Characterization of Acinetobacter baumannii Copper Resistance Reveals a Role in Virulence

Isolation and crystallization of copper resistance protein B (CopB) from Acinetobacter baumannii

Acinetobacter baumannii (A. baumannii) is an opportunistic, Gram-negative human pathogen, which is predominantly found in hospital patients. Its antimicrobial resistance is escalating, leading to less efficient treatments, and an increasing interest in identifying new therapeutic drugs. Metals as antimicrobials are vital in healthcare and agriculture, and copper-containing surfaces are known to reduce microbial counts, also in clinical settings. Indeed, copper (Cu) is an essential element required for survival in all organisms from bacteria to humans, but nevertheless elevated levels are highly toxic for cells. Through different regulatory mechanisms, cells maintain Cu homeostasis, and ion channels and transporters are critical in this process. Precise understanding of such ion transport requires insight into the protein structures of the involved proteins, which will also provide information important for applied sciences. Considering the medical significance of A. baumannii and the possibility to exploit Cu to handle such infections, channels and transporters represent appealing targets. Here we approached the putative outer membrane CopB (Copper resistance protein B) from A. baumannii that is postulated to conduct Cu, with characterization of its structure and function as well as to enable rational drug-design. To this end, we demonstrate in this work procedures to produce purified sample and to recover diffracting protein crystals of CopB. The protein was overproduced in E. coli and membrane extracted in a range of detergents. The solubilized protein was subjected to crystallization, which yielded hits that scatter X-rays to low resolution. Our findings have the potential to pave the way for subsequent drug discovery.

Characterization of the diversity of type IV secretion system-encoding plasmids in Acinetobacter

The multi-drug resistant pathogen Acinetobacter baumannii has gained global attention as an important clinical challenge. Owing to its ability to survive on surfaces, its capacity for horizontal gene transfer, and its resistance to front-line antibiotics, A. baumannii has established itself as a successful pathogen. Bacterial conjugation is a central mechanism for pathogen evolution. The epidemic multidrug-resistant A. baumannii ACICU harbours a plasmid encoding a Type IV Secretion System (T4SS) with homology to the E. coli F-plasmid, and plasmids with homologous gene clusters have been identified in several A. baumannii sequence types. However the genetic and host strain diversity, global distribution, and functional ability of this group of plasmids is not fully understood. Using systematic analysis, we show that pACICU2 belongs to a group of almost 120 T4SS-encoding plasmids within four different species of Acinetobacter and one strain of Klebsiella pneumoniae from human and environmental origin, and globally distributed across 20 countries spanning 4 continents. Genetic diversity was observed both outside and within the T4SS-encoding cluster, and 47% of plasmids harboured resistance determinants, with two plasmids harbouring eleven. Conjugation studies with an extensively drug-resistant (XDR) strain showed that the XDR plasmid could be successfully transferred to a more divergent A. baumanii, and transconjugants exhibited the resistance phenotype of the plasmid. Collectively, this demonstrates that these T4SS-encoding plasmids are globally distributed and more widespread among Acinetobacter than previously thought, and that they represent an important potential reservoir for future clinical concern.

Physiological Roles of an Acinetobacter-specific σ Factor

The Gram-negative pathogen Acinetobacter baumannii is considered an "urgent threat" to human health due to its propensity to become antibiotic resistant. Understanding the distinct regulatory paradigms used by A. baumannii to mitigate cellular stresses may uncover new therapeutic targets. Many γ-proteobacteria use the extracytoplasmic function (ECF) σ factor, RpoE, to invoke envelope homeostasis networks in response to stress. Acinetobacter species contain the poorly characterized ECF "SigAb;" however, it is unclear if SigAb has the same physiological role as RpoE. Here, we show that SigAb is a metal stress-responsive ECF that appears unique to Acinetobacter species and distinct from RpoE. We combine promoter mutagenesis, motif scanning, and ChIP-seq to define the direct SigAb regulon, which consists of sigAb itself, the stringent response mediator, relA, and the uncharacterized small RNA, "sabS." However, RNA-seq of strains overexpressing SigAb revealed a large, indirect regulon containing hundreds of genes. Metal resistance genes are key elements of the indirect regulon, as CRISPRi knockdown of sigAb or sabS resulted in increased copper sensitivity and excess copper induced SigAb-dependent transcription. Further, we found that two uncharacterized genes in the sigAb operon, "aabA" and "aabB", have anti-SigAb activity. Finally, employing a targeted Tn-seq approach that uses CRISPR-associated transposons, we show that sigAb, aabA, and aabB are important for fitness even during optimal growth conditions. Our work reveals new physiological roles for SigAb and SabS, provides a novel approach for assessing gene fitness, and highlights the distinct regulatory architecture of A. baumannii.

Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii

Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo-EM reconstructions of Acinetobacter baumannii TolQ in apo and TolR- bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a trans-membrane funnel leading towards a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton non-permeable stance, characterized by the TolQ pentamer's flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers' interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope.

Teaser

Apo TolQ and TolQ-TolR structures depict structural rearrangements required for cell envelope organization in bacterial cell division.

Complete genome analysis of copper resistant bacteria Pseudoalteromonas sp. CuT4-3 isolated from a deep-sea hydrothermal vent

Pseudoalteromonas sp. CuT4-3, a copper resistant bacterium, was isolated from deep-sea hydrothermal sulfides on the Southwest Indian Ridge (SWIR), is an aerobic, mesophilic and rod-shaped bacterium belonging to the family Pseudoalteromonadaceae (class Gammaproteobacteria, order Alteromonadales). In this study, we present the complete genome sequence of strain CuT4-3, which consists of a single circular chromosome comprising 3,660,538 nucleotides with 41.05% G + C content and two circular plasmids comprising 792,064 nucleotides with 40.36% G + C content and 65,436 nucleotides with 41.50% G + C content. In total, 4078 protein coding genes, 105 tRNA genes, and 25 rRNA genes were obtained. Genomic analysis of strain CuT4-3 identified numerous genes related to heavy metal resistance (especially copper) and EPS production. The genome of strain CuT4-3 will be helpful for further understanding of its adaptive strategies, particularly its ability to resist heavy metal, in the deep-sea hydrothermal vent environment.

Development and Evaluation of an Immunoinformatics-Based Multi-Peptide Vaccine against Acinetobacter baumannii Infection

Multi-drug-resistant (MDR) Acinetobacter baumannii is an opportunistic pathogen associated with hospital-acquired infections. Due to its environmental persistence, virulence, and limited treatment options, this organism causes both increased patient mortality and incurred healthcare costs. Thus, prophylactic vaccination could be ideal for intervention against MDR Acinetobacter infection in susceptible populations. In this study, we employed immunoinformatics to identify peptides containing both putative B- and T-cell epitopes from proteins associated with A. baumannii pathogenesis. A novel Acinetobacter Multi-Epitope Vaccine (AMEV2) was constructed using an A. baumannii thioredoxin A (TrxA) leading protein sequence followed by five identified peptide antigens. Antisera from A. baumannii infected mice demonstrated reactivity to rAMEV2, and subcutaneous immunization of mice with rAMEV2 produced high antibody titer against the construct as well as peptide components. Immunization results in increased frequency of IL-4-secreting splenocytes indicative of a Th2 response. AMEV2-immunized mice were protected against intranasal challenge with a hypervirulent strain of A. baumannii and demonstrated reduced bacterial burden at 48 h. In contrast, all mock vaccinated mice succumbed to infection within 3 days. Results presented here provide insight into the effectiveness of immunoinformatic-based vaccine design and its potential as an effective strategy to combat the rise of MDR pathogens.

Deciphering the structure of a multi-drug resistant Acinetobacter baumannii short-chain dehydrogenase reductase

The rapidly increasing threat of multi-drug-resistant Acinetobacter baumannii infections globally, encompassing a range of clinical manifestations from skin and soft tissue infections to life-threatening conditions like meningitis and pneumonia, underscores an urgent need for novel therapeutic strategies. These infections, prevalent in both hospital and community settings, present a formidable challenge to the healthcare system due to the bacterium's widespread nature and dwindling effective treatment options. Against this backdrop, the exploration of bacterial short-chain dehydrogenase reductases (SDRs) emerges as a promising avenue. These enzymes play pivotal roles in various critical bacterial processes, including fatty acid synthesis, homeostasis, metabolism, and contributing to drug resistance mechanisms. In this study, we present the first examination of the X-ray crystallographic structure of an uncharacterized SDR enzyme from A. baumannii. The tertiary structure of this SDR is distinguished by a central parallel β-sheet, consisting of seven strands, which is flanked by eight α-helices. This configuration exhibits structural parallels with other enzymes in the SDR family, underscoring a conserved architectural theme within this enzyme class. Despite the current ambiguity regarding the enzyme's natural substrate, the importance of many SDR enzymes as targets in anti-bacterial agent design is well-established. Therefore, the detailed structural insights provided in this study open new pathways for the in-silico design of therapeutic agents. By offering a structural blueprint, our findings may provide a platform for future research aimed at developing targeted treatments against this and other multi-drug-resistant infections.

DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

Introduction

Acinetobacter baumannii strain 17978 is an opportunistic pathogen possessing a DNA damage response (DDR) in which multiple error-prone polymerase genes are co-repressed by a UmuD homolog, UmuDAb, and the small Acinetobacter-specific protein DdrR. Additionally, these regulators coactivate nine other genes. We identified the DNA damage-inducible transcriptome for wildtype, umuDAb, and recA strains, and later established the ddrR DDR transcriptome. However, the ATCC 17978 reference genome had several assembly errors and lacked the 44 kb virulence locus, AbaAL44, that is present in the strain 17978 UN.

Methods

For this project, we combined our earlier single-end read RNAseq data with the ddrR paired-end reads and aligned these data to the improved 17978 UN genome assembly that resembled our laboratory strain, 17978 JH.

Results

New DESeq2 analyses verified previous differentially expressed genes (DEGs) but also found 339 genes in 17978 JH that were not annotated or physically present in the older genome assembly. Sixty-three were differentially expressed after DNA damage, and 182 had differential basal expression when comparing umuDAb, ddrR, or recA strains to wildtype, with 94 genes' expression unchanged. This work identified and characterized the 55 gene DNA damage-repressible transcriptome, 98% of which required either umuDAb or ddrR for repression. Two-thirds of these DEGs required both regulators. We also identified 110 genes repressed only in the ddrR strain, ~50% of which were due to increased basal expression levels. Basal gene expression in the ddrR mutant was further dysregulated independent of the DDR. Over 800 genes were upregulated, and over 1200 genes were downregulated compared to wildtype expression. Half of A. baumannii's essential genes were upregulated in the ddrR strain, including cell division genes, and two-thirds of these were downregulated in the umuDAb strain.

Discussion

The ddrR mutant upregulated genes enriched in translation, RNA metabolism, protein metabolism, AA/FA/cell-structure synthesis, and transport, while downregulating genes enriched in quorum sensing, biofilm production, secretion systems, pilus production, cell adhesion, and aromatics and chlorine degradation. Our data underscore the need for accurate and appropriately matched genome assemblies and indicate that ddrR affects approximately 60% of the genome, rendering it a potential target for Acinetobacter baumannii infection treatment.

Comparative genomic analysis of two Arctic Pseudomonas strains reveals insights into the aerobic denitrification in cold environments

BACKGROUND

Biological denitrification has been commonly adopted for the removal of nitrogen from sewage effluents. However, due to the low temperature during winter, microorganisms in the wastewater biological treatment unit usually encounter problems such as slow cell growth and low enzymatic efficiency. Hence, the isolation and screening of cold-tolerant aerobic denitrifying bacteria (ADB) have recently drawn attention. In our previous study, two Pseudomonas strains PMCC200344 and PMCC200367 isolated from Arctic soil demonstrated strong denitrification ability at low temperatures. The two Arctic strains show potential for biological nitrogen removal from sewage in cold environments. However, the genome sequences of these two organisms have not been reported thus far.

RESULTS

Here, the basic characteristics and genetic diversity of strains PMCC200344 and PMCC200367 were described, together with the complete genomes and comparative genomic results. The genome of Pseudomonas sp. PMCC200344 was composed of a circular chromosome of 6,478,166 bp with a G + C content of 58.60% and contained a total of 5,853 genes. The genome of Pseudomonas sp. PMCC200367 was composed of a circular chromosome of 6,360,061 bp with a G + C content of 58.68% and contained 5,801 genes. Not only prophages but also genomic islands were identified in the two Pseudomonas strains. No plasmids were observed. All genes of a complete set of denitrification pathways as well as various putative cold adaptation and heavy metal resistance genes in the genomes were identified and analyzed. These genes were usually detected on genomic islands in bacterial genomes.

CONCLUSIONS

These analytical results provide insights into the genomic basis of microbial denitrification in cold environments, indicating the potential of Arctic Pseudomonas strains in nitrogen removal from sewage effluents at low temperatures.

Genetic Basis of Acinetobacter sp. K1 Adaptation Mechanisms to Extreme Environmental Conditions

Anthropogenic pollution often leads to the generation of technosols, technogenic soils with inhospitable conditions for all living organisms including microbiota. Aluminum production near Ziar nad Hronom (Slovakia) resulted in the creation of a highly alkaline and heavy-metal-rich brown mud landfill, from which a bacterial strain of a likely new species of the genus Acinetobacter, Acinetobacter sp. K1, was isolated. The whole-genome sequence analysis of this strain confirmed the presence of operon units enabling tolerance to the heavy metals copper, zinc, cobalt, cadmium, chromium, and metalloid arsenic, which are functionally active. Despite the predominance of plasmid-related sequences in the K1 genome, the results indicate that most of the resistance genes are chromosomally encoded. No significant alkali tolerance of Acinetobacter sp. K1 was observed in vitro, suggesting that community level mechanisms are responsible for the survival of this strain in the highly alkaline, brown mud bacterial community.

Comparative Transcriptomic Profiling of Pellicle and Planktonic Cells from Carbapenem-Resistant Acinetobacter baumannii

Acinetobacter baumannii forms air-liquid interface pellicles that boost its ability to withstand desiccation and increase survival under antibiotic pressure. This study aims to delve into the transcriptomic profiles of pellicle cells from clinical strains of carbapenem-resistant A. baumannii (CRAB). The total RNA was extracted from pellicle cells from three pellicle-forming CRAB strains and planktonic cells from three non-pellicle-forming CRAB strains, subject to RNA sequencing using Illumina HiSeq 2500 system. A transcriptomic analysis between pellicle and planktonic cells, along with differential expression genes (DEGs) analysis and enrichment analysis of annotated COGs, GOs, and KEGGs, was performed. Our analysis identified 366 DEGs in pellicle cells: 162 upregulated genes and 204 downregulated genes. The upregulated ABUW_1624 (yiaY) gene and downregulated ABUW_1550 gene indicated potential involvement in fatty acid degradation during pellicle formation. Another upregulated ABUW_2820 (metQ) gene, encoding the D-methionine transporter system, hinted at its contribution to pellicle formation. The upregulation of two-component systems, CusSR and KdpDE, which implies the regulation of copper and potassium ions in a CRAB pellicle formation was also observed. These findings provide valuable insights into the regulation of gene expression during the formation of pellicles in CRAB, and these are potential targets that may aid in the eradication of CRAB infections.

Acinetobacter Metabolism in Infection and Antimicrobial Resistance

Acinetobacter infections have high rates of mortality due to an increasing incidence of infections by multidrug-resistant (MDR) and extensively-drug-resistant (XDR) strains. Therefore, new therapeutic strategies for the treatment of Acinetobacter infections are urgently needed. Acinetobacter spp. are Gram-negative coccobacilli that are obligate aerobes and can utilize a wide variety of carbon sources. Acinetobacter baumannii is the main cause of Acinetobacter infections, and recent work has identified multiple strategies A. baumannii uses to acquire nutrients and replicate in the face of host nutrient restriction. Some host nutrient sources also serve antimicrobial and immunomodulatory functions. Hence, understanding Acinetobacter metabolism during infection may provide new insights into novel infection control measures. In this review, we focus on the role of metabolism during infection and in resistance to antibiotics and other antimicrobial agents and discuss the possibility that metabolism may be exploited to identify novel targets to treat Acinetobacter infections.

Genomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6

Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si's abundance in the earth's crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, Enterobacter sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 protein-coding genes. In taxogenomic terms, it is similar to E. hormaechei subsp. xiangfangensis based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). LR6 genomic data provided insight into potential genes involved in stress response, secondary metabolite production, and growth promotion. The LR6 genome contains two aquaporins, of which the aquaglyceroporin (GlpF) is responsible for the uptake of metalloids including arsenic (As) and antimony (Sb). The yeast survivability assay confirmed the metalloid transport activity of GlpF. As a biofertilizer, LR6 isolate has a great deal of tolerance to high temperatures (45 °C), salinity (7%), and acidic environments (pH 9). Most importantly, the present study provides an understanding of plant-growth-promoting activity of the silicate-solubilizing bacterium, its adaptation to various stresses, and its uptake of different metalloids including As, Ge, and Si.

Lipocalin-2 is an essential component of the innate immune response to Acinetobacter baumannii infection

Acinetobacter baumannii is an opportunistic pathogen and an emerging global health threat. Within healthcare settings, major presentations of A. baumannii include bloodstream infections and ventilator-associated pneumonia. The increased prevalence of ventilated patients during the COVID-19 pandemic has led to a rise in secondary bacterial pneumonia caused by multidrug resistant (MDR) A. baumannii. Additionally, due to its MDR status and the lack of antimicrobial drugs in the development pipeline, the World Health Organization has designated carbapenem-resistant A. baumannii to be its priority critical pathogen for the development of novel therapeutics. To better inform the design of new treatment options, a comprehensive understanding of how the host contains A. baumannii infection is required. Here, we investigate the innate immune response to A. baumannii by assessing the impact of infection on host gene expression using NanoString technology. The transcriptional profile observed in the A. baumannii infected host is characteristic of Gram-negative bacteremia and reveals expression patterns consistent with the induction of nutritional immunity, a process by which the host exploits the availability of essential nutrient metals to curtail bacterial proliferation. The gene encoding for lipocalin-2 (Lcn2), a siderophore sequestering protein, was the most highly upregulated during A. baumannii bacteremia, of the targets assessed, and corresponds to robust LCN2 expression in tissues. Lcn2^-/- mice exhibited distinct organ-specific gene expression changes including increased transcription of genes involved in metal sequestration, such as S100A8 and S100A9, suggesting a potential compensatory mechanism to perturbed metal homeostasis. In vitro, LCN2 inhibits the iron-dependent growth of A. baumannii and induces iron-regulated gene expression. To elucidate the role of LCN2 in infection, WT and Lcn2^-/- mice were infected with A. baumannii using both bacteremia and pneumonia models. LCN2 was not required to control bacterial growth during bacteremia but was protective against mortality. In contrast, during pneumonia Lcn2^-/- mice had increased bacterial burdens in all organs evaluated, suggesting that LCN2 plays an important role in inhibiting the survival and dissemination of A. baumannii. The control of A. baumannii infection by LCN2 is likely multifactorial, and our results suggest that impairment of iron acquisition by the pathogen is a contributing factor. Modulation of LCN2 expression or modifying the structure of LCN2 to expand upon its ability to sequester siderophores may thus represent feasible avenues for therapeutic development against this pathogen.

A lack of therapeutic options has prompted the World Health Organization to designate multidrug-resistant Acinetobacter baumannii as its priority critical pathogen for research into new treatment strategies. The mechanisms employed by A. baumannii to cause disease and the host tactics exercised to constrain infection are not fully understood. Here, we further characterize the innate immune response to A. baumannii infection. We identify nutritional immunity, a process where the availability of nutrient metals is exploited to restrain bacterial growth, as being induced during infection. The gene encoding for lipocalin-2 (Lcn2), a protein that can impede iron uptake by bacteria, is highly upregulated in infected mice, and corresponds to robust LCN2 detection in the tissues. We find that LCN2 is crucial to reducing mortality from A. baumannii bacteremia and inhibits dissemination of the pathogen during pneumonia. In wild-type and Lcn2-deficient mice, broader transcriptional profiling reveals expression patterns consistent with the known response to Gram-negative bacteremia. Although the role of LCN2 in infection is likely multifactorial, we find its antimicrobial effects are at least partly exerted by impairing iron acquisition by A. baumannii. Facets of nutritional immunity, such as LCN2, may be exploited as novel therapeutics in combating A. baumannii infection.

Identification of cuprotosis-mediated subtypes, the development of a prognosis model, and influence immune microenvironment in hepatocellular carcinoma

Purpose

Cuprotosis is a newly discovered form of non-apoptotic regulated cell death and is characterized by copper-dependent and associated with mitochondrial respiration. However, the prognostic significance and function of cuprotosis-related genes (CRGs) in hepatocellular carcinoma (HCC) are unknown. This study aims to develop cuprotosis-mediated patterns-related gene (CMPRG) prediction models for the prognosis of patients with HCC, exploring the functional underlying the CRGs on the influence of tumor microenvironment (TME) features.

Experimental design

This study obtained transcriptome profiling and the corresponding clinical information from the TCGA and GEO databases. Besides, the Cox regression model with LASSO was implemented to build a multi-gene signature, which was then validated in an internal validation set and two external validation sets through Kaplan-Meier, DCA, and ROC analyses.

Results

According to the LASSO analysis, we screened out a cuprotosis-mediated pattern 5-gene combination (including PBK; MMP1; GNAZ; GPC1 and AKR1D1). A nomogram was constructed for the presentation of the final model. The ROC curve assessed the model’s predictive ability, which resulted in an area under the curve (AUC) values ranging from 0.604 to 0.787 underwent internal and two external validation sets. Meanwhile, the risk score divided the patients into two groups of high and low risk, and the survival rate of high-risk patients was significantly lower than that of low-risk patients (P<0.01). The risk score could be an independent prognostic factor in the multifactorial Cox regression analysis (P<0.01). Functional analysis revealed that immune status, mutational loads, and drug sensitivity differed between the two risk groups.

Conclusions

In summary, we identified three cuprotosis-mediated patterns in HCC. And CMPRGs are a promising candidate biomarker for HCC early detection, owing to their strong performance in predicting HCC prognosis and therapy. Quantifying cuprotosis-mediated patterns in individual samples may help improve the understanding of multiomic characteristics and guide the development of targeted therapy for HCC.

Unique underlying principles shaping copper homeostasis networks

Abstract

Copper is essential in cells as a cofactor for key redox enzymes. Bacteria have acquired molecular components that sense, uptake, distribute, and expel copper ensuring that cuproenzymes are metallated and steady-state metal levels are maintained. Toward preventing deleterious reactions, proteins bind copper ions with high affinities and transfer the metal via ligand exchange, warranting that copper ions are always complexed. Consequently, the directional copper distribution within cell compartments and across cell membranes requires specific dynamic interactions and metal exchange between cognate holo-apo protein partners. These metal exchange reactions are determined by thermodynamic and kinetics parameters and influenced by mass action. Then, copper distribution can be conceptualized as a molecular system of singular interacting elements that maintain a physiological copper homeostasis. This review focuses on the impact of copper high-affinity binding and exchange reactions on the homeostatic mechanisms, the conceptual models to describe the cell as a homeostatic system, the various molecule functions that contribute to copper homeostasis, and the alternative system architectures responsible for copper homeostasis in model bacteria.

Graphical Abstract

Fresh produce as a potential vehicle for transmission of Acinetobacter baumannii

Acinetobacter baumannii is a Gram-negative bacterium that has gained a stronghold inside healthcare settings. Due to the ability of A. baumannii to acquire antibiotic resistance easily, its presence in food products could pose a major threat to the public health. The aim of this study therefore, was to investigate the prevalence of A. baumannii in fresh produce and study their genetic diversity. A total of 234 samples of vegetables and fruits were collected. A. baumannii isolates were identified using CHROMagar and two different PCR assays. Also, the isolates were tested for their ability to resist antibiotics and form biofilms. The genetic diversity of the isolates was determined using multi-locus sequence typing (MLST). Of the 234 samples collected, 10 (6.5%) and 7 (8.75%) A. baumannii isolates were recovered from vegetables and fruits, respectively. Antibiotic susceptibility testing revealed that 4 of these isolates were extensively drug-resistant (XDR). All isolates were able to form biofilms and MLST analysis revealed 6 novel strains. This study demonstrated that fresh produce constitutes a reservoir for A. baumannii, including strong biofilm formers and XDR strains. This represents a significant concern to public health because vegetables and fruits may serve as a vehicle for the spread of A. baumannii and antibiotic resistance into the community and healthcare settings.

Promising Acinetobacter baumannii Vaccine Candidates and Drug Targets in Recent Years

In parallel to the uncontrolled use of antibiotics, the emergence of multidrug-resistant bacteria, like Acinetobacter baumannii, has posed a severe threat. A. baumannii predominates in the nosocomial setting due to its ability to persist in hospitals and survive antibiotic treatment, thereby eventually leading to an increasing prevalence and mortality due to its infection. With the increasing spectra of drug resistance and the incessant collapse of newly discovered antibiotics, new therapeutic countermeasures have been in high demand. Hence, recent research has shown favouritism towards the long-term solution of designing vaccines. Therefore, being a realistic alternative strategy to combat this pathogen, anti-A. Baumannii vaccines research has continued unearthing various antigens with variable results over the last decade. Again, other approaches, including pan-genomics, subtractive proteomics, and reverse vaccination strategies, have shown promise for identifying promiscuous core vaccine candidates that resulted in chimeric vaccine constructs. In addition, the integration of basic knowledge of the pathobiology of this drug-resistant bacteria has also facilitated the development of effective multiantigen vaccines. As opposed to the conventional trial-and-error approach, incorporating the in silico methods in recent studies, particularly network analysis, has manifested a great promise in unearthing novel vaccine candidates from the A. baumannii proteome. Some studies have used multiple A. baumannii data sources to build the co-functional networks and analyze them by k-shell decomposition. Additionally, Whole Genomic Protein Interactome (GPIN) analysis has utilized a rational approach for identifying essential proteins and presenting them as vaccines effective enough to combat the deadly pathogenic threats posed by A. baumannii. Others have identified multiple immune nodes using network-based centrality measurements for synergistic antigen combinations for different vaccination strategies. Protein-protein interactions have also been inferenced utilizing structural approaches, such as molecular docking and molecular dynamics simulation. Similar workflows and technologies were employed to unveil novel A. baumannii drug targets, with a similar trend in the increasing influx of in silico techniques. This review integrates the latest knowledge on the development of A. baumannii vaccines while highlighting the in silico methods as the future of such exploratory research. In parallel, we also briefly summarize recent advancements in A. baumannii drug target research.

Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and human macrophages

The opportunistic pathogen Acinetobacter baumannii possesses stress tolerance strategies against host innate immunity and antibiotic killing. However, how the host-pathogen-antibiotic interaction affects the overall molecular regulation of bacterial pathogenesis and host response remains unexplored. Here, we simultaneously investigate proteomic changes in A. baumannii and macrophages following infection in the absence or presence of the polymyxins. We discover that macrophages and polymyxins exhibit complementary effects to disarm several stress tolerance and survival strategies in A. baumannii, including oxidative stress resistance, copper tolerance, bacterial iron acquisition and stringent response regulation systems. Using the spoT mutant strains, we demonstrate that bacterial cells with defects in stringent response exhibit enhanced susceptibility to polymyxin killing and reduced survival in infected mice, compared to the wild-type strain. Together, our findings highlight that better understanding of host-pathogen-antibiotic interplay is critical for optimization of antibiotic use in patients and the discovery of new antimicrobial strategy to tackle multidrug-resistant bacterial infections.

Genetic Dissection of Antibiotic Adjuvant Activity

Small molecule adjuvants that enhance the activity of established antibiotics represent promising agents in the battle against antibiotic resistance. Adjuvants generally act by inhibiting antibiotic resistance processes, and specifying the process acted on is a critical step in defining an adjuvant's mechanism of action. This step is typically carried out biochemically by identifying molecules that bind adjuvants and then inferring their roles in resistance. Here, we present a complementary genetic strategy based on identifying mutations that both sensitize cells to antibiotic and make them "adjuvant blind." We tested the approach in Acinetobacter baumannii AB5075 using two adjuvants: a well-characterized β-lactamase inhibitor (avibactam) and a compound enhancing outer membrane permeability (aryl 2-aminoimidazole AI-1). The avibactam studies showed that the adjuvant potentiated one β-lactam (ceftazidime) through action on a single β-lactamase (GES-14) and a second (meropenem) by targeting two different enzymes (GES-14 and OXA-23). Mutations impairing disulfide bond formation (DsbAB) also reduced potentiation, possibly by impairing β-lactamase folding. Mutations reducing AI-1 potentiation of canonical Gram-positive antibiotics (vancomycin and clarithromycin) blocked lipooligosaccharide (LOS/LPS) synthesis or its acyl modification. The results indicate that LOS-mediated outer membrane impermeability is targeted by the adjuvant and show the importance of acylation in the resistance. As part of the study, we employed Acinetobacter baylyi as a model to verify the generality of the A. baumannii results and identified the principal resistance genes for ceftazidime, meropenem, vancomycin, and clarithromycin in A. baumannii AB5075. Overall, the work provides a foundation for analyzing adjuvant action using a comprehensive genetic approach. IMPORTANCE One strategy to confront the antibiotic resistance crisis is through the development of adjuvant compounds that increase the efficacy of established drugs. A key step in the development of a natural product adjuvant as a drug is identifying the resistance process it undermines to enhance antibiotic activity. Previous procedures designed to accomplish this have relied on biochemical identification of cell components that bind adjuvant. Here, we present a complementary strategy based on identifying mutations that eliminate adjuvant activity.

Spatiotemporal dynamics of the resistome and virulome of riverine microbiomes disturbed by a mining mud tsunami

Aquatic ecosystems are highly vulnerable to anthropogenic activities. However, it remains unclear how the microbiome responds to press disturbance events in these ecosystems. We examined the impact of the world's largest mining disaster (Brazil, 2015) on sediment microbiomes in two disturbed rivers compared to an undisturbed river during 390 days post-disturbance. The diversity and structure of the virulome and microbiome, and of antibiotic and metal resistomes, consistently differed between the disturbed and undisturbed rivers, particularly at day 7 post-disturbance. 684 different ARGs were predicted, 38% were exclusive to the disturbed rivers. Critical antibiotic resistance genes (ARGs), e.g., mcr and ereA2, were significantly more common in the disturbed microbiomes. 401 different ARGs were associated with mobile genetic elements (MGEs), 95% occurred in the disturbed rivers. While plasmids were the most common MGEs with a broad spectrum of ARGs, spanning 16 antibiotic classes, integrative conjugative elements (ICEs) and integrons disseminated ARGs associated with aminoglycoside and tetracycline, and aminoglycoside and beta-lactam, respectively. A significant increase in the relative abundance of class 1 integrons, ICEs, and pathogens was identified at day 7 in the disturbed microbiomes, 72-, 14- and 3- fold higher, respectively, compared with the undisturbed river. Mobile ARGs associated with ESKAPEE group pathogens, while metal resistance genes and virulence factor genes in nonpathogenic hosts predominated in all microbiomes. Network analysis showed highly interconnected ARGs in the disturbed communities, including genes targeting antibiotics of last resort. Interactions between copper and beta-lactam/aminoglycoside/macrolide resistance genes, mostly mobile and critical, were also uncovered. We conclude that the mud tsunami resulted in resistome expansion, enrichment of pathogens, and increases in promiscuous and mobile ARGs. From a One Health perspective, mining companies need to move toward more environmentally friendly and socially responsible mining practices to reduce risks associated with pathogens and critical and mobile ARGs.

Copper Homeostatic Mechanisms and Their Role in the Virulence of Escherichia coli and Salmonella enterica

Copper is an essential micronutrient that also exerts toxic effects at high concentrations. This review summarizes the current state of knowledge on copper handling and homeostasis systems in Escherichia coli and Salmonella enterica. We describe the mechanisms by which transcriptional regulators, efflux pumps, detoxification enzymes, metallochaperones, and ancillary copper response systems orchestrate cellular response to copper stress. E. coli and S. enterica are important pathogens of humans and animals. We discuss the critical role of copper during killing of these pathogens by macrophages and in nutritional immunity at the bacterial-pathogen-host interface. In closing, we identify opportunities to advance our understanding of the biological roles of copper in these model enteric bacterial pathogens.

The First Saudi Study Investigating the Plasmid-borne Aminoglycoside and Sulfonamide Resistance among Acinetobacter baumannii Clinical Isolates Genotyped by RAPD-PCR: the Declaration of a Novel Allelic Variant Called aac(6')-SL and Three Novel Mutations in the sul1 Gene in the Acinetobacter Plasmid (s)

Background

Acinetobacter baumannii (A. baumannii) is one of the most important nosocomial pathogens responsible for a wide range of infections.

Aim

This study aimed to investigate the existence of the plasmidic genes encoding for aminoglycoside modifying enzymes (AMEs), 16S rRNA methyltransferases (RMT), and the altered dihydropetroate synthase (DHPS) encoded by the sul1 gene among A. baumannii clinical isolates collected from Taif, Kingdom of Saudi Arabia (KSA). The mutations in aac(6ʹ)-Ib and sul1 genes were also investigated.

Methods

Forty A. baumannii clinical isolates were investigated for their susceptibility to ten antibiotics. The plasmid DNA was extracted and screened for nine genes encoding for aminoglycoside resistance in addition to the sul1 gene. The clonal relatedness was determined by random amplified polymorphic DNA (RAPD)-PCR. Mutation in aac(6ʹ)-Ib and the sul1 genes were detected by capillary electrophoresis sequencing (CES).

Results

All isolates were A. baumannii in which 42.5% of them exhibited a high level of aminoglycoside resistance (HLAR). The most prevalent AMEs and RMT encoding genes were aph(3ʹ)-VI, the two aac(6ʹ) gene variants [aac(6ʹ)-Ib and aac(6ʹ)-SL], ant(3ʹʹ)-I, and armA in which 90%, 87.5%, 85%, and 45% of isolates tested positive, respectively. The other investigated aminoglycoside resistant encoding genes, namely aac(3)-II, aac(6ʹ)-II, and rmtB, were not detected. Only 15% of isolates harbored the sul1 gene. RAPD-PCR classified the 40 isolates into three clusters in which cluster II was the main cluster. DNA sequencing revealed that 34.29% (12/35) of isolates tested positive for aac(6ʹ)-Ib were found to harbor a common missense mutation in position 102 indicating a novel allelic variant named aac(6ʹ)-SL. Also, DNA sequencing revealed three missense mutations in the sul1 gene.

Conclusion

This is the first Saudi study to investigate the plasmid borne aminoglycoside and sulfonamide resistance genes among A. baumannii clinical isolates. A novel allelic variant for aac(6ʹ)-Ib was detected in addition to novel mutations in the sul1 gene.

Identification of Two Variants of Acinetobacter baumannii Strain ATCC 17978 with Distinct Genotypes and Phenotypes

Acinetobacter baumannii is a nosocomial pathogen that exhibits substantial genomic plasticity. Here, the identification of two variants of A. baumannii ATCC 17978 that differ based on the presence of a 44-kb accessory locus, named AbaAL44 (A. baumannii accessory locus 44 kb), is described. Analyses of existing deposited data suggest that both variants are found in published studies of A. baumannii ATCC 17978 and that American Type Culture Collection (ATCC)-derived laboratory stocks comprise a mix of these two variants. Yet, each variant exhibits distinct interactions with the host in vitro and in vivo. Infection with the variant that harbors AbaAL44 (A. baumannii 17978 UN) results in decreased bacterial burdens and increased neutrophilic lung inflammation in a mouse model of pneumonia, and affects the production of interleukin 1 beta (IL-1β) and IL-10 by infected macrophages. AbaAL44 harbors putative pathogenesis genes, including those predicted to encode a type I pilus cluster, a catalase, and a cardiolipin synthase. The accessory catalase increases A. baumannii resistance to oxidative stress and neutrophil-mediated killing in vitro. The accessory cardiolipin synthase plays a dichotomous role by promoting bacterial uptake and increasing IL-1β production by macrophages, but also by enhancing bacterial resistance to cell envelope stress. Collectively, these findings highlight the phenotypic consequences of the genomic dynamism of A. baumannii through the evolution of two variants of a common type strain with distinct infection-related attributes.

The Molecular Basis of Acinetobacter baumannii Cadmium Toxicity and Resistance

Acinetobacter species are ubiquitous Gram-negative bacteria that can be found in water, in soil, and as commensals of the human skin. The successful inhabitation of Acinetobacter species in diverse environments is primarily attributable to the expression of an arsenal of stress resistance determinants, which includes an extensive repertoire of metal ion efflux systems. Metal ion homeostasis in the hospital pathogen Acinetobacter baumannii contributes to pathogenesis; however, insights into its metal ion transporters for environmental persistence are lacking. Here, we studied the impact of cadmium stress on A. baumannii. Our functional genomics and independent mutant analyses revealed a primary role for CzcE, a member of the cation diffusion facilitator (CDF) superfamily, in resisting cadmium stress. We also show that the CzcCBA heavy metal efflux system contributes to cadmium efflux. Collectively, these systems provide A. baumannii with a comprehensive cadmium translocation pathway from the cytoplasm to the periplasm and subsequently the extracellular space. Furthermore, analysis of the A. baumannii metallome under cadmium stress showed zinc depletion, as well as copper enrichment, both of which are likely to influence cellular fitness. Overall, this work provides new knowledge on the role of a broad arsenal of membrane transporters in A. baumannii metal ion homeostasis. IMPORTANCE Cadmium toxicity is a widespread problem, yet the interaction of this heavy metal with biological systems is poorly understood. Some microbes have evolved traits to proactively counteract cadmium toxicity, including Acinetobacter baumannii, which is notorious for persisting in harsh environments. Here, we show that A. baumannii utilizes a dedicated cadmium efflux protein in concert with a system that is primarily attuned to zinc efflux to efficiently overcome cadmium stress. The molecular characterization of A. baumannii under cadmium stress revealed how active cadmium efflux plays a key role in preventing the dysregulation of bacterial metal ion homeostasis, which appeared to be a primary means by which cadmium exerts toxicity upon the bacterium.

Genome Analysis of Acinetobacter lwoffii Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates

Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of A. lwoffii and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical A. lwoffii isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter.

The Influence of Copper Homeostasis Genes copA and copB on Xylella fastidiosa Virulence Is Affected by Sap Copper Concentration

Xylella fastidiosa is a xylem-limited plant pathogenic bacterium that causes diseases worldwide in crops such as grape, citrus, and olive. Although copper (Cu)-containing compounds are not used for management of X. fastidiosa-caused diseases, they are widely used in X. fastidiosa hosts in vineyards and orchards. The accumulation of Cu in soils and, therefore, plant saps, could be a challenge for X. fastidiosa survival. Here, the molecular basis of Cu homeostasis was studied in relation to virulence. Although homologous Cu-related genes copA (X. fastidiosa loci PD0100) and copB (PD0101) have been characterized in other bacteria, their functions differ among bacterial species. In vitro, both copA and copB mutants were more sensitive to Cu than the wild-type (WT) strain. Interestingly, the copA mutant was more sensitive to Cu shock, while the copB mutant was more sensitive to chronic Cu treatments. In tobacco greenhouse experiments with normal watering, both mutants reduced virulence compared with WT. But when Cu was added as a drench treatment, both copA and copB mutants had increased disease severity approximately 20 and 50% compared with mutants without Cu added, respectively, which were significantly higher than the approximately 5% observed for WT under the same conditions. These results indicate that the pathogen's Cu homeostasis affects virulence and is influenced by Cu concentration in the environment. Understanding Cu homeostasis in X. fastidiosa will help discern the outcome of Cu treatments and the adaptation of this pathogen to the xylem of plants that have been exposed to high Cu concentrations because of agricultural practices.

The YcnI protein from Bacillus subtilis contains a copper-binding domain

Bacteria require a precise balance of copper ions to ensure that essential cuproproteins are fully metalated while also avoiding copper-induced toxicity. The Gram-positive bacterium Bacillus subtilis maintains appropriate copper homeostasis in part through the ycn operon. The ycn operon comprises genes encoding three proteins: the putative copper importer YcnJ, the copper-dependent transcriptional repressor YcnK, and the uncharacterized Domain of Unknown Function 1775 (DUF1775) containing YcnI. DUF1775 domains are found across bacterial phylogeny, and bioinformatics analyses indicate that they frequently neighbor domains implicated in copper homeostasis and transport. Here, we investigated whether YcnI can interact with copper and, using electron paramagnetic resonance and inductively coupled plasma-MS, found that this protein can bind a single Cu(II) ion. We determine the structure of both the apo and copper-bound forms of the protein by X-ray crystallography, uncovering a copper-binding site featuring a unique monohistidine brace ligand set that is highly conserved among DUF1775 domains. These data suggest a possible role for YcnI as a copper chaperone and that DUF1775 domains in other bacterial species may also function in copper homeostasis.

Transformation of pig manure by passage through the gut of black soldier fly larvae (Hermetia illucens): Metal speciation, potential pathogens and metal-related functional profiling

Black soldier fly larvae (BSFL) have great potential in livestock manure disposal. However, the changes in metal speciation, microbial communities, potential pathogens during the manure transformation process by BSFL is still largely uncharacterized, as well as the underlying metal tolerance mechanism of larval gut microbiome. Here we used BSFL to convert pig manure (PM) into larval feces (BF), and investigated the metal and microbial changes in the conversion process. Physicochemical parameters (e.g. pH, electrical conductivity, total nitrogen, total phosphorus and total potassium) in PM were significantly altered compared to BF. After conversion, less than 10% of Cu and Zn were accumulated in larval bodies. The bioavailable fraction of Cu (88.3%-86.2%) and Zn (80.6%-82.3%) occupied as the primary form in PM and BF. Genera Enterococcus, Clostridium_sensu_stricto_1, Terrisporobacter and Romboutsia were substantially enriched in the final BSFL gut (GF) compared with initial gut (GI). BSFL transformation substantially reduced pathogen abundances (decreased by 89%) derived from pig manure. Functional genes involved in metal homeostasis and resistance (e.g. CutC, pcoC, cusR, zurR and zntB) were obviously strengthened (by 2.3-7.7 folds) in GF than in GI, which might partly explain the metal tolerance ability of BSFL during the livestock manure transformation process.

Recent Advances in Genetic Tools for Acinetobacter baumannii

Acinetobacter baumannii is classified as a top priority pathogen by the World Health Organization (WHO) because of its widespread resistance to all classes of antibiotics. This makes the need for understanding the mechanisms of resistance and virulence critical. Therefore, tools that allow genetic manipulations are vital to unravel the mechanisms of multidrug resistance (MDR) and virulence in A. baumannii. A host of current strategies are available for genetic manipulations of A. baumannii laboratory-strains, including ATCC® 17978TM and ATCC® 19606T, but depending on susceptibility profiles, these strategies may not be sufficient when targeting strains newly obtained from clinic, primarily due to the latter's high resistance to antibiotics that are commonly used for selection during genetic manipulations. This review highlights the most recent methods for genetic manipulation of A. baumannii including CRISPR based approaches, transposon mutagenesis, homologous recombination strategies, reporter systems and complementation techniques with the spotlight on those that can be applied to MDR clinical isolates.

Cu Homeostasis in Bacteria: The Ins and Outs

Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.