The Acinetobacter baumannii disinfectant resistance protein, AmvA, is a spermidine and spermine efflux pump

Structural basis for spermidine recognition and modulation of Acinetobacter baumannii multidrug efflux regulator AmvR

Acinetobacter baumannii is a gram-negative, opportunistic pathogen frequently associated with hospital-acquired infections. Due to its resistance to multiple antibiotics, it is emerging as a major nosocomial pathogen, causing a wide range of severe infections such as pneumonia, meningitis, and bloodstream infections. In many cases, the intrinsic activities of efflux pumps contribute to the development of drug resistance. The polyamine-binding protein AmvR regulates the multidrug efflux pump AmvA, which is pivotal for transporting polyamines, an abundant and prevalent class of amino acid-derived metabolites. Here, we report the crystal structure of the AmvR protein bound to its physiological substrate, spermidine, thereby offering structural and functional insights into AmvR. By employing electrophoretic mobility shift assays and DNase I footprinting, we identified the recognition sites of the intragenic regions of amvR and amvA by AmvR. Moreover, a fluorescence reporter assay revealed that AmvR repressed the expressions of AmvA and AmvR. In addition, isothermal titration calorimetry indicated that spermidine may be a natural ligand of AmvR. Collectively, these experiments provided a better understanding of substrate recognition for the discovery of potential inhibitors. Furthermore, our results revealed that substrate binding triggers a localized conformational change in the AmvR protein, as supported by size-exclusion chromatography and static light scattering, suggesting a distinctive regulatory mechanism within the TetR family transcription factors.

IMPORTANCE

Multidrug efflux pumps are key contributors to clinically significant drug resistance in various gram-negative pathogens responsible for hospital-acquired infections. These pathogens often possess multiple genes that encode potential multidrug efflux pumps. Identifying the specific regulatory proteins that control the expression of these pumps, along with elucidating the regulatory mechanisms triggered by effectors, presents a complex challenge. In this study, we have resolved the crystal structures of AmvR in both its unbound and spermidine-bound states. To the best of our knowledge, this represents the first validated structural model of a polyamine-bound transcriptional regulator. Through detailed structural analysis and functional assays, we have pinpointed the critical residues in AmvR responsible for substrate recognition, providing a foundation for the development of future inhibitors.

A decade of genomic and phenotypic adaptation of carbapenem-resistant Acinetobacter baumannii

Introduction

Acinetobacter baumannii exhibits high genomic plasticity, enabling it to acquire virulence factors and antibiotic resistance (AR). Understanding its evolutionary adaptations is crucial for developing effective therapeutic strategies.

Methods

Thirty clinical isolates collected from two distinct time periods, defined as older (2010-2013), and recent (2022-2023),- were compared phenotypically (antibiotic resistance, growth, biofilm formation, desiccation tolerance, invasiveness) and genotypically (whole-genome sequencing).

Results

All isolates displayed an extensively drug-resistant phenotype. Overall, respiratory isolates harbored a higher content of antibiotic-resistant genes (ARGs), with older isolates showing 12.5% increases in the average number of ARGs compared to recent urine isolates (P = 0.02). More than 50% of the strains with faster growth, stronger biofilm formation, and increased lung cell invasiveness were recent respiratory isolates, while over 70% of older isolates showed greater desiccation tolerance and bladder cell invasiveness. Eleven virulence factor genes were shared between old and recent respiratory isolates, and eight were common between recent urinary and respiratory strains with no overlap among urinary isolates. Statistically significant positive correlations were observed between fast-growing and strong biofilm-forming respiratory isolates as well as their lung cell invasiveness. Conversely, negative correlations were found between collection time, isolation site, and host cell invasiveness. Analysis of macrocolony types revealed no link to phenotypic behavior.

Conclusion

Significant genetic variability was found between past and recent isolates. Older isolates had more genes involved in adhesion and nutrient uptake, while recent respiratory strains demonstrated increased biofilm formation and invasiveness, reflecting adaptation to clinical pressures. These findings highlight the dynamic evolution of A. baumannii, providing insights for future therapeutic strategies and infection control.

The Slow Pandemic: Emergence of Antimicrobial Resistance in the Postadvent of SARS-CoV-2 Pandemic

Background: The unprecedented outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically changed the global approach to public health, emphasizing the importance of measures to control and prevent infections. In response to the COVID-19 crisis, stringent hygiene practices and surface disinfection have become the norm, with an unprecedented surge in the use of disinfectants and antiseptics (DAs). Main Text: While these measures have been crucial in curbing the spread of the virus, an emerging concern has taken center stage: the potential impact of the prolonged and widespread use of antimicrobial compounds in these products on the development of antibiotic resistance. Antimicrobial resistance (AMR) has long been recognized as one of the most pressing global health threats. Quaternary ammonium compounds (QAC) such as benzalkonium chloride, benzethonium chloride, and cetylpyridinium chloride, which are extensively used in DAs formulations, have gained less attention in the context of AMR. Conclusion: A high abundance of QACs was detected in wastewater, and certain bacteria such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterococcus species developed resistance to these compounds over time. We analyzed the available evidence from the scientific literature, examining the presence and concentrations of QACs in different water sources, and their resistance mechanisms. This review aimed to shed light on the multifaceted challenges that arise from the dual battle against the COVID-19 pandemic and the ongoing global fight against AMR.

Targeting Acinetobacter baumannii resistance-nodulation-division efflux pump transcriptional regulators to combat antimicrobial resistance

Regulatory elements controlling gene expression fine-tune bacterial responses to environmental cues, including antimicrobials, to optimize survival. Acinetobacter baumannii, a pathogen notorious for antimicrobial resistance, relies on efficient efflux systems. Though the role of efflux systems in antibiotic expulsion are well recognized, the regulatory mechanisms controlling their expression remain understudied. This review explores the current understanding of these regulators, aiming to inspire strategies to combat bacterial resistance and improve therapeutic outcomes.

Gut Microbiome-Driven metabolites influence skin pigmentation in TYRP1 mutant Oujiang Color Common Carp

The gut microbiome plays a key role in regulating the gut-skin axis, and host genetics partially influence this regulation. The study investigated the role of gut microbiota and host genetics in the gut-skin axis, focusing on the unusual "coffee-like" color phenotype observed in TYRP1 mutant Oujiang Color Common Carp. We employed comparative high-throughput omics data from wild-type and mutant fish to quantify the influence of both genetics and gut microbes on skin transcriptomic expression and blood metabolites. We found 525 differential metabolites (DMs) and 45 distinct gut microbial genera in TYRP1 mutant fish compared to wild type. Interaction and causal mediation analyses revealed a complex interplay. The TYRP1 mutation likely triggers an inflammatory pathway involving Acinetobacter bacteria, Leukotrience-C4 and Spermine. This inflammatory response appears to be counterbalanced by an anti-inflammatory cardiovascular genetic network. The net effect is the upregulation of COMT, PLG, C2, C3, F10, TDO2, MHC1, and SERPINF2, leading to unusual coffee-like coloration. This study highlights the intricate interplay between gut microbiota, host genetics, and metabolic pathways in shaping complex phenotypes.

Impact of the Stress Response on Quaternary Ammonium Compound Disinfectant Susceptibility in Serratia Species

The well-known problem of antibiotic resistance foreshadows a similar threat posed by microbial resistance to biocides such as disinfectants and antiseptics. These products are vital for infection control, yet their overuse during the COVID-19 pandemic has accelerated the development of resistant microorganisms. This study investigates the molecular mechanisms underlying disinfectant resistance in Serratia sp. HRI. The transcriptomic responses of Serratia sp. HRI were used to identify significant gene expression changes during exposure to QACs and revealed increased methionine transport and polyamine synthesis. Polyamines, crucial in cellular stress responses, were notably upregulated, suggesting a pivotal role of the stress response in disinfectant resistance. Further, our susceptibility tests revealed a marked decrease in susceptibility to QACs under various stress conditions, supporting the hypothesis that stress responses, mediated by polyamines, decrease susceptibility to QACs. This research highlights polyamines as key players in disinfectant resistance, offering novel insights into resistance mechanisms and antimicrobial susceptibility. Our findings emphasise the need for continued investigation into disinfectant resistance and the role of stress responses, particularly polyamine-mediated mechanisms, to direct strategies for preserving disinfectant efficacy and developing future antimicrobial agents.

Characterization of the carbapenem-resistant Acinetobacter baumannii clinical reference isolate BAL062 (CC2:KL58:OCL1): resistance properties and capsular polysaccharide structure

The carbapenem-resistant Acinetobacter baumannii isolate BAL062 is a clinical reference isolate used in several recent experimental studies. It is from a ventilator-associated pneumonia (VAP) patient in an intensive care unit at the Hospital for Tropical Diseases (HTD), Ho Chi Minh City, Vietnam in 2009. Here, BAL062 was found to belong to the B sub-lineage of global clone 2 (GC2) isolates in the previously reported outbreak (2008 and 2012) of carbapenem-resistant VAP A. baumannii at the HTD. While related sub-lineage B outbreak isolates were extensively antibiotic-resistant and carry GC2-associated genomic resistance islands, AbGRI1, AbGRI2, and AbGRI3, BAL062 has lost AbGRI3 and three aminoglycoside resistance genes, armA, aacA4, and aphA1, leading to amikacin, tobramycin and kanamycin susceptibility. The location of Tn2008VAR found in the chromosome of this sub-lineage was also corrected. Like many of the outbreak isolates, BAL062 carries the KL58 gene cluster at the capsular polysaccharide (CPS) synthesis locus and an annotation key is provided. As information about K type is important for the development of novel CPS-targeting therapies, the BAL062 K58-type CPS structure was established using NMR spectroscopy. It is most closely related to K2 and K93, sharing similar configurations and linkages between K units, and contains the rare higher monosaccharide, 5,7-diacetamido-3,5,7,9-tetradeoxy-d-glycero-l-manno-non-2-ulosonic acid (5,7-di-N-acetyl-8-epipseudaminic acid; 8ePse5Ac7Ac), the 8-epimer of Pse5Ac7Ac (5,7-di-N-acetylpseudaminic acid). Inspection of publicly available A. baumannii genomes revealed a wide distribution of the KL58 locus in geographically diverse isolates belonging to several sequence types that were recovered over two decades from clinical, animal, and environmental sources.IMPORTANCEMany published experimental studies aimed at developing a clearer understanding of the pathogenicity of carbapenem-resistant Acinetobacter baumannii strains currently causing treatment failure due to extensive antibiotic resistance are undertaken using historic, laboratory-adapted isolates. However, it is ideal if not imperative that recent clinical isolates are used in such studies. The clinical reference isolate characterized here belongs to the dominant A. baumannii GC2 clone causing extensively resistant infections and has been used in various recent studies. The correlation of resistance profiles and resistance gene data is key to identifying genes available for gene knockout and complementation analyses, and we have mapped the antibiotic resistance genes to find candidates. Novel therapies, such as bacteriophage or monoclonal antibody therapies, currently under investigation as alternatives or adjuncts to antibiotic treatment to combat difficult-to-treat CRAb infections often exhibit specificity for specific structural epitopes of the capsular polysaccharide (CPS), the outer-most polysaccharide layer. Here, we have solved the structure of the CPS type found in BAL062 and other extensively resistant isolates. As consistent gene naming and annotation are important for locus identification and interpretation of experimental studies, we also have correlated automatic annotations to the standard gene names.

Impact of acidic and alkaline conditions on Staphylococcus aureus and Acinetobacter baumannii interactions and their biofilms

Bacterial biofilms pose significant challenges due to their association with antibiotic resistance, metabolic adaptation, and survival under harsh conditions. Among notable pathogens forming biofilms, Staphylococcus aureus and Acinetobacter baumannii are concerning pathogens in nosocomial settings. However, their behaviour under acidic (pH 4.5) and alkaline (pH10.5) conditions, especially in co-culture setups, remains insufficiently understood. This study investigates these aspects, by examining growth rates, biofilm formation, pH shifts, phenotypic analysis, and gene expression profiles. The results showed A. baumannii exhibited reduced  growth and biofilm formation at pH 4.5, while S. aureus showed slow growth and low biofilm formation at pH10.5 in mono-cultures. S. aureus leaned towards an acidic pH (6-6.5), whereas A. baumannii shifted towards an alkaline pH (8-9). In co-culture environments, growth rates and biofilm formation increased across all pH conditions, converging towards a neutral pH over time. Phenotypic motility assays indicated that A. baumannii exhibited greater motility in alkaline conditions, while S. aureus showed increased staphyloxanthin production under acidic conditions. Gene expression analyses revealed that the fibronectin-binding protein A (FnbA) and N-acetylglucosaminyl-transferase (icaA) genes, responsible for initial attachment during biofilm formation, were highly expressed in acidic co-culture condition but poorly expressed in alkaline condition. In A. baumannii, the outer membrane protein A (OmpA) gene associated with adhesion and virulence, was upregulated in co-culture. The LuxR gene involved in quorum sensing was upregulated in acidic conditions and poorly expressed at pH 10.5. This study elucidates the metabolic adaptability and biofilm formation tendencies of S. aureus towards acidic conditions and A. baumannii towards alkaline conditions, providing insights for better management of biofilm-related infections.

Efficacy of sodium hypochlorite in overcoming antimicrobial resistance and eradicating biofilms in clinical pathogens from pressure ulcers

Sodium hypochlorite (NaOCl) is widely recognized for its broad-spectrum antimicrobial efficacy in skin wound care. This study investigates the effectiveness of NaOCl against a range of bacterial and fungal isolates from pressure ulcer (PU) patients. We analyzed 20 bacterial isolates from PU patients, comprising carbapenem-resistant Klebsiella pneumoniae (CRKP), multidrug-resistant Acinetobacter baumannii (MDRAB), methicillin-resistant Staphylococcus aureus (MRSA), methicillin-susceptible Staphylococcus aureus (MSSA), along with 5 Candida albicans isolates. Antibiotic resistance profiles were determined using standard susceptibility testing. Whole-genome sequencing (WGS) was employed to identify antimicrobial resistance genes (ARGs) and disinfectant resistance genes (DRGs). Genetic determinants of biofilm formation were also assessed. The antimicrobial activity of NaOCl was evaluated by determining the minimum inhibitory concentration (MIC) and the minimal biofilm eradication concentration (MBEC) for both planktonic and biofilm-associated cells. CRKP and MDRAB showed resistance to fluoroquinolones and carbapenems, while MRSA exhibited resistance to β-lactams and levofloxacin. MSSA displayed a comparatively lower resistance profile. WGS identified significant numbers of ARGs in CRKP and MDRAB, with fewer DRGs compared to MRSA and MSSA. All isolates possessed genes associated with fimbriae production and adhesion, correlating with pronounced biofilm biomass production. NaOCl demonstrated substantial antimicrobial activity against both planktonic cells and biofilms. The MIC90 for planktonic bacterial cells was 0.125 mg/mL, and the MBEC90 ranged from 0.225 to 0.5 mg/mL. For planktonic C. albicans, the MIC90 was 0.150 mg/mL, and the MBEC90 was 0.250 mg/mL. These results highlight the challenge in treating biofilm-associated infections and underscore the potential of NaOCl as a robust antimicrobial agent against difficult-to-treat biofilm infections at concentrations lower than those typically found in commercial disinfectants.

Transcriptomic signature of bacteria exposed to benzalkonium chloride

The COVID-19 pandemic has highlighted our reliance on biocides, the increasing prevalence of resistance to biocides is a risk to public health. Bacterial exposure to the biocide, benzalkonium chloride (BAC), resulted in a unique transcriptomic profile, characterised by both a short and long-term response. Differential gene expression was observed in four main areas: motility, membrane composition, proteostasis, and the stress response. A metabolism shift to protect the proteome and the stress response were prioritised suggesting these are main resistance mechanisms. Whereas "well-established" mechanisms, such as biofilm formation, were not found to be differentially expressed after exposure to BAC.

Types and Mechanisms of Efflux Pump Systems and the Potential of Efflux Pump Inhibitors in the Restoration of Antimicrobial Susceptibility, with a Special Reference to Acinetobacter baumannii

Bacteria express a plethora of efflux pumps that can transport structurally varied molecules, including antimicrobial agents and antibiotics, out of cells. Thus, efflux pump systems participate in lowering intracellular concentrations of antibiotics, which allows phenotypic multidrug-resistant (MDR) bacteria to survive effectively amid higher concentrations of antibiotics. Acinetobacter baumannii is one of the classic examples of pathogens that can carry multiple efflux pump systems, which allows these bacteria to be MDR-to-pan-drug resistant and is now considered a public health threat. Therefore, efflux pumps in A. baumannii have gained major attention worldwide, and there has been increased interest in studying their mechanism of action, substrates, and potential efflux pump inhibitors (EPIs). Efflux pump inhibitors are molecules that can inhibit efflux pumps, rendering pathogens susceptible to antimicrobial agents, and are thus considered potential therapeutic agents for use in conjunction with antibiotics. This review focuses on the types of various efflux pumps detected in A. baumannii, their molecular mechanisms of action, the substrates they transport, and the challenges in developing EPIs that can be clinically useful in reference to A. baumannii.

Healthcare Equipment and Personnel Reservoirs of Carbapenem-Resistant Acinetobacter baumannii Epidemic Clones in Intensive Care Units in a Tunisian Hospital

Carbapenem-resistant Acinetobacter baumannii (CRAB) strains can cause severe and difficult-to-treat infections in patients with compromised general health. CRAB strains disseminate rapidly in nosocomial settings by patient-to-patient contact, through medical devices and inanimate reservoirs. The occurrence of CRAB in patients residing in the intensive care units (ICUs) of the Sahloul University hospital in Sousse, Tunisia is high. The objective of the current study was to determine whether the surfaces of items present in five ICU wards and the medical personnel there operating could serve as reservoirs for CRAB strains. Furthermore, CRAB isolates from patients residing in the ICUs during the sampling campaign were analyzed for genome comparison with isolates from the ICUs environment. Overall, 206 items were screened for CRAB presence and 27 (14%) were contaminated with a CRAB isolate. The items were located in several areas of three ICUs. Eight of the 54 (15%) screened people working in the wards were colonized by CRAB on the hands. Patients residing in the ICUs were infected with CRAB strains sharing extensive genomic similarity with strains recovered in the nosocomial environment. The strains belonged to three sub-clades of the internationally disseminated clone (ST2). A clone emerging in the Mediterranean basin (ST85) was detected as well. The strains were OXA-23 or NDM-1 producers and were also pan-aminoglycoside resistant due to the presence of the armA gene. Hygiene measures are urgent to be implemented in the Sahloul hospital to avoid further spread of difficult-to-treat CRAB strains and preserve health of patients and personnel operating in the ICU wards.

DksA is a conserved master regulator of stress response in Acinetobacter baumannii

Coordination of bacterial stress response mechanisms is critical for long-term survival in harsh environments for successful host infection. The general and specific stress responses of well-studied Gram-negative pathogens like Escherichia coli are controlled by alternative sigma factors, archetypically RpoS. The deadly hospital pathogen Acinetobacter baumannii is notoriously resistant to environmental stresses, yet it lacks RpoS, and the molecular mechanisms driving this incredible stress tolerance remain poorly defined. Here, using functional genomics, we identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in A. baumannii. Transcriptomics, phenomics and in vivo animal studies revealed that DksA controls ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization in a niche-specific manner. Phylogenetically, DksA was highly conserved and well-distributed across Gammaproteobacteria, with 96.6% containing DksA, spanning 88 families. This study lays the groundwork for understanding DksA as a major regulator of general stress response and virulence in this important pathogen.

Acinetobacter baumannii ATCC 17978 encodes a microcin system with antimicrobial properties for contact-independent competition

Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen that persists in the hospital environment and causes various clinical infections, primarily affecting immunocompromised patients. A. baumannii has evolved a wide range of mechanisms to compete with neighbouring bacteria. One such competition strategy depends on small secreted peptides called microcins, which exert antimicrobial effects in a contact-independent manner. Here, we report that A. baumannii ATCC 17978 (AB17978) encodes the class II microcin 17 978 (Mcc17978) with antimicrobial activity against closely related Acinetobacter, and surprisingly, also Escherichia coli strains. We identified the genetic locus encoding the Mcc17978 system in AB17978. Using classical bacterial genetic approaches, we determined that the molecular receptor of Mcc17978 in E. coli is the iron-catecholate transporter Fiu, and in Acinetobacter is Fiu's homolog, PiuA. In bacteria, the Ferric uptake regulator (Fur) positively regulates siderophore systems and microcin systems under iron-deprived environments. We found that the Mcc17978 system is upregulated under low-iron conditions commonly found in the host environment and identified a putative Fur binding site upstream of the mcc17978 gene. When we tested the antimicrobial activity of Mcc17978 under different levels of iron availability, we observed that low iron levels not only triggered transcriptional induction of the microcin, but also led to enhanced microcin activity. Taken together, our findings suggest that A. baumannii may utilize microcins to compete with other microbes for resources during infection.

A suite of modular, all-synthetic suicide vectors for allelic exchange mutagenesis in multidrug resistant Acinetobacter strains

BACKGROUND

Acinetobacter baumannii is an opportunistic human pathogen that causes a variety of infections in immunosuppressed individuals and patients in intensive care units. The success of this pathogen in nosocomial settings can be directly attributed to its persistent nature and its ability to rapidly acquire multidrug resistance. It is now considered to be one of the top priority pathogens for development of novel therapeutic approaches. Several high-throughput techniques have been utilised to identify the genetic determinants contributing to the success of A. baumannii as a global pathogen. However, targeted gene-function studies remain challenging due to the lack of appropriate genetic tools.

RESULTS

Here, we have constructed a series of all-synthetic allelic exchange vectors - pALFI1, pALFI2 and pALFI3 - with suitable selection markers for targeted genetic studies in highly drug resistant A. baumannii isolates. The vectors follow the Standard European Vector Architecture (SEVA) framework for easy replacement of components. This method allows for rapid plasmid construction with the mutant allele, efficient conjugational transfer using a diaminopimelic acid-dependent Escherichia coli donor strain, efficient positive selection using the suitable selection markers and finally, sucrose-dependent counter-selection to obtain double-crossovers.

CONCLUSIONS

We have used this method to create scar-less deletion mutants in three different strains of A. baumannii, which resulted in up to 75% deletion frequency of the targeted gene. We believe this method can be effectively used to perform genetic manipulation studies in multidrug resistant Gram-negative bacterial strains.

Inhibition of Multidrug Efflux Pumps Belonging to the Major Facilitator Superfamily in Bacterial Pathogens

Bacterial pathogens resistant to multiple structurally distinct antimicrobial agents are causative agents of infectious disease, and they thus constitute a serious concern for public health. Of the various bacterial mechanisms for antimicrobial resistance, active efflux is a well-known system that extrudes clinically relevant antimicrobial agents, rendering specific pathogens recalcitrant to the growth-inhibitory effects of multiple drugs. In particular, multidrug efflux pump members of the major facilitator superfamily constitute central resistance systems in bacterial pathogens. This review article addresses the recent efforts to modulate these antimicrobial efflux transporters from a molecular perspective. Such investigations can potentially restore the clinical efficacy of infectious disease chemotherapy.

Cross-protection and cross-feeding between Klebsiella pneumoniae and Acinetobacter baumannii promotes their co-existence

Acinetobacter baumannii and Klebsiella pneumoniae are opportunistic pathogens frequently co-isolated from polymicrobial infections. The infections where these pathogens co-exist can be more severe and recalcitrant to therapy than infections caused by either species alone, however there is a lack of knowledge on their potential synergistic interactions. In this study we characterise the genomes of A. baumannii and K. pneumoniae strains co-isolated from a single human lung infection. We examine various aspects of their interactions through transcriptomic, phenomic and phenotypic assays that form a basis for understanding their effects on antimicrobial resistance and virulence during co-infection. Using co-culturing and analyses of secreted metabolites, we discover the ability of K. pneumoniae to cross-feed A. baumannii by-products of sugar fermentation. Minimum inhibitory concentration testing of mono- and co-cultures reveals the ability for A. baumannii to cross-protect K. pneumoniae against the cephalosporin, cefotaxime. Our study demonstrates distinct syntrophic interactions occur between A. baumannii and K. pneumoniae, helping to elucidate the basis for their co-existence in polymicrobial infections.

Overuse of food-grade disinfectants threatens a global spread of antimicrobial-resistant bacteria

Food-grade disinfectants are extensively used for microbial decontamination of food processing equipment. In recent years, food-grade disinfectants have been increasingly used. However, the overuse of disinfectants causes another major issue, which is the emergence and spread of antimicrobial-resistant bacteria on a global scale. As the ongoing pandemic takes global attention, bacterial infections with antibiotic resistance are another ongoing pandemic that often goes unnoticed and will be the next real threat to humankind. Here, the effects of food-grade disinfectant overuse on the global emergence and spread of antimicrobial-resistant bacteria were reviewed. It was found that longtime exposure to the most common food-grade disinfectants promoted resistance to clinically important antibiotics in pathogenic bacteria, namely cross-resistance. Currently, the use of disinfectants is largely unregulated. The mechanisms of cross-resistance are regulated by intrinsic molecular mechanisms including efflux pumps, DNA repair system, modification of the molecular target, and metabolic adaptation. Cross-resistance can also be acquired by mobile genetic elements. Long-term exposure to disinfectants has an impact on the dissemination of antimicrobial resistance in soil, plants, animals, water, and human gut environments.

Multidrug-Resistant Biofilms (MDR): Main Mechanisms of Tolerance and Resistance in the Food Supply Chain

Biofilms are mono- or multispecies microbial communities enclosed in an extracellular matrix (EPS). They have high potential for dissemination and are difficult to remove. In addition, biofilms formed by multidrug-resistant strains (MDRs) are even more aggravated if we consider antimicrobial resistance (AMR) as an important public health issue. Quorum sensing (QS) and horizontal gene transfer (HGT) are mechanisms that significantly contribute to the recalcitrance (resistance and tolerance) of biofilms, making them more robust and resistant to conventional sanitation methods. These mechanisms coordinate different strategies involved in AMR, such as activation of a quiescent state of the cells, moderate increase in the expression of the efflux pump, decrease in the membrane potential, antimicrobial inactivation, and modification of the antimicrobial target and the architecture of the EPS matrix itself. There are few studies investigating the impact of the use of inhibitors on the mechanisms of recalcitrance and its impact on the microbiome. Therefore, more studies to elucidate the effect and applications of these methods in the food production chain and the possible combination with antimicrobials to establish new strategies to control MDR biofilms are needed.

Making sense of drug-efflux transporters in the physiological environment

Bacterial drug-efflux transporters act synergistically with diffusion barriers of cellular membranes and other resistance mechanisms to protect cells from antibiotics and toxic metabolites. Their critical roles in clinical antibiotic and multidrug resistance are well established. In addition, a large body of evidence has been accumulated in support of their important contributions to bacterial growth and proliferation during infections. However, how these diverse functions of drug transporters are integrated at the level of bacterial cell physiology remains unclear. This opinion briefly summarizes the current understanding of substrate specificities and physiological roles of drug-efflux pumps from Resistance-Nodulation-Division (RND) superfamily of proteins in two ESKAPE pathogens Pseudomonas aeruginosa and Acinetobacter baumannii. Based on the analysis of phenotypic and transcriptomic studies in vitro and in vivo, we propose that RND pumps of Gram-negative bacteria fall into three categories: constitutively expressed, regulated, and silent. These three categories of efflux pumps participate in different physiological programs, which are not involved in the central metabolism and bacterial growth.

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.

Efflux Pump Mediated Antimicrobial Resistance by Staphylococci in Health-Related Environments: Challenges and the Quest for Inhibition

The increasing emergence of antimicrobial resistance in staphylococcal bacteria is a major health threat worldwide due to significant morbidity and mortality resulting from their associated hospital- or community-acquired infections. Dramatic decrease in the discovery of new antibiotics from the pharmaceutical industry coupled with increased use of sanitisers and disinfectants due to the ongoing COVID-19 pandemic can further aggravate the problem of antimicrobial resistance. Staphylococci utilise multiple mechanisms to circumvent the effects of antimicrobials. One of these resistance mechanisms is the export of antimicrobial agents through the activity of membrane-embedded multidrug efflux pump proteins. The use of efflux pump inhibitors in combination with currently approved antimicrobials is a promising strategy to potentiate their clinical efficacy against resistant strains of staphylococci, and simultaneously reduce the selection of resistant mutants. This review presents an overview of the current knowledge of staphylococcal efflux pumps, discusses their clinical impact, and summarises compounds found in the last decade from plant and synthetic origin that have the potential to be used as adjuvants to antibiotic therapy against multidrug resistant staphylococci. Critically, future high-resolution structures of staphylococcal efflux pumps could aid in design and development of safer, more target-specific and highly potent efflux pump inhibitors to progress into clinical use.