Andrew J. Roe

Graphical Phylogenetic tree highlighting members of the kingdom Animalia with characterized Streptomyces interactions. Images have been coloured using stereoimages of Streptomyces colonies.

Vascular injury and coagulopathy are key drivers of mortality in bacterial sepsis. In Neisseria meningitidis infection, endothelial adhesion and thrombosis cause the characteristic petechial rash and, in the most severe cases, purpura fulminans. Although antibiotics rapidly kill bacteria, inflammation and vascular injury often persist or worsen after bacterial clearance, suggesting ongoing toxicity from released bacterial components. Here we identify bacterial histone-like proteins (HLPs), small positively charged DNA-binding proteins conserved across bacterial species, as previously unrecognized mediators of vascular damage. In vitro HLPs are released following antibiotic exposure, disrupting endothelial integrity. In patients with severe sepsis, they are detectable in plasma and tissue, colocalising with areas of vascular leak and coagulopathy. Non-anticoagulant heparins and anti-HLP antibodies neutralize HLP-induced endothelial disruption and toxicity in vitro and in vivo . These findings reveal HLPs as antibiotic-released bacterial toxins and suggest new therapeutic strategies to prevent vascular injury in sepsis. One sentence summary: Antibiotic treatment of meningococcal and other sepsis causative bacteria triggers the release of histone-like proteins (HLPs) that damage the endothelium and drive coagulopathy, but these effects can be neutralized by non-anticoagulant heparins or anti-HLP antibodies.

Attaching and effacing pathogens, including enterohemorrhagic Escherichia coli (EHEC), colonize their preferred intestinal niche by sensing diverse host-, diet-, and microbiota-derived signals and coordinating the expression of virulence factors. D-serine, a host metabolite abundant in urine but scarce in the intestine, restricts EHEC colonization by transcriptionally repressing the type 3 secretion system (T3SS) while activating the SOS stress response. However, the mechanism underlying virulence regulation by D-serine remains unestablished. Here, we show that multiple amino acids, including L-serine converge on this pathway, repressing the T3SS without inducing the SOS response. Transcriptomic analyses showed a common response to D- and L-serine dominated by repression of nitrogen stress response genes. Mutational analysis identified the response regulators NtrC and Nac as essential mediators of T3SS repression by both serine enantiomers. Disruption of L-serine deaminase enzymes crucially revealed that T3SS repression depends on cytoplasmic ammonia/ammonium release rather than sensing of intact serine. While EHEC lacks canonical D-serine catabolic capacity, through metabolomics we provide evidence of oxidative deamination activity, capable of producing this regulatory signal. Together, these findings establish a mechanistic link between amino acid catabolism, nitrogen stress signaling, and virulence regulation in EHEC, highlighting how metabolic flux fine-tunes pathogen adaptation to intestinal niches.

OBJECTIVES: Secondary infections are a common occurrence in critically ill COVID-19 patients. These are difficult to identify, and antibiotic usage is high in this population. Identification of biomarkers for secondary infections would help to ensure antibiotics are being utilized only for patients who require them. This study sought to identify a panel of biomarkers capable of distinguishing critically ill COVID-19 patients with and without secondary infections. DESIGN: A multicenter retrospective cohort study. SETTING: Three critical care units in Scotland, United Kingdom. PATIENTS: One hundred five patients admitted to critical care with COVID-19, and 49 healthy volunteer controls. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Serial blood samples were obtained from critically ill COVID-19 patients with and without confirmed secondary infections, and a single sample was collected from healthy volunteers to provide baseline metabolic profiles. Metabolomic analysis was performed using liquid chromatography-mass spectrometry, and metabolites that were significantly different between patients with and without secondary infections were identified. Additionally, metabolites capable of distinguishing Gram-positive from Gram-negative organisms were also investigated. Forty patients developed a secondary infection during the study period. A significant increase in metabolites creatine and 2-hydroxyisovalerylcarnitine, and a significant reduction in S-methyl-L-cysteine were detected in patients with secondary infections. This metabolite panel could identify patients with secondary infections with an area under the curve (AUC) of 0.83 (95% CI, 0.68–0.97). Metabolites differentiating Gram-positive and Gram-negative infections included betaine, N(6)-methyllysine, and phosphatidylcholines (PCs; 38:6), PC(38:4), PC(40:6), and PC(36:4) with an AUC of 0.88 (95% CI, 0.68–1.0). CONCLUSIONS: Metabolomic profiling of critically ill COVID-19 shows promise for identification of novel biomarkers for secondary infections. Larger validation studies will help to confirm these findings.

Bacteria use diverse defence systems to resist phage predation, many of which cluster within mobile genetic elements (MGEs) and defence islands. In Pseudomonas aeruginosa, genomic and pathogenicity islands—such as the pathogenicity islands (PAPI), genomic islands (PAGI), and Liverpool epidemic strain islands (LESGI)—have been linked to virulence and adaptation, but their contribution to the organization and spread of defence systems remains unexplored. Here, we show that these islands serve as hubs for the assembly and spread of defence systems, revealing an underappreciated role in shaping the bacterium’s antiviral arsenal. We identify 11 conserved hotspots that encode defence and anti-defence genes, but rarely co-occur with virulence factors, resistance genes, or interbacterial competition modules. The frequent co-occurrence of defence and anti-defence genes within these loci points to an ongoing, intense molecular arms race between bacteria, MGEs, and lytic phages. Notably, these hotspots are found beyond their original island contexts, appearing across diverse Pseudomonas species and, in some cases, other genera. Together, our findings expand the known bacterial immunity landscape in P. aeruginosa, redefine the roles of these islands as defence and anti-defence reservoirs, and establish a framework for scalable discovery and annotation of novel defence and anti-defence systems in bacterial genomes.

Enterohaemorrhagic Escherichia coli causes sporadic, and sometimes large-scale, food poisoning outbreaks, for which antibiotic treatment in humans is contraindicated. As an alternative form of therapy, previous studies developed the family of salicylidene acylhydrazide (SA) anti-virulence compounds. One target of the SA compounds is AdhE, an enzyme that converts acetyl-CoA to ethanol and vice versa. AdhE oligomerizes, forming helicoidal filaments, heterogeneous in length, called spirosomes. We show it is possible to only partially fractionate AdhE spirosomes because in vitro they oligomerize in the absence of stimuli, and that spirosome formation is necessary to regulate the direction of AdhE enzymatic reactions. We also show that the SA compound ME0054 binds and perturbs AdhE spirosomes, enhancing the conversion of ethanol to acetyl-CoA. This mechanistic understanding of how ME0054 impacts AdhE function will help in the development of SA compounds as novel anti-virulence inhibitors.

Shiga Toxin-Producing E. coli (STEC) are a group of acute small intestine pathogens responsible for foodborne outbreaks of bloody diarrhoea. The expression of Shiga toxins (Stx) carried by STEC can initiate Haemolytic Uremic Syndrome (HUS), a major cause of acute renal failure in children. Here, we investigate the anti-virulence potential of Aurodox - a natural product of Streptomyces goldiniensis. Previously, we have shown that Aurodox downregulates the expression of the T3SS, inhibiting epithelial cell colonisation in vitro. Here, we use the Citrobacter rodentium DBS770 (Cr Stx2_dact) model of STEC infection to demonstrate that Aurodox protects mice against Citrobacter rodentium-associated colonic hyperplasia and Stx-mediated renal injury. Given antibiotic-associated dysbiosis of the gut is associated with inflammation and the emergence of opportunistic pathogens, we examined the effect of Aurodox on the faecal bacteriome. We show that although the microbial community is altered following Aurodox treatment, changes are distinct from those associated with traditional antibiotic therapies.

We present the manufacture and characterisation of a 3D‐printed, low‐cost optical microscope using both a 3D‐printed chassis and 3D‐printed illumination and imaging optics. The required commercial components, consisting of a basic camera for image acquisition and light emitting diode controlled by a Raspberry Pi for illumination, are integrated into the 3D‐printed microscope with the full design shown for ease of replication. Our 3D‐printed microscope uses a single 3D‐printed objective lens with a 2.9× magnification and a numerical aperture of 0.07. To benchmark the imaging performance of the system, we used standard test targets and histological specimens, namely, a Giemsa‐stained blood smear sample and a thin section of mouse kidney stained with haemotoxylin and eosin. We demonstrated that subcellular resolution was obtained, and we corroborated this by imaging individual red blood cells and intricate anatomical details of the stained mouse kidney section. All of this was achieved using entirely 3D‐printed hardware and optics, at a fraction of the cost of a commercial bright‐field microscope, while presenting remarkable potential for customisation and increased accessibility for diagnostic imaging applications.

We present the manufacture and characterisation of a fully 3D printed, low-cost optical microscope using both a 3D printed chassis and 3D printed illumination and imaging optics. The required commercial components, consisting of a basic camera for image acquisition and light emitting diode controlled by a Raspberry Pi for illumination, are integrated into the 3D printed microscope with the full design shown for ease of replication. Our 3D printed microscope uses a single 3D printed objective lens with a 2.9x magnification and a numerical aperture of 0.07. To benchmark the imaging performance of the system, we used standard test targets and histological specimens, namely, a Giemsa-stained blood smear sample and a thin section of mouse kidney stained with Haemotoxylin and Eosin. We demonstrated that sub-cellular resolution was obtained, and we corroborated this by imaging individual red blood cells and intricate anatomical details of the stained mouse kidney section. All of this was achieved using entirely 3D printed hardware and optics, at a fraction of the cost of a commercial brightfield microscope, while presenting remarkable potential for customisation and increased accessibility for diagnostic imaging applications.

Gram-negative pathogens pose a significant threat due to their propensity for causing various infections, often coupled with formidable resistance to conventional antibiotic treatments. The development of antivirulence (AV) compounds emerges as a promising alternative strategy by disrupting virulence mechanisms rather than targeting bacterial viability. Aurodox has exhibited promising AV properties in previous studies by blocking the expression and function of the LEE-encoded type 3 secretion system (T3SS) in enterohaemorrhagic Escherichia coli , an injectosome that translocates effector proteins directly into host target cells. However, aurodox’s efficacy against the T3SS of other pathogens remained unanswered. Using quantitative real-time polymerase chain reaction, we show that aurodox exerts inhibitory effects on selected T3SS including those of Salmonella Typhimurium, Yersinia pseudotuberculosis and Vibrio parahaemolyticus . Imaging of RAW 264.7 cells infected with S . Typhimurium showed that aurodox protects against late stages of infection by blocking the expression of the SPI-2 T3SS. To elucidate a conserved mechanism of action, we compared transcriptomic datasets from both E. coli and S . Typhimurium treated with aurodox to identify orthologous genes differentially expressed in response to aurodox treatment across both pathogens. This study sheds light on potential mechanisms driving the action of this promising AV compound.