Editorial commentary: Polymyxin-resistant Acinetobacter baumannii: urgent action needed

Exploring Aspartate Transcarbamoylase: A Promising Broad-Spectrum Target for Drug Development

Pyrimidine nucleotides are essential for a wide variety of cellular processes and are synthesized either via a salvage pathway or through de novo biosynthesis. The latter is particularly important in proliferating cells, such as infectious diseases and cancer cells. Aspartate transcarbamoylase (ATCase) catalyzes the first committed and rate-limiting step in the de novo pyrimidine biosynthesis pathway, making it an attractive therapeutic target for various diseases. This review summarizes the development of a series of allosteric ATCase inhibitors, advancing them as potential candidates for malarial, tuberculosis and cancer therapies. Furthermore, it explores the potential for these compounds to be expanded into drugs targeting neglected tropical diseases, antimicrobial-resistant infections caused by the ESKAPE pathogens, and their possible application as herbicides. We identify the likely equivalent allosteric pocket in these systems and perform a structure and sequence-based analysis of the residues comprising it, providing a rationale for continued exploration of this compound series as both specific and broad-range inhibitors. The review concludes by emphasizing the importance of continued research into ATCase inhibitors, given their potential broad applicability in treating diverse diseases to enhance both human health and agricultural practices.

Colistin resistance in carbapenem non-susceptible Acinetobacter baumanii in a tertiary care hospital in India: clinical characteristics, antibiotic susceptibility and molecular characterization

INTRODUCTION

Acinetobacter baumanii (AB) is a bacterium of concern in the hospital setup due to its ability to thrive in unfavorable conditions and the rapid emergence of antibiotic resistance. Carbapenem resistance in this organism is disheartening, further clouded by the emergence of colistin resistance.

AIM

The present prospective study aims to note the epidemiology, molecular profile, and clinical outcome of patients with colistin resistance AB infections in a multispecialty tertiary care setup in Odisha, Eastern India.

METHODS

All AB strains received from March 2021 to February 2022, identified by Vitek2 (Biomerieux) and confirmed by oxa-51 genes, were included. Carbapenem and colistin resistance were identified as per CLSI guidelines. Known mutations for blaOXA-23-like, blaIMP, blaVIM, blaKP, lpxA, lpxC, pmrA, pmrB, and plasmid mediated mcr (mcr1-5) were screened by conventional PCR techniques. The clinical outcome was noted retrospectively from case sheets. Data was entered in MS Excel and tabulated using SPSS software.

RESULTS

In the study period, 350 AB were obtained, of which 317(90.5%) were carbapenem resistant (CRAB). Among the CRAB isolates, 19 (5.9%) were colistin resistant (ABCoR). The most valuable antibiotics in the study were tigecycline (65.4% in ABCoI; 31.6% in ABCoR) and minocycline (44.3% in CI; 36.8% in CR). There was a significant difference in mortality among ABCoI and ABCoR infections. bla OXA was the predominant carbapenem resistance genotype, while pmrA was the predominant colistin resistant genotype. There were no plasmid mediated mcr genes detected in the present study.

Engineering Phage Tail Fiber Protein as a Wide-Spectrum Probe for Acinetobacter baumannii Strains with a Recognition Rate of 100

As a multidrug-resistant pathogen, Acinetobacter baumannii has long been identified as one of the most common nosocomial bacteria. High-performance recognition probes for wide-spectrum detection of A. baumannii are highly desired to achieve efficient diagnosis and timely treatment of infectious diseases induced by this pathogen. An engineering tail fiber protein (ETFP) named as Gp50 encoded by lytic phage Abp9 was expressed in Escherichia coli and identified as a binding protein for A. baumannii. According to the results of genome sequencing of an A. baumannii wild strain and phage-resistant strains, the binding receptor of ETFP Gp50 is inferred to be a lipopolysaccharide distributed on the bacterial surface. The engineering protein did not show lytic activity to A. baumannii, which facilitates the development of reliable diagnosis kits and biosensors with high flexibility and low false-negative rate. The results of specificity study show that ETFP Gp50 is a species-specific binding protein with a recognition rate of 100% for all tested 77 A. baumannii strains, while that of the natural phage Abp9 is only 27.3%. With the engineering protein, a fluorescence method was developed to detect A. baumannii with a detection range of 2.0 × 10² to 2.0 × 10⁸ cfu mL^-1. The method has been used for the quantification of A. baumannii in a diverse sample matrix with acceptable reliability. The work demonstrates the application potential of ETFP Gp50 as an ideal recognition probe for rapid screening of A. baumannii strains in a complicated sample matrix.

Comparative metabolomics reveals key pathways associated with the synergistic activity of polymyxin B and rifampicin combination against multidrug-resistant Acinetobacter baumannii

Multidrug-resistant (MDR) Acinetobacter baumannii presents a critical challenge to human health worldwide and polymyxins are increasingly used as a last-line therapy. Due to the rapid emergence of resistance during polymyxin monotherapy, synergistic combinations (e.g. with rifampicin) are recommended to treat A. baumannii infections. However, most combination therapies are empirical, owing to a dearth of understanding on the mechanism of synergistic antibacterial killing. In the present study, we employed metabolomics to investigate the synergy mechanism of polymyxin B-rifampicin against A. baumannii AB5075, an MDR clinical isolate. The metabolomes of A. baumannii AB5075 were compared at 1 and 4 h following treatments with polymyxin B alone (0.75 mg/L, i.e. 3 × MIC), rifampicin alone (1 mg/L, i.e. 0.25 × MIC) and their combination. Polymyxin B monotherapy significantly perturbed glycerophospholipid and fatty acid metabolism at 1 h, reflecting its activity on bacterial outer membrane. Rifampicin monotherapy significantly perturbed glycerophospholipid, nucleotide and amino acid metabolism, which are related to the inhibition of RNA synthesis. The combination treatment significantly perturbed the metabolism of nucleotides, amino acids, fatty acids and glycerophospholipids at 1 and 4 h. Notably, the intermediate metabolite pools from pentose phosphate pathway were exclusively enhanced by the combination, while most metabolites from the nucleotide and amino acid biosynthesis pathways were significantly decreased. Overall, the synergistic activity of the combination was initially driven by polymyxin B which impacted pathways associated with outer membrane biogenesis; and subsequent effects were mainly attributed to rifampicin via the inhibition of RNA synthesis. This study is the first to reveal the synergistic killing mechanism of polymyxin-rifampicin combination against polymyxin-susceptible MDR A. baumannii at the network level. Our findings provide new mechanistic insights for optimizing this synergistic combination in patients.

[New antibiotics for severe infections due to multidrug-resistant pathogens : Definitive treatment and escalation]

Multidrug-resistant pathogens often lead to treatment failure of antimicrobial regimens. After a period of imbalance between the occurrence/spread of resistance mechanisms and the development of new substances, some new substances have meanwhile been approved and many more are currently undergoing clinical testing. They are particularly effective against specific resistance mechanisms/pathogens and should be preserved for definitive treatment of an isolated pathogen. In the absence of alternatives reserve antibiotics, such as aztreonam and colistin have experienced a renaissance. They are again used in special infection scenarios and clinically tested in combination with new substances. Despite the introduction and development of new substances the building of resistance will at some time also render these (at least partially) ineffective. Therefore, their implementation must be carried out according to the antibiotic or infectious diseases stewardship.

A Diverse Panel of Clinical Acinetobacter baumannii for Research and Development

Over the past two decades, Acinetobacter baumannii has emerged as a leading cause of nosocomial infections worldwide. Of particular concern are panresistant strains, leading the World Health Organization (WHO) to designate carbapenem-resistant A. baumannii as a priority 1 (critical) pathogen for research and development of new antibiotics. A key component in supporting this effort is accessibility to diverse and clinically relevant strains for testing. Here, we describe a panel of 100 diverse A. baumannii strains for use in this endeavor. Whole-genome sequencing was performed on 3,505 A. baumannii isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. Isolates were cultured from clinical samples at health care facilities around the world between 2001 and 2017. Core-genome multilocus sequence typing and high-resolution single nucleotide polymorphism (SNP)-based phylogenetic analyses were used to select a final panel of 100 strains that captured the genetic diversity of the collection. Comprehensive antibiotic susceptibility testing was also performed on all 100 isolates using 14 clinically relevant antibiotics. The final 100-strain diversity panel contained representative strains from 70 different traditional Pasteur scheme multilocus sequence types, including major epidemic clones. This diversity was also reflected in antibiotic susceptibility and antimicrobial resistance (AMR) gene content, with phenotypes ranging from pansensitive to panresistant, and over 100 distinct AMR gene alleles identified from 32 gene families. This panel provides the most diverse and comprehensive set of A. baumannii strains for use in developing solutions for combating antibiotic resistance. The panel and all available metadata, including genome sequences, will be available to industry and academic institutions and federal and other laboratories free of charge.

Colistin-Resistant Acinetobacter Baumannii Bacteremia: A Serious Threat for Critically Ill Patients

The prevalence of acinetobacter baumannii (AB) as a cause of hospital infections has been rising. Unfortunately, emerging colistin resistance limits therapeutic options and affects the outcome. The aim of the study was to confirm our clinically-driven hypothesis that intensive care unit (ICU) patients with AB resistant-to-colistin (ABCoR) bloodstream infection (BSI) develop fulminant septic shock and die. We conducted a 28-month retrospective observational study including all patients developing AB infection on ICU admission or during ICU stay. From 622 screened patients, 31 patients with BSI sepsis were identified. Thirteen (41.9%) patients had ABCoR BSI and 18/31 (58.1%) had colistin-susceptible (ABCoS) BSI. All ABCoR BSI patients died; of them, 69% (9/13) presented with fulminant septic shock and died within the first 3 days from its onset. ABCoR BSI patients compared to ABCoS BSI patients had higher mortality (100% vs. 50%, respectively (p = 0.001)), died sooner (p = 0.006), had lower pH (p = 0.004) and higher lactate on ICU admission (p = 0.0001), and had higher APACHE II (p = 0.01) and Charlson Comorbidity Index scores (p = 0.044). In conclusion, we documented that critically ill patients with ABCoR BSI exhibit fulminant septic shock with excessive mortality. Our results highlight the emerging clinical problem of AB colistin resistance among ICU patients.

Unlocking NuriPep 1653 From Common Pea Protein: A Potent Antimicrobial Peptide to Tackle a Pan-Drug Resistant Acinetobacter baumannii

While the antibiotic era has come and gone, antimicrobial peptides (AMPs) hold promise as novel therapies to treat multidrug resistant (MDR) pathogens in an age where the threat of multidrug resistance escalates worldwide. Here, we report the bactericidal properties of NuriPep 1653, a novel 22 mer and non-modified peptide. NuriPep 1653 was identified within the sequence of the non-antimicrobial P54 protein, which is involved in nutrient reservoir activity in Pisum sativum. Total bacterial clearance of Acinetobacter baumannii cells (1 × 108 cells/mL) was observed using only 4 × MIC (48 μg/mL) of NuriPep 1653 after just 20 min of treatment. We uncovered a synergistic interaction between NuriPep 1653 and another antimicrobial peptide, colistin. The MIC of NuriPep 1653 and colistin dropped from 12 and 8 μg/mL to 2 and 1 μg/mL, respectively, when they were combined. NuriPep 1653 exhibits no cytotoxicity in different human cell lines and has a low propensity to induce bacterial resistance in a colistin resistant clinical isolate of A. baumannii. The existence of these peptides embedded in proteins unearths potentially new classes of antimicrobials with activity against clinically relevant pathogens. Our findings push the boundaries of traditional peptide discovery and represent a leading edge for natural bioactive compounds which may have a common existence in nature but remain unexposed.

Dissecting Colistin Resistance Mechanisms in Extensively Drug-Resistant Acinetobacter baumannii Clinical Isolates

The discovery of antibiotics revolutionized modern medicine and enabled us to cure previously deadly bacterial infections. However, a progressive increase in antibiotic resistance rates is a major and global threat for our health care system. Colistin represents one of our last-resort antibiotics that is still active against most Gram-negative bacterial pathogens, but increasing resistance is reported worldwide, in particular due to the plasmid-encoded protein MCR-1 present in pathogens such as Escherichia coli and Klebsiella pneumoniae. Here, we showed that colistin resistance in A. baumannii, a top-priority pathogen causing deadly nosocomial infections, is mediated through different avenues that result in increased activity of homologous phosphoethanolamine (PetN) transferases. Considering that MCR-1 is also a PetN transferase, our findings indicate that PetN transferases might be the Achilles heel of superbugs and that direct targeting of them may have the potential to preserve the activity of polymyxin antibiotics.

Nosocomial infections with Acinetobacter baumannii are a global problem in intensive care units with high mortality rates. Increasing resistance to first- and second-line antibiotics has forced the use of colistin as last-resort treatment, and increasing development of colistin resistance in A. baumannii has been reported. We evaluated the transcriptional regulator PmrA as potential drug target to restore colistin efficacy in A. baumannii. Deletion of pmrA restored colistin susceptibility in 10 of the 12 extensively drug-resistant A. baumannii clinical isolates studied, indicating the importance of PmrA in the drug resistance phenotype. However, two strains remained highly resistant, indicating that PmrA-mediated overexpression of the phosphoethanolamine (PetN) transferase PmrC is not the exclusive colistin resistance mechanism in A. baumannii. A detailed genetic characterization revealed a new colistin resistance mechanism mediated by genetic integration of the insertion element ISAbaI upstream of the PmrC homolog EptA (93% identity), leading to its overexpression. We found that eptA was ubiquitously present in clinical strains belonging to the international clone 2, and ISAbaI integration upstream of eptA was required to mediate the colistin-resistant phenotype. In addition, we found a duplicated ISAbaI-eptA cassette in one isolate, indicating that this colistin resistance determinant may be embedded in a mobile genetic element. Our data disprove PmrA as a drug target for adjuvant therapy but highlight the importance of PetN transferase-mediated colistin resistance in clinical strains. We suggest that direct targeting of the homologous PetN transferases PmrC/EptA may have the potential to overcome colistin resistance in A. baumannii.

Acinetobacter spp. as nosocomial pathogens: Epidemiology and resistance features

The genus Acinetobacter is a major cause of nosocomial infections; it is increasingly being associated with various epidemics and has become a widespread concern in a variety of hospitals worldwide. Multi-antibiotic resistant Acinetobacter baumannii, is now recognized to be of great clinical significance. Numerous reports relay to the spread of A. baumannii in the hospital settings which leads to enhanced nosocomial outbreaks associated with high death rates. However, many other Acinetobacter spp. also can cause nosocomial infections. This review focused on the role of Acinetobacter spp. as nosocomial pathogens in addition to their persistence, antimicrobial resistance patterns and epidemiology.

Acinetobacter spp. Infections in Malaysia: A Review of Antimicrobial Resistance Trends, Mechanisms and Epidemiology

Acinetobacter spp. are important nosocomial pathogens, in particular the Acinetobacter baumannii-calcoaceticus complex, which have become a global public health threat due to increasing resistance to carbapenems and almost all other antimicrobial compounds. High rates of resistance have been reported among countries in Southeast Asia, including Malaysia. In this review, we examine the antimicrobial resistance profiles of Acinetobacter spp. hospital isolates from Malaysia over a period of nearly three decades (1987–2016) with data obtained from various peer-reviewed publications as well as the Malaysian National Surveillance on Antibiotic Resistance (NSAR). NSAR data indicated that for most antimicrobial compounds, including carbapenems, the peak resistance rates were reached around 2008–2009 and thereafter, rates have remained fairly constant (e.g., 50–60% for carbapenems). Individual reports from various hospitals in Peninsular Malaysia do not always reflect the nationwide resistance rates and often showed higher rates of resistance. We also reviewed the epidemiology and mechanisms of resistance that have been investigated in Malaysian Acinetobacter spp. isolates, particularly carbapenem resistance and found that bla_OXA-23 is the most prevalent acquired carbapenemase-encoding gene. From the very few published reports and whole genome sequences that are available, most of the Acinetobacter spp. isolates from Malaysia belonged to the Global Clone 2 (GC2) CC92 group with ST195 being the predominant sequence type. The quality of data and analysis in the national surveillance reports could be improved and more molecular epidemiology and genomics studies need to be carried out for further in-depth understanding of Malaysian Acinetobacter spp. isolates.

Clinical and Pathophysiological Overview of Acinetobacter Infections: a Century of Challenges

Acinetobacter is a complex genus, and historically, there has been confusion about the existence of multiple species. The species commonly cause nosocomial infections, predominantly aspiration pneumonia and catheter-associated bacteremia, but can also cause soft tissue and urinary tract infections. Community-acquired infections by Acinetobacter spp. are increasingly reported. Transmission of Acinetobacter and subsequent disease is facilitated by the organism's environmental tenacity, resistance to desiccation, and evasion of host immunity. The virulence properties demonstrated by Acinetobacter spp. primarily stem from evasion of rapid clearance by the innate immune system, effectively enabling high bacterial density that triggers lipopolysaccharide (LPS)-Toll-like receptor 4 (TLR4)-mediated sepsis. Capsular polysaccharide is a critical virulence factor that enables immune evasion, while LPS triggers septic shock. However, the primary driver of clinical outcome is antibiotic resistance. Administration of initially effective therapy is key to improving survival, reducing 30-day mortality threefold. Regrettably, due to the high frequency of this organism having an extreme drug resistance (XDR) phenotype, early initiation of effective therapy is a major clinical challenge. Given its high rate of antibiotic resistance and abysmal outcomes (up to 70% mortality rate from infections caused by XDR strains in some case series), new preventative and therapeutic options for Acinetobacter spp. are desperately needed.

Antibiotic resistance: What is so special about multidrug-resistant Gram-negative bacteria?

In the past years infections caused by multidrug-resistant Gram-negative bacteria have dramatically increased in all parts of the world. This consensus paper is based on presentations, subsequent discussions and an appraisal of current literature by a panel of international experts invited by the Rudolf Schülke Stiftung, Hamburg. It deals with the epidemiology and the inherent properties of Gram-negative bacteria, elucidating the patterns of the spread of antibiotic resistance, highlighting reservoirs as well as transmission pathways and risk factors for infection, mortality, treatment and prevention options as well as the consequences of their prevalence in livestock. Following a global, One Health approach and based on the evaluation of the existing knowledge about these pathogens, this paper gives recommendations for prevention and infection control measures as well as proposals for various target groups to tackle the threats posed by Gram-negative bacteria and prevent the spread and emergence of new antibiotic resistances.

Untargeted metabolomics analysis reveals key pathways responsible for the synergistic killing of colistin and doripenem combination against Acinetobacter baumannii

Combination therapy is deployed for the treatment of multidrug-resistant Acinetobacter baumannii, as it can rapidly develop resistance to current antibiotics. This is the first study to investigate the synergistic effect of colistin/doripenem combination on the metabolome of A. baumannii. The metabolite levels were measured using LC-MS following treatment with colistin (2 mg/L) or doripenem (25 mg/L) alone, and their combination at 15 min, 1 hr and 4 hr (n = 4). Colistin caused early (15 min and 1 hr) disruption of the bacterial outer membrane and cell wall, as demonstrated by perturbation of glycerophospholipids and fatty acids. Concentrations of peptidoglycan biosynthesis metabolites decreased at 4 hr by doripenem alone, reflecting its mechanism of action. The combination induced significant changes to more key metabolic pathways relative to either monotherapy. Down-regulation of cell wall biosynthesis (via D-sedoheptulose 7-phosphate) and nucleotide metabolism (via D-ribose 5-phosphate) was associated with perturbations in the pentose phosphate pathway induced initially by colistin (15 min and 1 hr) and later by doripenem (4 hr). We discovered that the combination synergistically killed A. baumannii via time-dependent inhibition of different key metabolic pathways. Our study highlights the significant potential of systems pharmacology in elucidating the mechanism of synergy and optimizing antibiotic pharmacokinetics/pharmacodynamics.

Rapid dissemination of colistin and carbapenem resistant Acinetobacter baumannii in Central Greece: mechanisms of resistance, molecular identification and epidemiological data

Background

Colistin-resistant/carbapenem-resistant Acinetobacter baumannii is a significant challenge for antibiotic treatment and infection control policies. Since 2012, in Central Greece an increase of colistin/pan- resistant A. baumannii has occurred, indicating the need for further analysis.

Methods

A total of 86 colistin-resistant/carbapenem-resistant out of 1228 A. baumannii clinical isolates, consecutively collected between 2012 and 2014 in a tertiary Greek hospital of Central Greece, as well as one environmental isolate from surveillance cultures were studied. Molecular typing and mechanisms of resistance to colistin and to carbapenems were assessed, whereas, epidemiological and clinical data of the patients were reviewed.

Results

During the study period, the rate of colistin resistance gradually increased and reached 21.1 % in 2014. All colistin-resistant/carbapenem-resistant A. baumannii belonged to 3LST ST101 clone that corresponds to the international clonal lineage II. Carbapenem resistance was associated with the presence of bla_oxa-23-like, while resistance to colistin probably correlated with G54E and R109H amino acid substitutions in PmrA and PmrC, respectively.

Conclusions

Epidemiological data of the patients indicated that the first detection of colistin-resistant/carbapenem-resistant ST101 clone in the University Hospital of Larissa (UHL) was associated with a patient who previously had received colistin, while, the movement of the infected patients into the hospital probably resulted to its spread.

Mechanisms of antimicrobial resistance in Gram-negative bacilli

The burden of multidrug resistance in Gram-negative bacilli (GNB) now represents a daily issue for the management of antimicrobial therapy in intensive care unit (ICU) patients. In Enterobacteriaceae, the dramatic increase in the rates of resistance to third-generation cephalosporins mainly results from the spread of plasmid-borne extended-spectrum beta-lactamase (ESBL), especially those belonging to the CTX-M family. The efficacy of beta-lactam/beta-lactamase inhibitor associations for severe infections due to ESBL-producing Enterobacteriaceae has not been adequately evaluated in critically ill patients, and carbapenems still stands as the first-line choice in this situation. However, carbapenemase-producing strains have emerged worldwide over the past decade. VIM- and NDM-type metallo-beta-lactamases, OXA-48 and KPC appear as the most successful enzymes and may threaten the efficacy of carbapenems in the near future. ESBL- and carbapenemase-encoding plasmids frequently bear resistance determinants for other antimicrobial classes, including aminoglycosides (aminoglycoside-modifying enzymes or 16S rRNA methylases) and fluoroquinolones (Qnr, AAC(6′)-Ib-cr or efflux pumps), a key feature that fosters the spread of multidrug resistance in Enterobacteriaceae. In non-fermenting GNB such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, multidrug resistance may emerge following the sole occurrence of sequential chromosomal mutations, which may lead to the overproduction of intrinsic beta-lactamases, hyper-expression of efflux pumps, target modifications and permeability alterations. P. aeruginosa and A. baumannii also have the ability to acquire mobile genetic elements encoding resistance determinants, including carbapenemases. Available options for the treatment of ICU-acquired infections due to carbapenem-resistant GNB are currently scarce, and recent reports emphasizing the spread of colistin resistance in environments with high volume of polymyxins use elicit major concern.

Infection Control Programs and Antibiotic Control Programs to Limit Transmission of Multi-Drug Resistant Acinetobacter baumannii Infections: Evolution of Old Problems and New Challenges for Institutes

Background: Acinetobacter baumannii complex (A. baumannii) has been isolated worldwide. The rapid spread of multidrug-resistant A. baumannii complex (MDRAB) in clinical settings has made choosing an appropriate antibiotic to treat these infections and executing contact precautions difficult for clinicians. Although controlling the transmission of MDRAB is a high priority for institutions, there is little information about MDRAB control. Therefore, this study evaluated infection control measures for A. baumannii infections, clusters and outbreaks in the literature. Methods: We performed a review of OVID Medline (from 1980 to 2015), and analyzed the literature. Results: We propose that both infection control programs and antibiotic control programs are essential for control of MDRAB. The first, effective control of MDRAB infections, requires compliance with a series of infection control methods including strict environmental cleaning, effective sterilization of reusable medical equipment, concentration on proper hand hygiene practices, and use of contact precautions, together with appropriate administrative guidance. The second strategy, effective antibiotic control programs to decrease A. baumannii, is also of paramount importance. Conclusion: We believe that both infection control programs and antibiotics stewardship programs are essential for control of MDRAB infections.