With the high rise in Salmonella infections and emergence of antibiotic resistance, developing a novel strategy to control the pathogen is imperative. Earlier studies have revealed that ethanolamine (EA) metabolism plays a crucial role in Salmonella intestinal colonization; however, the potential of this metabolism as a therapeutic target remains unexplored. The EA metabolic enzymes are localized within a proteinaceous microcompartment (MCP) shell composed of thousands of copies of shell proteins encoded by five genes from the eut operon. Our study reveals that supplementation of EA and vitamin B12 in both rich and minimal media enhances biofilm formation, motility, and tolerance to antibiotics. Conversely, mutants deficient in EA metabolism due to defective MCP shell exhibited no physiological fitness. Fascinatingly, these mutants exhibited enhanced susceptibility to various antibiotics and lower expression of biofilm and curli. Also, a mutation in one of the major shell proteins reduced intramacrophage viability of Salmonella. Notably, phenotypes were restored upon ectopic expression of corresponding genes. Mutations in the MCP shell proteins downregulated the expression of genes related to pathogenicity. Overall, this study sheds new light on understanding the relationship between EA metabolism and bacterial physiology that would pave the way for developing novel therapeutic interventions against Salmonella.

Staphylococcus epidermidis (SE) is a common human skin coloniser, which is often the cause of medical device-associated infections. SE population is composed of two clonal lineages, A/C and B, with distinct pathogenic potential. Although pH is known to change during infection when SE crosses the host skin to access the bloodstream, the impact of this pH alteration on SE pathogenicity is poorly understood. Recognizing how SE deals with pH increments will help designing effective prevention and treatment strategies against SE infections. To investigate the metabolic adaptations of representative A/C and B strains to pH, we mimicked skin and blood pH conditions (5.5 and 7.4) and followed biomass formation, growth media pH and exometabolites over time. Although both strains share some metabolic patterns, specificities were identified for each strain and pH condition. The B strain was better adapted to use diverse carbon sources and at blood pH has a more active TCA cycle and amino acid catabolism. At blood pH, the B strain depletes formate from the extracellular media, while its extracellular accumulation by the A/C strain could work as a host invasion strategy. For both SE strains, TCA cycle regulation, purine biosynthesis and glutamate uptake could be associated with virulence, particularly biofilm production, especially relevant for ICE25 which is able to produce high adherence biofilm. The uptake and consumption of saccharides follow similar profiles and seem to be pH-regulated by both strains. The dynamic study of SE exometabolome has contributed to understanding the intracellular processes and their relationship with virulence.

Leptospira interrogans, the agent of leptospirosis, employs complex virulence mechanisms that are not fully understood at a systems level. To elucidate the regulatory landscape of its pathogenicity, we used Weighted Gene Co-expression Network Analysis (WGCNA) on a comprehensive transcriptomic dataset to map the architecture of its virulence programs. Our analysis revealed that the L. interrogans transcriptome is organized into distinct, functionally coherent modules. We discovered that known virulence factors are significantly concentrated in two key modules: a "lightgrey" module that orchestrates host colonization and immune evasion, containing genes for surface adhesion (loa22, ompL1) and defense (lipL21); and a "black" module that functions as an arsenal for tissue invasion (colA), stress adaptation (clpB), and cytotoxicity (sph2). Furthermore, by contextualizing genes within this network, our approach implicated numerous uncharacterized genes (e.g., from the PF07598 family) in pathogenesis due to their strong co-expression with established virulence factors. These findings provide a systems-level blueprint of the regulatory networks driving leptospirosis, offering a rich resource of functionally validated gene modules and novel targets for the development of next-generation vaccines and therapeutics. These findings not only deepen the understanding of L. interrogans virulence regulation but also provide a conceptual framework for integrating transcriptomic data into systems-level models of bacterial pathogenesis, paving the way for translational applications in diagnostics and vaccine design.

A marked difference in virulence was observed between two subpopulations of the Edwardsiella piscicida FSW910410 strain, originally isolated from olive flounder (Paralichthys olivaceus). While the strain maintained under routine laboratory culture conditions retained high virulence, the same strain stored long-term at -80 °C lost its ability to induce disease in olive flounder. Comparative in vivo assays demonstrated complete avirulence in the frozen-stored subpopulation, contrasting with high mortality rates induced by the virulent counterpart. Despite over 99 % genomic sequence identity and identical virulence gene repertoires, the two subpopulations differed significantly in their ability to evade host immune responses. Whole-genome methylation profiling revealed comparable levels of N6-methyladenine (m[6]A) but notably reduced levels of cytosine methylation (m[4]C/m[5]C) in the avirulent subpopulation, particularly in genes associated with type III and type VI secretion systems (T3SS and T6SS). Quantitative RT-PCR analyses confirmed substantially lower expression of T3SS and T6SS genes in the avirulent strain. These results suggest that epigenetic modifications, especially cytosine methylation, may contribute to the observed differences in virulence, although additional regulatory mechanisms cannot be excluded. Collectively, the data highlight the complex interplay of genomic and epigenetic factors that may influence bacterial pathogenicity during prolonged storage or passage.

Klebsiella pneumoniae is a Gram-negative bacterium and an important pathogen implicated in both hospital- and community-acquired pneumonia. K. pneumoniae strains are either classical, hypervirulent (hvKp), or antibiotic-resistant. There are several virulence factors of K. pneumoniae that helps immune evasion and survivability within the host. This review emphasizes the host immune interactions of K. pneumoniae. Evasion strategies of the pathogen and complex risk factors of the infection have been explained. Different diagnostic approaches, such as computed tomography, PCR, and Lateral Flow Immunoassay (LF), have been used for the diagnosis of K. pneumoniae. Multidrug-resistant Klebsiella pneumoniae (MDRKP) has emerged as a significant global public health concern, with higher cases of carbapenem-resistant K. pneumoniae (CRKP). CRKP caused more than 7000 deaths annually in Europe. Although K.pneumoniae has several mechanisms of antibiotic resistance, resistance to β-lactams, specifically carbapenems, causes a notable difference. Newer β-lactam/β-lactamase inhibitor combinations, such as ceftazidime-avibactam and cefiderocol are preferred for KPC-producing infections. This review emphasizes the ongoing challenges in translating therapeutic advancements into successful clinical outcomes, as well as the persisting complications in K. pneumoniae research, including the unsolved differences between hypervirulent and classical strains. Alternative methods, including bacteriophage therapy, antimicrobial peptides, and immunotherapy, are being studied for tackling CRKP. This review addresses recent advances in understanding Klebsiella pneumoniae-induced pneumonia, emphasizing how virulence factors interact with immune defences. Additionally, we highlight key challenges in antimicrobial resistance, current therapeutic strategies, K. pneumoniae's implications for infection control and antibiotic stewardship. Overall, this review aims to contribute to a deeper understanding of K. pneumoniae and to guide future interventions for effective prevention, control, and treatment strategies.

Biofilm formation is governed by quorum sensing (QS) and intracellular signaling, with cyclic di-GMP (c-di-GMP) acting as a key regulator that modulates biofilm stability in response to environmental cues. The present study aims to explore the regulatory network between QS, c-di-GMP signaling, and amyloid production in the marine biofilm-forming bacterium Pseudomonas aeruginosa PFL-P1 under various physicochemical stressors. P. aeruginosa PFL-P1 demonstrated adaptability to diverse conditions typical of marine habitats, attributed to the activity of diguanylate cyclase (dgc86) and phosphodiesterase (pde94) genes regulating c-di-GMP turnover. Gene expression analysis revealed a coordinated regulatory network during biofilm development, with significant upregulation of dgc86, pde94, fapC (functional amyloid synthesis), lasI, rhlI (QS), and nahAc [polycyclic aromatic hydrocarbon (PAH) degradation] at 48 h, indicating a mature biofilm. Under acidic condition (pH 4), all genes except pde94 exhibited an adaptive response (p<0.0001). Salinity ≤1 % enhanced gene expression, whereas salinity ≥5 % suppressed it due to osmotic stress (p<0.0001). At 40 °C, dgc86 (p=0.0457) and fapC (p=0.0444) were upregulated, promoting biofilm stability. Pyrene exposure induced significant upregulation of dgc86, lasI, rhlI, and nahAc (p<0.05), enhancing biofilm formation and PAH degradation while downregulating pde94. Supplementation with C4-HSL and 3OC12-HSL upregulated these genes, reinforcing the role of QS in biofilm regulation. Terrein, a QS and c-di-GMP inhibitor downregulated fapC and nahAc, disrupting biofilm formation and PAH degradation. The strong correlation between c-di-GMP levels, amyloid production, and its high binding affinity to FapC (-11.8 kcal/mol) suggests a dual role for c-di-GMP as a signaling molecule and molecular chaperone in amyloid assembly.

Over the years, anthrax has become endemic in the state of Andhra Pradesh, India, posing risk for both animals and humans and spreading to the bordering state of Karnataka. The incidence is on the rise and the spread covering the entire state. The article is aimed at projecting spatio-temporal distribution of anthrax in the state of Andhra Pradesh highlighting possible reasons influencing the transmission dynamics in animals and resultant risk to humans. A select sub-sample of these were analyzed by Whole Genome Sequencing. From 2009 to 2024, 122 animal anthrax outbreaks were recorded, whereas 21 human anthrax outbreaks were reported from 2004 to 2024 in the state of Andhra Pradesh. Animal anthrax outbreaks were reported throughout the year with short peaks during March to October, covering high summer and rainy season. Most affected species were sheep (84 %), followed by Bovines (9 %) and Goats (4 %). Spill over was detected in Pig and Hog deer, and a probable transmission in humans. The recent spread of anthrax in livestock across the state, particularly to adjoining pasture lands of Odisha, Karnataka and Tamil Nadu due to migration for grazing might have led to the recent hot spots around state boundaries and forest fringes, calls for effective intervention to stop the spread.

Capsule is a key virulence factor for Bacillus anthracis. In this study, we examined the onset of capsule expression and the ultrastructure of capsule expressed in vitro and in infected hosts. We determined by immunofluorescence and immunoelectron microscopy that capsule was produced as early as 15 min after onset of germination. Further analysis revealed bacilli were often fully encapsulated when they emerged from the exosporium. Using conventional fixative to prepare samples for electron microscopy resulted in loss of capsular material, but using a fixative containing ruthenium red and lysine acetate preserved it. Transmission electron microscopy using enhanced fixation revealed that B. anthracis grown in vitro were surrounded by a thick capsule layer comprised of globular structures and a slime layer. When examined using the enhanced fixation, extracellular bacilli in tissues from moribund animals were surrounded by a thick capsule layer, and had long branching strands like those observed on live but not fixed bacilli by fluorescence microscopy. Scanning electron microscopy using enhanced fixation similarly revealed B. anthracis within spleen sinusoids were covered with long branching strands that appeared to tether them to host cells. This is the first report describing the presence of long capsule strands during infection in vivo.

Bacillus anthracis, the causative agent of anthrax, poses a persistent threat in endemic regions. In this study, eight archived B. anthracis isolates from the year 2018-2019 were successfully revived, highlighting the resilience of spores and the effectiveness of long-term storage in maintaining virulence. Genomic DNA was extracted using three methods: Qiagen DNeasy kit, Zymo bead-based method, and phenol-chloroform extraction. The inclusion of ampicillin during initial incubation in the phenol-chloroform method enhanced DNA yield by selectively eliminating vegetative cells without inducing sporulation. The highest DNA concentration of 3710 ng/μL was obtained using this method. PCR analysis confirmed the presence of pXO1 and pXO2 virulence plasmids, along with the chromosomal rpoB gene, using OIE-recommended primers. The rpoB marker was chosen over 16S rRNA for its superior resolution among closely related strains. Phylogenetic analysis with bootstrap replicates revealed conserved sequences in plasmid genes, while rpoB exhibited notable diversity, suggesting chromosomal variation among the isolates. These findings contribute to ongoing anthrax surveillance and molecular epidemiology efforts in Karnataka, India, and underscore the potential of combining plasmid and chromosomal markers in understanding strain-level variation. Further whole genome sequencing (WGS) will provide deeper insights into the genomic diversity and evolutionary dynamics of B. anthracis.

Bacillus anthracis, a rod-shaped, spore-forming bacterium, is the causative agent of anthrax. The life cycle of B. anthracis involves sporulation and germination processes that are precisely regulated by distinct sigma factors and associated proteins. Its pathogenicity is primarily attributed to a tripartite toxin consisting of lethal factor (LF), edema factor (EF) and protective antigen (PA), as well as an antiphagocytic capsule of Poly-γ-D-Glutamate. The virulence of B. anthracis is further regulated by various post-translational modifications (PTMs), including protein phosphorylation, acetylation, glycosylation, hydroxylation, and lipidation. These modifications play a key role in modulating bacterial virulence by influencing enzymatic activity and protein expression. This review summarizes the role of PTMs in the regulation of B. anthracis virulence. A deeper understanding of how these PTMs contribute to B. anthracis pathogenesis may offer new insights into novel enzyme targets, strategies to disrupt toxin production and the development of therapeutic approaches to combat anthrax infections.

Listeria monocytogenes is primarily a saprophytic bacterium, but it can transition into a pathogenic form when ingested by humans, vertebrates, or invertebrates, thereby initiating infection and proliferating within the host. This bacterium serves as a model for studying the molecular and cellular mechanisms by which environmental microorganisms adapt to mammalian and other host systems, thereby promoting the successful colonization and survival of these microorganisms. Environmental contamination is a significant factor in the transmission of listeriosis and other foodborne diseases. This review provides a comprehensive examination of the microbiological characteristics of L. monocytogenes. It systematically evaluates host-pathogen interactions, focusing on a range of clinically relevant isolates and their pathogenic mechanisms. Furthermore, it evaluates in vitro models employed to investigate the virulence factors of the pathogen while also considering the role of animal models, including Drosophila melanogaster and other insect species, in elucidating infection dynamics. In addition, it discusses the host's innate immune response, specifically highlighting the molecular and cellular pathways activated upon infection, thereby providing a comprehensive understanding of the pathogen's interactions with the host's immune system.

Methods for assembly and annotation of whole genomic sequences were compared for six strains of avian pathogenic Escherichia coli (APEC). Two vertically transferred E. coli clones, represented by three isolates all belonging to pulse field genome electrophoresis (PFGE) type 65- sequence type (ST)95 and three isolates belonging to PFGE type 47- ST131, were selected for Illumina short read sequencing. There was no significant difference between SPAdes and CLC Genomic Workbench for benchmark parameters to assemble the short reads. The six strains were also sequenced by long read sequencing (Nanopore) and these reads were hybrid assembled with the short reads. Unicycler provided a lower number of contigs and higher NG50 compared to Flye. No significant differences between total length of genomes were obtained from the four assemblers. At least 2.1 and 0.9 % of coding gene sequences (CDSs) annotated with Rapid annotations using subsystems technology (RAST) and PROKKA, respectively were wrongly annotated. The errors were most often associated to CDS of shorter length (<150 nt) with functions such as transposases, mobile genetic elements or being hypothetical. The investigation points out the importance of controlling automatic annotations and suggest further work to improve annotations in strains not belonging to the K12 or B lineages.

Phages are bacterial viruses considered as therapeutics for treatment of serious infections with antibiotic-resistant pathogens. In Staphylococcus aureus, resistance to cell wall targeting antibiotics is common in the methicillin resistant (MRSA) or vancomycin-intermediate susceptible (VISA) strains. Furthermore, the cell wall anchors the primary phage receptor, the wall teichoic acid (WTA) glycopolymers. Here we demonstrate that mutations resulting in VISA development affect phage susceptibility of clinically and laboratory evolved strains. For clinical strains we observed both increased and decreased susceptibility compared to the ancestral vancomycin susceptible strains when infected with the therapeutically relevant myoviruses, ΦIPLA-RODI, Stab20, Stab21 and ΦK. For laboratory strains adapted to vancomycin from the MRSA strain, JE2, we observed variable resistance development to the phages ΦIPLA-RODI, Stab21 and ΦK with one strain becoming completely phage resistant. In contrast, half of the VISA strains became susceptible to Stab20 to which JE2 is resistant. These changes in part correlated with altered WTA glycosylation patterns as shown by WTA-specific antibodies and for the resistant strain resulted in compromised phage therapy as shown in a Galleria mellonella infection model. This study highlights the need for understanding antibiotic-driven alterations in bacterial physiology when developing phage-based therapies using combination treatments with antibiotics and phages.