Acinetobacter baumannii is a hospital-associated pathogen with unique fatty acid homeostasis features. This includes a reliance on desaturases for proliferation, due to an inability to generate unsaturated fatty acids during the synthesis cycles. However, there are various unexplained gaps in A. baumannii fatty acid homeostasis, such as the desaturation of de novo synthesized fatty acids. We identified a conserved desaturase (DesC) with a rare structural feature that may have roles in coordinating fatty acids with acyl carrier protein conjugants. We showed that DesC can generate fatty acids with cis double bonds in the delta-9 position. Profiling of A. baumannii fatty acids and mRNA transcripts emphasized its significance during fatty acid synthesis. DesC was found to be most critical in mouse niches where A. baumannii relies on fatty acid synthesis. This work has contributed to our understanding of core metabolic features that are key to the disease potential of A. baumannii.

Antimicrobial resistance is a growing threat to human health and agriculture. Sulfur-containing compounds and elemental sulfur have a long history of use as antimicrobials, but challenges related to solubility and formulation have limited their broad application. Recent advances in sulfur polymer chemistry have enabled the development of novel sulfur-rich materials with antimicrobial activity. However, most of these materials are water-insoluble, limiting their use in biomedical and agricultural applications. Here, we report the synthesis of a linear poly(trisulfide) via photochemical ring-opening polymerization of a cyclic trisulfide monomer bearing a carboxylic acid. Deprotonation of the carboxylic acid renders the poly(trisulfide) fully water soluble, with concomitant chain scission via S-S cleavage. The resulting poly(trisulfide) oligomers exhibited potent antifungal activity against Candida albicans (MIC < 8 µg/mL), and stronger inhibition of the Gram-positive bacterium Staphylococcus aureus (MIC = 16 µg/mL) compared to the Gram-negative Escherichia coli (MIC > 512 µg/mL). In control experiments, the monomer did not show potent antifungal or antibacterial activity. This work demonstrates a simple and controllable synthesis of a poly(trisulfide) species that serves as a prodrug: treatment with NaOH converts the polymer to water-soluble oligomers with antimicrobial activity. This approach is a new direction for biological applications of sulfur polymers and a new strategy to address antimicrobial resistance.

Microbiome-mediated impacts of global change on human metabolic health remain understudied. Type 2 diabetes (T2D) is shaped by nutrition, host and environmental factors, with rapidly increasing global prevalence. Soil microbiomes shift with ecosystem degradation and may influence human metabolism through altering food quality and gut microbiomes, including metabolite exposures without requiring colonization. Here, we investigated functional overlaps between soil microbiomes across ecosystem degradation gradients (USA, Australia) and gut microbiomes in T2D versus normal health (Sweden, China). We developed a method to translate metagenomic functional pathways to potential metabolism of biochemical compounds. In silico trend analyses revealed consistent shifts relevant to energy harvesting and management. Both T2D gut microbiomes and degraded soil microbiomes exhibited increased potential metabolism for sugars and decreased potential metabolism for lignin and monomethyl branched-chain fatty acids. Our findings suggest ecosystem degradation may contribute to T2D pathogenesis through nutrient-depleted food and/or adverse shaping of gut microbiome functional capacities.

25 September, 2024. Research Square has withdrawn this preprint as it was requested after the work was already published at a peer reviewed journal, which is in conflict with our editorial policy regarding postprints.

SUMMARY The lipid homeostasis pathways of bacterial pathogens have been studied comprehensively for their biochemical functionality. However, new and refined technologies have supported the interrogation of bacterial lipid and fatty acid homeostasis mechanisms in more complex environments, such as mammalian host niches. In particular, emerging findings on the breadth and depth of host fatty acid uptake have demonstrated their importance beyond merely fatty acid utilization for membrane synthesis, as they can contribute to virulence factor regulation, pathogenesis, and group-based behaviors. Lipid homeostasis is also intertwined with other metabolic and physiological processes in the bacterial cells, which appear to be largely unique per species, but overarching themes can be derived. This review combines the latest biochemical and structural findings and places these in the context of bacterial pathogenesis, thereby shedding light on the far-reaching implications of lipid homeostasis on bacterial success.

Multidrug-resistant bacterial pathogens like vancomycin-resistant Enterococcus faecium (VREfm) are a critical threat to human health1. Daptomycin is a last-resort antibiotic for VREfm infections with a novel mode of action2, but for which resistance has been widely reported but is unexplained. Here we show that rifaximin, an unrelated antibiotic used prophylactically to prevent hepatic encephalopathy in patients with liver disease3, causes cross-resistance to daptomycin in VREfm. Amino acid changes arising within the bacterial RNA polymerase in response to rifaximin exposure cause upregulation of a previously uncharacterized operon (prdRAB) that leads to cell membrane remodelling and cross-resistance to daptomycin through reduced binding of the antibiotic. VREfm with these mutations are spread globally, making this a major mechanism of resistance. Rifaximin has been considered ‘low risk’ for the development of antibiotic resistance. Our study shows that this assumption is flawed and that widespread rifaximin use, particularly in patients with liver cirrhosis, may be compromising the clinical use of daptomycin, a major last-resort intervention for multidrug-resistant pathogens. These findings demonstrate how unanticipated antibiotic cross-resistance can undermine global strategies designed to preserve the clinical use of critical antibiotics. Rifaximin use, particularly in patients with liver cirrhosis, may be compromising the clinical use of daptomycin.

Klebsiella pneumoniae is consistently ranked among the most problematic multidrug-resistant bacterial pathogens in healthcare systems. Developing novel treatments requires a better understanding of its interaction with the host environment. Although bacteria can synthesize fatty acids, emerging findings suggest a potential preference for their acquisition from the host. Fatty acid profiling of mice revealed a dramatic increase in the level of hepatic lipids during K. pneumoniae infection. The K. pneumoniae fatty acid composition and uptake capabilities were found to be largely clonally conserved. Correlations between fatty acid uptake, outer membrane vesicle production, and cell permeability were observed, but this did not translate to alterations in cell morphology, capsule production, or antimicrobial susceptibility. Importantly, hyper-capsulation did not prevent the uptake of hydrophobic fatty acids. The uptake of a saturated fatty acid by hypervirulent K. pneumoniae isolate may provide insights into the clinical association of K. pneumoniae infections with hyperlipidemic and/or obese individuals.

The dissemination of multi-drug resistant Acinetobacter baumannii threatens global healthcare systems and necessitates the development of novel therapeutic options. The Gram-negative bacterial cell envelope provides a first defensive barrier against antimicrobial assault. Essential components of this multi-layered complex are the phospholipid-rich membranes. Phosphatidylglycerol phosphate (PGP) phosphatases are responsible for a key step in the biosynthesis of a major phospholipid species, phosphatidylglycerol (PG), but these enzymes have also been implicated in the biogenesis of other cell envelope components. Our bioinformatics analyses identified two putative PGP candidates in the A. baumannii genome, PgpA and PgpB. Phospholipid analyses of isogenic pgpA mutants in two distinct A. baumannii strains revealed a shift in the desaturation levels of phosphatidylethanolamine (PE) phospholipid species, possibly due to the activation of the phospholipid desaturase DesA. We also investigated the impact of the inner membrane phosphatases on other cell envelope components, which revealed a role of PgpB in the maintenance of the A. baumannii peptidoglycan layer, and consequently carbapenem resistance. Collectively, this work provides novel insights into the roles of PGP phosphatases on the global lipidomic landscape of A. baumannii and their interconnectivity with the biogenesis of other cell envelope components. The non-essentiality of these candidates exemplifies metabolic versatility of A. baumannii, which is believed to be key to its success as global pathogen.

Gram-negative bacteria such as Acinetobacter baumannii sequester host lipids from the site of infection for incorporation into lipid synthesis pathways, altering the membrane lipidome. Changes in membrane composition from the incorporation of host-derived polyunsaturated fatty acids (PUFAs) help restore sensitivity to antimicrobials in several species of Gram-negative bacteria. Using coarse-grained simulations based on lipidomic data of A. baumannii inner membrane collected under three different growth conditions, we show PUFA-incorporation alters membrane biophysical properties, increasing the phase separation between ordered and disordered lipid domains resulting in thinner, less ordered membranes. We show that the changes in A. baumannii membrane biophysical properties on the incorporation of PUFA-containing lipids alter the conformational cycling of RND multidrug efflux pumps and restore sensitivity to some antimicrobials. Finally, we examine the interaction of antimicrobial peptides (AMP) with the simulated A. baumannii membranes to identify the effect of lipid saturation and alterations in membrane properties has on AMP-induced membrane disruption.

ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in the developing world, predominantly affecting the pediatric age group, with malnutrition being a common co-morbidity. Lipids are key nutritional components, and their abundance and composition are likely to influence the pathobiology of S. flexneri. S. flexneri expresses a plethora of polysaccharides on its cell surface, but how this hydrophilic surface layer influences S. flexneri interaction with hydrophobic host molecules, such as fatty acids and lipids, is not well understood. In this study, we sought to interrogate how this hydrophilic layer affects S. flexneri during its intracellular lifestyle and how lipid homeostasis changes in both the host and pathogen. We characterized changes in S. flexneri cell envelope composition and surface-associated glycolipids, in particular lipopolysaccharide (LPS), during different phases of infection. We found that a dynamic capacity in LPS expression is necessary for the pathogen to manage delicate interaction with host fatty acids and maintain optimum virulence. Additionally, through confocal immunofluorescent microscopy, coupled with transcriptional and lipid analyses, we demonstrate that S. flexneri induces major host lipid remodeling during infection, by hijacking host lipid homeostasis pathways to its own benefit. Finally, this study suggests that fatty acid supplementation can influence the persistence and magnitude of S. flexneri infection. This work provides novel insights into the potential roles of balanced and sufficient dietary fatty acid intake in protection against gastroenteric pathogen infection. IMPORTANCE Bacterial pathogens have vastly distinct sites that they inhabit during infection. This requires adaptation due to changes in nutrient availability and antimicrobial stress. The bacterial surface is a primary barrier, and here, we show that the bacterial pathogen Shigella flexneri increases its surface decorations when it transitions to an intracellular lifestyle. We also observed changes in bacterial and host cell fatty acid homeostasis. Specifically, intracellular S. flexneri increased the expression of their fatty acid degradation pathway, while the host cell lipid pool was significantly depleted. Importantly, bacterial proliferation could be inhibited by fatty acid supplementation of host cells, thereby providing novel insights into the possible link between human malnutrition and susceptibility to S. flexneri .

Shigella flexneri is theprimarycausative agent of worldwide shigellosis. As the pathogen transversesthe distinct niches of the gastrointestinal tract it necessitatesdynamic adaptation strategies to mitigate host antimicrobials suchas dietary fatty acids (FAs) and the bile salt, deoxycholate (DOC).This study investigates the dynamics of the S. flexneri cell envelope, by interrogating adaptations following FA or DOCexposure. We deciphered the effects of FAs and DOC on bacterial membranefatty acid and lipopolysaccharide (LPS) compositions. We identifiednovel LPS-based strategies by the pathogen to support resistance tothese host compounds. In particular, expression of S. flexneri very-long O antigen (VL-Oag) LPS wasfound to play a central role in stress mitigation, as VL-Oag protectsagainst antimicrobial FAs, but its presence rendered S. flexneri susceptible to DOC stress. Collectively,this work underpins the importance for S. flexneri to maintain appropriate regulation of cell envelope constituents,in particular VL-Oag LPS, to adequately adapt to diverse stressesduring infection.

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.

AIMS:This study examined the origins and evolution of the AdeABC, AdeFGH and AdeIJK efflux pumps in the Acinetobacter genus, including human and animal pathogens and species from non-clinical environments.METHODS:Comparative genome analyses were performed using the reference sequences for 70 Acinetobacter species to identify putative orthologs of AdeABC, AdeFGH and AdeIJK and their regulators. Sequence similarities and the genomic locations of coding sequences were correlated with phylogeny to infer modes of evolution. Intraspecies variation was assessed in species of interest using up to 236 complete genome sequences. Mutants overproducing adeIJK in A. baylyi were examined to identify regulators of this system in a non A. baumannii species.RESULTS:The results indicate that adeIJK has been a stable part of Acinetobacter genomes since the genesis of this genus, whereas adeABC and adeFGH were carried by less than half of the species, but showed some lineage specificity. The organisation and local genetic contexts of adeABC loci were particularly variable to the sub-species level, suggesting frequent recombination. Cognate regulatory systems were almost always found in the genomes of species encoding pumps. Mutations in adeN, which encodes a repressor of adeIJK, were selected by antibiotic exposure in A. baylyi, similar to previous findings in pathogenic lineages.CONCLUSIONS:The multidrug efflux capacity of clinical Acinetobacter strains stems from accessory and core genetic features. AdeIJK is likely to have ancient core function(s) that have promoted its maintenance, whereas recent antibiotic use may be driving the evolution of the AdeABC pump.

Shigella flexneri implements the Wzy-dependent pathway to biosynthesize the O antigen (Oag) component of its surface lipopolysaccharide. The inner membrane polymerase Wzy(SF) catalyzes the repeat addition of undecaprenol-diphosphate-linked Oag (Und-PP-RUs) to produce a polysaccharide, the length of which is tightly regulated by two competing copolymerase proteins, Wzz(SF) (short-type Oag; 10 to 17 RUs) and Wzz(pHS-2) (very-long-type Oag; >90 RUs). The nature of the interaction between Wzy(SF) and Wzz(SF)/Wzz(pHS-2) in Oag polymerization remains poorly characterized, with the majority of the literature characterizing the individual protein constituents of the Wzy-dependent pathway. Here, we report instead a major investigation into the specific binding interactions of Wzy(SF) with its copolymerase counterparts. For the first time, a region of Wzy(S)(F) that forms a unique binding site for Wzz(pHS-2) has been identified. Specifically, this work has elucidated key Wzy(SF) moieties at the N- and C-terminal domains (NTD and CTD) that form an intramolecular pocket modulating the Wzz(pHS-2) interaction. Novel copurification data high-light that disruption of residues within this NTD-CTD pocket impairs the interaction with Wzz(pHS-2) without affecting Wzz(S)(F) binding, thereby specifically disrupting polymerization of longer polysaccharide chains. This study provides a novel understanding of the molecular interaction of Wzy(SF) with Wzz(SF)/Wzz(pHS-2) in the Wzy-dependent pathway and, furthermore, detects the Wzy/Wzz/Und-PP-Oag complex for the first time. Beyond S. flexneri, this work may be extended to provide insight into the interactions between protein homologues expressed by related species, especially members of Enterobacteriaceae, that produce dual Oag chain length determinants. IMPORTANCE Shigella flexneri is a pathogen causing significant morbidity and mortality, predominantly devastating the pediatric age group in developing countries. A major virulence factor contributing to S. flexneri pathogenesis is its surface lipopolysaccharide, which is comprised of three domains: lipid A, core oligosaccharide, and O antigen (Oag). The Wzy-dependent pathway is the most common biosynthetic mechanism implemented for Oag biosynthesis by Gram-negative bacteria, including S. flexneri. The nature of the interaction between the polymerase, Wzy(S)(F), and the polysaccharide copolymerases, Wzz(S)(F) and Wzz(p)(HS-2), in Oag polymerization is poorly characterized. This study investigates the molecular interplay between Wzy(SF) and its copolymerases, deciphering key interactions in the Wzy-dependent pathway that may be extended beyond S. flexneri, providing insight into Oag biosynthesis in Gram-negative bacteria.

Limited therapeutic options dictate the need for new classes of antimicrobials active against carbapenem-resistant Acinetobacter baumannii . Presented data confirm and extend penicillin binding protein 7/8 (PBP 7/8) as a high-value target in the CR A. baumannii strain HUMC1.

Metal ions are required by all organisms for the chemical processes that support life. However, in excess they can also exert toxicity within biological systems. During infection, bacterial pathogens such as Streptococcus pneumoniae are exposed to host-imposed metal intoxication, where the toxic properties of metals, such as copper, are exploited to aid in microbial clearance. However, previous studies investigating the antimicrobial efficacy of copper in vivo have reported variable findings. Here, we use a highly copper-sensitive strain of S. pneumoniae, lacking both copper efflux and intracellular copper buffering by glutathione, to investigate how copper stress is managed and where it is encountered during infection. We show that this strain exhibits highly dysregulated copper homeostasis, leading to the attenuation of growth and hyperaccumulation of copper in vitro. In a murine infection model, whole-tissue copper quantitation and elemental bioimaging of the murine lung revealed that infection with S. pneumoniae resulted in increased copper abundance in specific tissues, with the formation of spatially discrete copper hot spots throughout the lung. While the increased copper was able to reduce the viability of the highly copper-sensitive strain in a pneumonia model, copper levels in professional phagocytes and in a bacteremic model were insufficient to prosecute bacterial clearance. Collectively, this study reveals that host copper is redistributed to sites of infection and can impact bacterial viability in a hypersusceptible strain. However, in wildtype S. pneumoniae, the concerted actions of the copper homeostatic mechanisms are sufficient to facilitate continued viability and virulence of the pathogen. IMPORTANCE Streptococcus pneumoniae (the pneumococcus) is one of the world's foremost bacterial pathogens. Treatment of both localized and systemic pneumococcal infection is becoming complicated by increasing rates of multidrug resistance globally. Copper is a potent antimicrobial agent used by the mammalian immune system in the defense against bacterial pathogens. However, unlike other bacterial species, this copper stress is unable to prosecute pneumococcal clearance. This study determines how the mammalian host inflicts copper stress on S. pneumoniae and the bacterial copper tolerance mechanisms that contribute to maintenance of viability and virulence in vitro and in vivo. This work has provided insight into the chemical biology of the hostpneumococcal interaction and identified a potential avenue for novel antimicrobial development.

Streptococcus pneumoniae is the primary cause of community-acquired bacterial pneumonia with rates of penicillin and multidrug-resistance exceeding 80% and 40%, respectively. The innate immune response generates a variety of antimicrobial agents to control infection, including zinc stress. Here, we characterize the impact of zinc intoxication on S. pneumoniae, observing disruptions in central carbon metabolism, lipid biogenesis, and peptidoglycan biosynthesis. Characterization of the pivotal peptidoglycan biosynthetic enzyme GlmU indicates a sensitivity to zinc inhibition. Disruption of the sole zinc efflux pathway, czcD, renders S. pneumoniae highly susceptible to β-lactam antibiotics. To dysregulate zinc homeostasis in the wild-type strain, we investigated the safe-for-human-use ionophore 5,7-dichloro-2-[(dimethylamino)methyl]quinolin-8-ol (PBT2). PBT2 rendered wild-type S. pneumoniae strains sensitive to a range of antibiotics. Using an invasive ampicillin-resistant strain, we demonstrate in a murine pneumonia infection model the efficacy of PBT2 + ampicillin treatment. These findings present a therapeutic modality to break antibiotic resistance in multidrug-resistant S. pneumoniae.

Shigella flexneri utilises the Wzy-dependent pathway for the production of a plethora of complex polysaccharides, including the lipopolysaccharide O-antigen (Oag) component. The inner membrane protein WzySF polymerises Oag repeat units, whilst two co-polymerase proteins, WzzSF and WzzpHS-2, together interact with WzySF to regulate production of short- (S-Oag) and very long- (VL-Oag) Oag modal lengths, respectively. The 2D arrangement of WzySF transmembrane and soluble regions has been previously deciphered, however, attaining information on the 3D structural and conformational arrangement of WzySF, or any homologue, has proven difficult. For the first time, the current study detected insights into the in situ WzySF arrangement. In vitro assays using thiol-reactive PEG-maleimide were used to probe WzySF conformation, which additionally detected novel, unique conformational changes in response to interaction with intrinsic factors, including WzzSF and WzzpHS-2, and extrinsic factors, such as temperature. Site-directed mutagenesis of WzySF cysteine residues revealed the presence of a putative intramolecular disulphide bond, between cysteine moieties 13 and 60. Subsequent analyses highlighted both the structural and functional importance of WzySF cysteines. Substitution of WzySF cysteine residues significantly decreased biosynthesis of the VL-Oag modal length, without disruption to S-Oag production. This phenotype was corroborated in the absence of co-polymerase competition for WzySF interaction. These data suggest WzySF cysteine substitutions directly impair the interaction between Wzy/WzzpHS-2, without altering the Wzy/WzzSF interplay, and in combination with structural data, we propose that the N- and C-termini of WzySF are arranged in close proximity, and together may form the unique WzzpHS-2 interaction site.

Here, we report the 7.7-Mbp genome sequence of Rhodococcus sp. strain 9, which was isolated from Australian groundwater contaminated with phenols and trichloroethylene. This strain has previously been shown to efficiently degrade p -nitrophenol and high-molecular-weight polycyclic aromatic hydrocarbons (PAHs).

Exogenous polyunsaturated fatty acids (PUFAs) are readily incorporated into the synthesis pathways of A. baumannii membrane phospholipids, where they contribute to reduced bacterial fitness and increased antimicrobial susceptibility. Here we examine the impact of PUFA membrane modification on membrane organisation and biophysical properties using coarse grained MARTINI simulations of chemically representative membrane models developed from mass-spectrometry datasets of an untreated, arachidonic acid (AA) treated and docosahexaenoic acid (DHA) treated A. baumannii membranes. Enzymatic integration of AA or DHA into phospholipids of the A. baumannii membrane resulted in modulation of membrane biophysical properties. Membrane thickness decreased slightly following PUFA treatment, concomitant with changes in the lateral area per lipid of each lipid headgroup class. PUFA treatment resulted in a decrease in membrane ordering and an increase in lipid lateral diffusion. Changes in lateral membrane organisation were observed in the PUFA treated membranes, with a concurrent increase in ordered cardiolipin domains and disordered PUFA-containing domains. Notably, separation between ordered and disordered domains was enhanced and was more pronounced for DHA relative to AA, providing a possible mechanism for greater antimicrobial action of DHA relative to AA observed experimentally. Furthermore, the membrane active antimicrobial, pentamidine, preferentially adsorbs to cardiolipin domains of the A. baumannii model membranes. This interaction, and membrane penetration of pentamidine, was enhanced following PUFA treatment. Cumulatively, this work explores the wide-ranging effects of PUFA incorporation on the A. baumannii membrane and provides a molecular basis for bacterial inner membrane disruption by PUFAs.