA genes' expression was reduced. One of the mutations common to both heteroresistant strains was mapped within ppiA, a gene associated with iron homeostasis in other species. Static time-kill assays demonstrated that supplementing cation-adjusted Mueller-Hinton broth with human serum albumin (HAS), the main protein component of HPF, considerably reduced cefiderocol killing activity for all three strains tested. Notably, collateral resistance to amikacin was observed in both variants. We conclude that exposing CRAB to fluids with high HSA concentrations facilitates the rise of heteroresistance associated with point mutations and transcriptional upregulation of genes coding for β-lactamases and biofilm formation. The findings from this study hold significant implications for understanding the emergence of CRAB resistance mechanisms against cefiderocol treatment. This understanding is vital for the development of treatment guidelines that can effectively address the challenges posed by CRAB infections.

Acinetobacter baumannii Global Clone-Specific Resistomes Explored in Clinical Isolates Recovered from Egypt

Acinetobacter baumannii (A. baumannii) is a highly problematic pathogen with an enormous capacity to acquire or upregulate antibiotic drug resistance determinants. The genomic epidemiology and resistome structure of 46 A. baumannii clinical isolates were studied using whole-genome sequencing. The isolates were chosen based on reduced susceptibility to at least three classes of antimicrobial compounds and were initially identified using MALDI-TOF/MS, followed by polymerase chain reaction amplification of bla_OXA-51-like genes. The susceptibility profiles were determined using a broth microdilution assay. Multi-, extensive-, and pan-drug resistance was shown by 34.8%, 63.0%, and 2.2% of the isolates, respectively. These were most susceptible to colistin (95.7%), amikacin, and trimethoprim/sulfamethoxazole (32.6% each), while only 26.1% of isolates were susceptible to tigecycline. In silico multi-locus sequence typing revealed 8 Pasteur and 22 Oxford sequence types (STs) including four novel STs (ST^Oxf 2805, 2806, 2807, and 2808). The majority of the isolates belonged to Global Clone (GC) 2 (76.4%), GC5 (19.6%), GC4 (6.5%), GC9 (4.3%), and GC7 (2.2%) lineages. An extensive resistome potentially conferring resistance to the majority of the tested antimicrobials was identified in silico. Of all known carbapenem resistance genes, bla_OXA-23 was carried by most of the isolates (69.6%), followed by ISAba1-amplified bla_ADC (56.5%), bla_NDM-1 and bla_GES-11 (21.7% each), and bla_GES-35 (2.2%) genes. A significant correlation was found between carbapenem resistance and carO mutations, which were evident in 35 (76.0%) isolates. A lower proportion of carbapenem resistance was noted for strains possessing both bla_OXA-23- and bla_GES-11. Amikacin resistance was most probably mediated by armA, aac(6')-Ib9, and aph(3')-VI, most commonly coexisting in GC2 isolates. No mutations were found in pmrABC or lpxACD operons in the colistin-resistant isolates. Tigecycline resistance was associated with adeS (N268Y) and baeS (A436T) mutations. While the lineage-specific distribution of some genes (e.g., bla_ADC and bla_OXA-51-like alleles) was evident, some resistance genes, such as bla_OXA-23 and sul1, were found in all GCs. The data generated here highlight the contribution of five GCs in A. baumannii infections in Egypt and enable the comprehensive analysis of GC-specific resistomes, thus revealing the dissemination of the carbapenem resistance gene bla_OXA-23 in isolates encompassing all GCs.

Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex

Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.

Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors

Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.

Characterization of Virulent T4-Like Acinetobacter baumannii Bacteriophages DLP1 and DLP2

The world is currently facing a global health crisis due to the rapid increase in antimicrobial-resistant bacterial infections. One of the most concerning pathogens is Acinetobacter baumannii, which is listed as a Priority 1 pathogen by the World Health Organization. This Gram-negative bacterium has many intrinsic antibiotic resistance mechanisms and the ability to quickly acquire new resistance determinants from its environment. A limited number of effective antibiotics against this pathogen complicates the treatment of A. baumannii infections. A potential treatment option that is rapidly gaining interest is “phage therapy”, or the clinical application of bacteriophages to selectively kill bacteria. The myoviruses DLP1 and DLP2 (vB_AbaM-DLP_1 and vB_AbaM-DLP_2, respectively) were isolated from sewage samples using a capsule minus variant of A. baumannii strain AB5075. Host range analysis of these phages against 107 A. baumannii strains shows a limited host range, infecting 15 and 21 for phages DLP1 and DLP2, respectively. Phage DLP1 has a large burst size of 239 PFU/cell, a latency period of 20 min, and virulence index of 0.93. In contrast, DLP2 has a smaller burst size of 24 PFU/cell, a latency period of 20 min, and virulence index of 0.86. Both phages show potential for use as therapeutics to combat A. baumannii infections.

Molecular docking and dynamic approach to screen the drug candidate against the Imipenem-resistant CarO porin in Acinetobacter baumannii

The multidrug-resistant Acinetobacter baumannii is an emerging nosocomial pathogen in the healthcare sector. Intrinsic resistance in A. baumannii is a significant problem framing a perfect treatment regimen. Also, this organism showed more resistance towards the carbapenem antibiotics, especially for imipenem and meropenem. The development of carbapenem-resistant Acinetobacter baumannii is mainly due to the alteration or loss of the porin region in the outer membrane. The most well-known porin in Acinetobacter baumannii is CarO (carbapenem-associated outer membrane protein). The CarO protein, which functions as a porin channel for carbapenem inflow, may contribute to carbapenem resistance. The current study identifies a potent drug candidate with a better binding affinity to the carbapenem-resistant outer membrane protein. We investigated the specificity of carbapenems such as imipenem, meropenem, ertapenem, biapenem, doripenem, and fluoroquinolone drugs such as sitafloxacin against the imipenem-resistant CarO protein was demonstrated using the computational approaches molecular docking and dynamic simulation for 50 ns. As a result, the high to low enzyme-ligand complex's binding affinity exhibited a greater binding affinity for ertapenem -7.76 kcal·mol^-1 and sitafloxacin -7.75 kcal·mol^-1 than biapenem, doripenem, meropenem, and imipenem. The molecular dynamic simulation and the MMPBSA analysis depicted ertapenem -55.431±25.908 kJ/mol and sitafloxacin -47.154 ± 11.052 kJ/mol with better binding affinity and more stability against the imipenem resistant CarO protein when it compared to other antibiotics.

Dynamic state of plasmid genomic architectures resulting from XerC/D-mediated site-specific recombination in Acinetobacter baumannii Rep_3 superfamily resistance plasmids carrying blaOXA-58 - and TnaphA6-resistance modules

The acquisition of bla _OXA genes encoding different carbapenem-hydrolyzing class-D β-lactamases (CHDL) represents a main determinant of carbapenem resistance in the nosocomial pathogen Acinetobacter baumannii. The bla_OXA-58 gene, in particular, is generally embedded in similar resistance modules (RM) carried by plasmids unique to the Acinetobacter genus lacking self-transferability. The ample variations in the immediate genomic contexts in which bla_OXA-58 -containing RMs are inserted among these plasmids, and the almost invariable presence at their borders of non-identical 28-bp sequences potentially recognized by the host XerC and XerD tyrosine recombinases (pXerC/D-like sites), suggested an involvement of these sites in the lateral mobilization of the gene structures they encircle. However, whether and how these pXerC/D sites participate in this process is only beginning to be understood. Here, we used a series of experimental approaches to analyze the contribution of pXerC/D-mediated site-specific recombination to the generation of structural diversity between resistance plasmids carrying pXerC/D-bounded bla _OXA-58- and TnaphA6-containing RM harbored by two phylogenetically- and epidemiologically-closely related A. baumannii strains of our collection, Ab242 and Ab825, during adaptation to the hospital environment. Our analysis disclosed the existence of different bona fide pairs of recombinationally-active pXerC/D sites in these plasmids, some mediating reversible intramolecular inversions and others reversible plasmid fusions/resolutions. All of the identified recombinationally-active pairs shared identical GGTGTA sequences at the cr spacer separating the XerC- and XerD-binding regions. The fusion of two Ab825 plasmids mediated by a pair of recombinationally-active pXerC/D sites displaying sequence differences at the cr spacer could be inferred on the basis of sequence comparison analysis, but no evidence of reversibility could be obtained in this case. The reversible plasmid genome rearrangements mediated by recombinationally-active pairs of pXerC/D sites reported here probably represents an ancient mechanism of generating structural diversity in the Acinetobacter plasmid pool. This recursive process could facilitate a rapid adaptation of an eventual bacterial host to changing environments, and has certainly contributed to the evolution of Acinetobacter plasmids and the capture and dissemination of bla _OXA-58 genes among Acinetobacter and non-Acinetobacter populations co-residing in the hospital niche.

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii with Special Reference to Carbapenemases: A Systematic Review

Carbapenemases are β-lactamase enzymes that hydrolyze a variety of β-lactams including carbapenem and belong to different Ambler classes (A, B, D). These enzymes can be encoded by plasmid or chromosomal-mediated genes. The major issues associated with carbapenemases-producing organisms are compromising the activity and increasing the resistance to carbapenems which are the last resort antibiotics used in treating serious infections. The global increase of pathogen, carbapenem-resistant A. baumannii has significantly threatened public health. Thus, there is a pressing need for a better understanding of this pathogen, to know the various carbapenem resistance encoding genes and dissemination of resistance genes from A. baumannii which help in developing strategies to overcome this problem. The horizontal transfer of resistant determinants through mobile genetic elements increases the incidence of multidrug, extensive drug, and Pan-drug resistant A. baumannii. Therefore, the current review aims to know the various mechanisms of carbapenem resistance, categorize and discuss carbapenemases encoding genes and various mobile genetic elements, and the prevalence of carbapenemase genes in recent years in A. baumannii from various geographical regions.

Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination

Pathogenic Acinetobacter species, most notably Acinetobacter baumannii, are a significant cause of healthcare-associated infections worldwide. Acinetobacter infections are of particular concern to global health due to the high rates of multidrug resistance and extensive drug resistance. Widespread genome sequencing and analysis has determined that bacterial antibiotic resistance is often acquired and disseminated through the movement of mobile genetic elements, including insertion sequences (IS), transposons, integrons, and conjugative plasmids. In Acinetobacter specifically, resistance to carbapenems and cephalosporins is highly correlated with IS, as many ISAba elements encode strong outwardly facing promoters that are required for sufficient expression of β-lactamases to confer clinical resistance. Here, we review the role of mobile genetic elements in antibiotic resistance in Acinetobacter species through the framework of the mechanism of resistance acquisition and with a focus on experimentally validated mechanisms.

Gearing up for battle: Harnessing adaptive T cell immunity against gram-negative pneumonia

Pneumonia is one of the leading causes of morbidity and mortality worldwide and Gram-negative bacteria are a major cause of severe pneumonia. Despite advances in diagnosis and treatment, the rise of multidrug-resistant organisms and hypervirulent strains demonstrates that there will continue to be challenges with traditional treatment strategies using antibiotics. Hence, an alternative approach is to focus on the disease tolerance components that mediate immune resistance and enhance tissue resilience. Adaptive immunity plays a pivotal role in modulating these processes, thus affecting the incidence and severity of pneumonia. In this review, we focus on the adaptive T cell responses to pneumonia induced by Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. We highlight key factors in these responses that have potential for therapeutic targeting, as well as the gaps in current knowledge to be focused on in future work.

Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy

In 2016, a 68-year-old patient with a disseminated multidrug-resistant Acinetobacter baumannii infection was successfully treated using lytic bacteriophages. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The phages used in the initial treatment are related, T4-like myophages. Analysis of 19 A. baumannii isolates collected before and during phage treatment shows that resistance to the T4-like phages appeared two days following the start of treatment. We generate complete genomic sequences for three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment, supporting a clonal relationship. Furthermore, we use strain TP1 to select for increased resistance to five of the phages in vitro, and identify mutations that are also found in phage-insensitive isolates TP2 and TP3 (which evolved in vivo during phage treatment). These results support that in vitro investigations can produce results that are relevant to the in vivo environment.

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.

Evasion of Antimicrobial Activity in Acinetobacter baumannii by Target Site Modifications: An Effective Resistance Mechanism

Acinetobacter baumannii is a Gram-negative bacillus that causes multiple infections that can become severe, mainly in hospitalized patients. Its high ability to persist on abiotic surfaces and to resist stressors, together with its high genomic plasticity, make it a remarkable pathogen. Currently, the isolation of strains with high antimicrobial resistance profiles has gained relevance, which complicates patient treatment and prognosis. This resistance capacity is generated by various mechanisms, including the modification of the target site where antimicrobial action is directed. This mechanism is mainly generated by genetic mutations and contributes to resistance against a wide variety of antimicrobials, such as β-lactams, macrolides, fluoroquinolones, aminoglycosides, among others, including polymyxin resistance, which includes colistin, a rescue antimicrobial used in the treatment of multidrug-resistant strains of A. baumannii and other Gram-negative bacteria. Therefore, the aim of this review is to provide a detailed and up-to-date description of antimicrobial resistance mediated by the target site modification in A. baumannii, as well as to detail the therapeutic options available to fight infections caused by this bacterium.

Genetic Resistance Determinants in Clinical Acinetobacter pittii Genomes

Antimicrobial-resistant pathogenic bacteria are an increasing problem in public health, especially in the healthcare environment, where nosocomial infection microorganisms find their niche. Among these bacteria, the genus Acinetobacter which belongs to the ESKAPE pathogenic group harbors different multi-drug resistant (MDR) species that cause human nosocomial infections. Although A. baumannii has always attracted more interest, the close-related species A. pittii is the object of more study due to the increase in its isolation and MDR strains. In this work, we present the genomic analysis of five clinically isolated A. pittii strains from a Spanish hospital, with special attention to their genetic resistance determinants and plasmid structures. All the strains harbored different genes related to β-lactam resistance, as well as different MDR efflux pumps. We also found and described, for the first time in this species, point mutations that seem linked with colistin resistance, which highlights the relevance of this comparative analysis among the pathogenic species isolates.

An Outer Membrane Protein YiaD Contributes to Adaptive Resistance of Meropenem in Acinetobacter baumannii

Acinetobacter baumannii is an important nosocomial pathogen that can develop various resistance mechanisms to many antibiotics. However, little is known about how it evolves from an antibiotic sensitive to a resistant phenotype. In this study, we investigated the transition of outer membrane proteins (OMPs) under antibiotic stress and identified YiaD as an OMP marker involved in the development of adaptive resistance to meropenem (MEM) in A. baumannii. Following stimulation of a carbapenem-sensitive strain AB5116 with sub-MIC of MEM, yiaD showed significantly decreased expression, and this decrease continued with prolonged stimulation for 8 h. The downregulation of yiaD was not only observed in clinically sensitive strains but also in 45 carbapenem-resistant isolates that produced the β-lactamases TEM and OXA-23. However, the extent of the reduction of yiaD expression in resistant strains was less than that in sensitive strains. Lack of yiaD resulted in a 4-fold increase in the MIC of AB5116 to MEM. The same level of depressed susceptibility induced by yiaD deletion was observed in both a growth curve test and a survival rate assay. Moreover, the colony shape became enlarged and irregular after loss of yiaD, and the biofilm formation ability of A. baumannii was influenced by YiaD. These results suggest that YiaD could respond to the stimulus of MEM in A. baumannii with a downregulation trend that kept pace with the prolonged stimulation time, indicating that it participates in various routes to benefit MEM resistance evolution in both carbapenem-sensitive and -resistant A. baumannii strains.

IMPORTANCEAcinetobacter baumannii can develop various resistance mechanisms to carbapenems. However, the factors involved in the evolutionary process that leads from transition to the sensitive to resistant phenotype are not clear. The outer membrane protein YiaD of A. baumannii was downregulated under the stress of meropenem (MEM), and its expression level was continuously reduced with prolonged stimulation time. The downregulation of yiaD was not only observed in sensitive strains but also in carbapenem-resistant isolates producing the β-lactamases TEM and OXA-23. However, the extent of yiaD reduction was less in resistant strains than in sensitive strains. Lack of yiaD resulted in an increased MEM MIC, enlarged and irregular colonies, and decreased biofilm formation ability. These results suggest that YiaD responds to MEM stimulus in A. baumannii and participates in the adaptive resistance of MEM in both carbapenem-sensitive and -resistant strains.

Comparison of the outer membrane proteomes between clinical carbapenem-resistant and susceptible Acinetobacter baumannii

BACKGROUND AND AIM

Carbapenem resistance has become a major obstacle in combating Acinetobacter baumannii infections. Although enzymatic degradation by β-lactamases is the pivotal mechanism of carbapenem resistance, porin deficiency has also been implicated in the mechanism. In this study, outer membrane proteins (OMPs) pattern of a clinical multidrug-resistant A. baumannii isolate were analyzed in order to attain a deeper understanding of carbapenem resistance strategies.

METHODS

OMPs extracts respectively separated from carbapenem-resistant and -susceptible clinical A. baumannii isolates were compared using two-dimensional polyacrylamide gel electrophoresis. Differentially expressed proteins were identified by matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF).

RESULTS

Twenty-three differently expressed proteins were identified between the resistant and susceptible isolates. Among them, six were annotated convincingly as OMPs in UniProt database. CarO was found absent from the resistant isolate and the expression levels of Omp33-36 and Omp25 were significantly lower than that in the susceptible counterpart. Strikingly, a LysM domain/BON superfamily protein, which has been linked to carbapenem resistance in Klebsiella pneumoniae, was found underexpressed by 10-fold in the resistant isolate.

CONCLUSION

Our study verified some porins which have been proven to play an important role in bacterial resistance against carbapenems. Underexpression of the LysM domain/BON superfamily protein may indicate its possible engagement in bacterial drug resistance, but its actual role requires more investigation.

Integron Functionality and Genome Innovation: An Update on the Subtle and Smart Strategy of Integrase and Gene Cassette Expression Regulation

Integrons are considered hot spots for bacterial evolution, since these platforms allow one-step genomic innovation by capturing and expressing genes that provide advantageous novelties, such as antibiotic resistance. The acquisition and shuffling of gene cassettes featured by integrons enable the population to rapidly respond to changing selective pressures. However, in order to avoid deleterious effects and fitness burden, the integron activity must be tightly controlled, which happens in an elegant and elaborate fashion, as discussed in detail in the present review. Here, we aimed to provide an up-to-date overview of the complex regulatory networks that permeate the expression and functionality of integrons at both transcriptional and translational levels. It was possible to compile strong shreds of evidence clearly proving that these versatile platforms include functions other than acquiring and expressing gene cassettes. The well-balanced mechanism of integron expression is intricately related with environmental signals, host cell physiology, fitness, and survival, ultimately leading to adaptation on the demand.

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Isolated from the Intensive Care Unit in a Tertiary Teaching Hospital in Malaysia

The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) has now become a global sentinel event. CRAB infections often instigate severe clinical complications and are potentially fatal, especially for debilitated patients. The present study aimed to conduct molecular characterization on CRAB isolated from patients in the intensive care unit from 2015 to 2016 and determine the risk factors associated with patients’ mortality. One hundred CRAB isolates were retrospectively selected and included in this study. Antimicrobial susceptibility testing showed that all isolates remained susceptible to colistin, even though 62% of them conferred resistance to all other classes of antibiotics tested. OXA carbapenemase gene was found to be the predominant carbapenemase gene, with 99% of the isolates coharbouring bla_OXA-23-like and bla_OXA-51-like carbapenemase genes. All isolates were carrying intact CarO genes, with the presence of various degree of nucleotide insertion, deletion and substitution. Overall, PFGE subtyped the isolates into 13 distinct pulsotypes, with the presence of 2 predominant pulsotypes. Univariate analysis implied that age, infection/colonization by CRAB, ethnicity, comorbidity and CRAB specimen source were significantly associated with in-hospital mortality. Multivariate analysis identified a higher risk of mortality for patients who are of Chinese ethnicity with diabetes as an underlying disease. As CRAB infection could lead to high rate of mortality, comprehensive infection control measures are needed to minimize the spread of this pathogen.

Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance

Carbapenems-one of the important last-line antibiotics for the treatment of gram-negative infections-are becoming ineffective for treating Acinetobacter baumannii infections. Studies have identified multiple genes (and mechanisms) responsible for carbapenem resistance. In some A. baumannii strains, the presence/absence of putative resistance genes is not consistent with their resistance phenotype-indicating the genomic factors underlying carbapenem resistance in A. baumannii are not fully understood. Here, we describe a large-scale whole-genome genotype-phenotype association study with 349 A. baumannii isolates that extends beyond the presence/absence of individual antimicrobial resistance genes and includes the genomic positions and pairwise interactions of genes. Ten known resistance genes exhibited statistically significant associations with resistance to imipenem, a type of carbapenem: blaOXA-23, qacEdelta1, sul1, mphE, msrE, ant(3")-II, aacC1, yafP, aphA6, and xerD. A review of the strains without any of these 10 genes uncovered a clade of isolates with diverse imipenem resistance phenotypes. Finer resolution evaluation of this clade revealed the presence of a 38.6 kbp conserved chromosomal region found exclusively in imipenem-susceptible isolates. This region appears to host several HTH-type DNA binding transcriptional regulators and transporter genes. Imipenem-susceptible isolates from this clade also carried two mutually exclusive plasmids that contain genes previously known to be specific to imipenem-susceptible isolates. Our analysis demonstrates the utility of using whole genomes for genotype-phenotype correlations in the context of antibiotic resistance and provides several new hypotheses for future research.

Interplay between Meropenem and Human Serum Albumin on Expression of Carbapenem Resistance Genes and Natural Competence in Acinetobacter baumannii

Acinetobacter baumannii A118, a carbapenem-susceptible strain, and AB5075, carbapenem resistant, were cultured in lysogeny broth (LB) or LB with different supplements, such as 3.5% human serum albumin (HSA), human serum (HS), meropenem, or meropenem plus 3.5% HSA. Natural transformation levels were enhanced in A. baumannii A118 and AB5075 cultured in medium supplemented with 3.5% HSA. Addition of meropenem plus 3.5% HSA caused synergistic enhancement of natural transformation in A. baumannii A118. Medium containing 3.5% HSA or meropenem enhanced the expression levels of the competence and type IV pilus-associated genes. The combination meropenem plus 3.5% HSA produced a synergistic enhancement in the expression levels of many of these genes. The addition of HS, which has a high content of HSA, was also an inducer of these genes. Cultures in medium supplemented with HS or 3.5% HSA also affected resistance genes, which were expressed at higher or lower levels depending on the modification required to enhance resistance. The inducing or repressing activity of these modulators also occurred in three more carbapenem-resistant strains tested. An exception was the A. baumannii AMA16 blaNDM-1 gene, which was repressed in the presence of 3.5% HSA. In conclusion, HSA produces an enhancement of natural transformation and a modification in expression levels of competence genes and antibiotic resistance. Furthermore, when HSA is combined with carbapenems, which may increase the stress response, the expression of genes involved in natural competence is increased in A. baumannii. This process may favor the acquisition of foreign DNA and accelerate evolution.

Histone-like nucleoid-structuring protein (H-NS) regulatory role in antibiotic resistance in Acinetobacter baumannii

In the multidrug resistant (MDR) pathogen Acinetobacter baumannii the global repressor H-NS was shown to modulate the expression of genes involved in pathogenesis and stress response. In addition, H-NS inactivation results in an increased resistance to colistin, and in a hypermotile phenotype an altered stress response. To further contribute to the knowledge of this key transcriptional regulator in A. baumannii behavior, we studied the role of H-NS in antimicrobial resistance. Using two well characterized A. baumannii model strains with distinctive resistance profile and pathogenicity traits (AB5075 and A118), complementary transcriptomic and phenotypic approaches were used to study the role of H-NS in antimicrobial resistance, biofilm and quorum sensing gene expression. An increased expression of genes associated with β-lactam resistance, aminoglycosides, quinolones, chloramphenicol, trimethoprim and sulfonamides resistance in the Δhns mutant background was observed. Genes codifying for efflux pumps were also up-regulated, with the exception of adeFGH. The wild-type transcriptional level was restored in the complemented strain. In addition, the expression of biofilm related genes and biofilm production was lowered when the transcriptional repressor was absent. The quorum network genes aidA, abaI, kar and fadD were up-regulated in Δhns mutant strains. Overall, our results showed the complexity and scope of the regulatory network control by H-NS (genes involved in antibiotic resistance and persistence). These observations brings us one step closer to understanding the regulatory role of hns to combat A. baumannii infections.

In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology

Biological systems have evolved to utilize proteins to accomplish nearly all functional roles needed to sustain life. A majority of biological functions occur within the crowded environment inside cells and subcellular compartments where proteins exist in a densely packed complex network of protein-protein interactions. The structural biology field has experienced a renaissance with recent advances in crystallography, NMR, and CryoEM that now produce stunning models of large and complex structures previously unimaginable. Nevertheless, measurements of such structural detail within cellular environments remain elusive. This review will highlight how advances in mass spectrometry, chemical labeling, and informatics capabilities are merging to provide structural insights on proteins, complexes, and networks that exist inside cells. Because of the molecular detection specificity provided by mass spectrometry and proteomics, these approaches provide systems-level information that not only benefits from conventional structural analysis, but also is highly complementary. Although far from comprehensive in their current form, these approaches are currently providing systems structural biology information that can uniquely reveal how conformations and interactions involving many proteins change inside cells with perturbations such as disease, drug treatment, or phenotypic differences. With continued advancements and more widespread adaptation, systems structural biology based on in-cell labeling and mass spectrometry will provide an even greater wealth of structural knowledge.

Variability in carbapenemase activity of intrinsic OxaAb (OXA-51-like) β-lactamase enzymes in Acinetobacter baumannii

OBJECTIVES

To measure the variability in carbapenem susceptibility conferred by different OxaAb variants, characterize the molecular evolution of oxaAb and elucidate the contribution of OxaAb and other possible carbapenem resistance factors in the clinical isolates using WGS and LC-MS/MS.

METHODS

Antimicrobial susceptibility tests were performed on 10 clinical Acinetobacter baumannii isolates. Carbapenem MICs were evaluated for all oxaAb variants cloned into A. baumannii CIP70.10 and BM4547, with and without their natural promoters. Molecular evolution analysis of the oxaAb variants was performed using FastTree and SplitsTree4. Resistance determinants were studied in the clinical isolates using WGS and LC-MS/MS.

RESULTS

Only the OxaAb variants with I129L and L167V substitutions, OxaAb(82), OxaAb(83), OxaAb(107) and OxaAb(110) increased carbapenem MICs when expressed in susceptible A. baumannii backgrounds without an upstream IS element. Carbapenem resistance was conferred with the addition of their natural upstream ISAba1 promoter. LC-MS/MS analysis on the original clinical isolates confirmed overexpression of the four I129L and L167V variants. No other differences in expression levels of proteins commonly associated with carbapenem resistance were detected.

CONCLUSIONS

Elevated carbapenem MICs were observed by expression of OxaAb variants carrying clinically prevalent substitutions I129L and L167V. To drive carbapenem resistance, these variants required overexpression by their upstream ISAba1 promoter. This study clearly demonstrates that a combination of IS-driven overexpression of oxaAb and the presence of particular amino acid substitutions in the active site to improve carbapenem capture is key in conferring carbapenem resistance in A. baumannii and other mechanisms are not required.

Treatment of patients with serious infections due to carbapenem-resistant Acinetobacter baumannii: How viable are the current options?

This review critically appraises the published microbiologic and clinical data on the treatment of patients with carbapenem-resistant Acinetobacter baumannii infections. Despite being recognized as an urgent threat pathogen by the CDC and WHO, optimal treatment of patients with serious CRAB infections remains ill-defined. Few commercially available agents exhibit reliable in vitro activity against CRAB. Historically, polymyxins have been the most active agents in vitro, though interpretations of susceptibility data are difficult given issues surrounding MIC testing methodologies and lack of correlation between MICs and clinical outcomes. Most available preclinical and clinical data involve use of polymyxins, tetracyclines, and sulbactam, alone and in combination. As the number of viable treatment options is limited, combination therapy with a polymyxin is often used for patients with CRAB infections, despite the significant risk of nephrotoxicity. However, no treatment regimen has been found to reduce mortality, which exceeds 40% across most studies, or substantially improve clinical response. While some newer agents, such as eravacycline and cefiderocol, have demonstrated in vitro activity, clinical efficacy has not been fully established. New agents with clinically relevant activity against CRAB isolates and favorable toxicity profiles are sorely needed.

Highlights Regarding the Use of Metallic Nanoparticles against Pathogens Considered a Priority by the World Health Organization

The indiscriminate use of antibiotics has facilitated the growing resistance of bacteria, and this has become a serious public health problem worldwide. Several microorganisms are still resistant to multiple antibiotics and are particularly dangerous in the hospital and nursing home environment, and to patients whose care requires devices, such as ventilators and intravenous catheters. A list of twelve pathogenic genera, which especially included bacteria that were not affected by different antibiotics, was released by the World Health Organization (WHO) in 2017, and the research and development of new antibiotics against these genera has been considered a priority. The nanotechnology is a tool that offers an effective platform for altering the physicalchemical properties of different materials, thereby enabling the development of several biomedical applications. Owing to their large surface area and high reactivity, metallic particles on the nanometric scale have remarkable physical, chemical, and biological properties. Nanoparticles with sizes between 1 and 100 nm have several applications, mainly as new antimicrobial agents for the control of microorganisms. In the present review, more than 200 reports of various metallic nanoparticles, especially those containing copper, gold, platinum, silver, titanium, and zinc were analyzed with regard to their anti-bacterial activity. However, of these 200 studies, only 42 reported about trials conducted against the resistant bacteria considered a priority by the WHO. All studies are in the initial stage, and none are in the clinical phase of research.

Synergistic Antibacterial Effect of Casein-AgNPs Combined with Tigecycline against Acinetobacter baumannii

Acinetobacter baumannii (A. baumannii) is a common and challenging pathogen of nosocomial infections, due to its ability to survive on inanimate objects, desiccation tolerance, and resistance to disinfectants. In this study, we investigated an antibacterial strategy to combat A. baumannii via the combination of antibiotics and silver protein. This strategy used a functional platform consisting of silver nanoparticles (AgNPs) resurrected from silver-based calcium thiophosphate (SSCP) through casein and arginine. Then, the silver protein was combined with tigecycline, the first drug in glycylcycline antibiotic, to synergistically inhibit the viability of A. baumannii. The synergistic antibacterial activity was confirmed by the 96-well checkerboard method to determine their minimum inhibitory concentrations (MIC) and calculated for the combination index (CI). The MIC of the combination of silver protein and tigecycline (0.31 mg/mL, 0.16 µg/mL) was significantly lower than that of the individual MIC, and the CI was 0.59, which indicates a synergistic effect. Consequently, we integrated the detailed synergistic antibacterial properties when silver protein was combined with tigecycline. The result could make for a promising approach for the treatment of A. baumannii.

Phenotype profiles and adaptive preference of Acinetobacter johnsonii isolated from Ba River with different environmental backgrounds

Acinetobacter johnsonii is a potentially opportunistic pathogen widely distributed in nosocomial and natural environments, but little attention has been paid to this bacillus. Here A. johnsonii strains from Ba River with different pollution levels were isolated. In this study, we found that the increasing anthropogenic contaminants accounted for the emergence of multidrug-resistant (MDR) A. johnsonii strains. Correlation analysis results showed that the resistance phenotype of strains could be generated by co-selection of heavy metals or non-corresponding antibiotics. The whole genome sequence analysis showed that the relative heavy pollution of water selects strains containing more survival-relevant genes. We found that only some genes like bla_OXA-24 were responsible for its corresponding resistance profile. Additionally, the tolerance profiles toward heavy metals also attribute to the expression of efflux pumps rather than corresponding resistance genes. In summary, our finding revealed that the resistance profiles of A. johnsonii could be generated by cross or co-selection of anthropogenic contaminants and mediated by efflux pumps instead of corresponding resistance determinants. Our study also has deep-sight into the adaptive preference of bacteria in natural environments, and contributes to surveillance studies and MDR- A. johnsonii monitoring worldwide.

A plethora of carbapenem resistance in Acinetobacter baumannii: no end to a long insidious genetic journey

Acinetobacter baumannii, notorious for causing nosocomial infections especially in patients admitted to intensive care unit (ICU) and burn units, is best at displaying resistance to all existing antibiotic classes. Consequences of high potential for antibiotic resistance has resulted in extensive drug or even pan drug resistant A. baumannii. Carbapenems, mainly imipenem and meropenem, the last resort for the treatment of A. baumannii infections have fallen short due to the emergence of carbapenem resistant A. baumannii (CRAB). Though enzymatic degradation by production of class D β-lactamases (Oxacillinases) and class B β-lactamases (Metallo β-lactamases) is the core mechanism of carbapenem resistance in A. baumannii; however over-expression of efflux pumps such as resistance-nodulation cell division (RND) family and variant form of porin proteins such as CarO have been implicated for CRAB inception. Transduction and outer membrane vesicles-mediated transfer play a role in carbapenemase determinants spread. Colistin, considered as the most promising antibacterial agent, nevertheless faces adverse effects flaws. Cefiderocol, eravacycline, new β-lactam antibiotics, non-β-lactam-β-lactamase inhibitors, polymyxin B-derived molecules and bacteriophages are some other new treatment options streamlined.

Dissemination mechanisms of NDM genes in hospitalized patients

Background

NDM-producing Enterobacteriaceae are a major clinical concern worldwide. We characterized NDM-positive pathogens isolated from patients and assessed the dissemination patterns of the bla_NDM genes in a hospital setting.

Methods

Eleven NDM-positive Enterobacteriaceae (three Enterobacter hormaechei, six Klebsiella pneumoniae and two Escherichia coli) were isolated from nine patients over a 1 year period. Antimicrobial susceptibility was assessed by MICs. A combination of short- and long-read WGS was used for genome analysis. Clinical treatment history of patients was linked with genetic features of individual isolates to investigate the dissemination patterns of the bla_NDM genes and NDM-positive strains.

Results

bla_NDM in clonal K. pneumoniae were transmitted between two patients. In other instances, an identical IncC plasmid encoding NDM-1 was transmitted between E. coli and K. pneumoniae isolated from the same patient, and an IncX3 plasmid, carrying bla_NDM-1 or bla_NDM-5, was harboured in non-clonal E. hormaechei. Varying patterns of IS elements were identified as a critical transmission mechanism in association with bla_NDM genes.

Conclusions

Multiple transmission patterns were identified in hospitalized patients, including dissemination of clonal bacterial strains carrying resistance genes and horizontal transfer of resistance genes among divergent bacterial strains. Controlling spread of NDM is complex: while attention to standard infection control practices is critically important, this needs to be matched by aggressive efforts to limit unnecessary antimicrobial use, to minimize the selection for and risk of transfer of ‘high mobility’ resistance genes among Enterobacteriaceae.

Acinetobacter baumannii Antibiotic Resistance Mechanisms

Acinetobacter baumannii is a Gram-negative ESKAPE microorganism that poses a threat to public health by causing severe and invasive (mostly nosocomial) infections linked with high mortality rates. During the last years, this pathogen displayed multidrug resistance (MDR), mainly due to extensive antibiotic abuse and poor stewardship. MDR isolates are associated with medical history of long hospitalization stays, presence of catheters, and mechanical ventilation, while immunocompromised and severely ill hosts predispose to invasive infections. Next-generation sequencing techniques have revolutionized diagnosis of severe A. baumannii infections, contributing to timely diagnosis and personalized therapeutic regimens according to the identification of the respective resistance genes. The aim of this review is to describe in detail all current knowledge on the genetic background of A. baumannii resistance mechanisms in humans as regards beta-lactams (penicillins, cephalosporins, carbapenems, monobactams, and beta-lactamase inhibitors), aminoglycosides, tetracyclines, fluoroquinolones, macrolides, lincosamides, streptogramin antibiotics, polymyxins, and others (amphenicols, oxazolidinones, rifamycins, fosfomycin, diaminopyrimidines, sulfonamides, glycopeptide, and lipopeptide antibiotics). Mechanisms of antimicrobial resistance refer mainly to regulation of antibiotic transportation through bacterial membranes, alteration of the antibiotic target site, and enzymatic modifications resulting in antibiotic neutralization. Virulence factors that may affect antibiotic susceptibility profiles and confer drug resistance are also being discussed. Reports from cases of A. baumannii coinfection with SARS-CoV-2 during the COVID-19 pandemic in terms of resistance profiles and MDR genes have been investigated.

How to Enter a Bacterium: Bacterial Porins and the Permeation of Antibiotics

Despite tremendous successes in the field of antibiotic discovery seen in the previous century, infectious diseases have remained a leading cause of death. More specifically, pathogenic Gram-negative bacteria have become a global threat due to their extraordinary ability to acquire resistance against any clinically available antibiotic, thus urging for the discovery of novel antibacterial agents. One major challenge is to design new antibiotics molecules able to rapidly penetrate Gram-negative bacteria in order to achieve a lethal intracellular drug accumulation. Protein channels in the outer membrane are known to form an entry route for many antibiotics into bacterial cells. Up until today, there has been a lack of simple experimental techniques to measure the antibiotic uptake and the local concentration in subcellular compartments. Hence, rules for translocation directly into the various Gram-negative bacteria via the outer membrane or via channels have remained elusive, hindering the design of new or the improvement of existing antibiotics. In this review, we will discuss the recent progress, both experimentally as well as computationally, in understanding the structure-function relationship of outer-membrane channels of Gram-negative pathogens, mainly focusing on the transport of antibiotics.