Quinn, M. C. | Search bioRxiv

bioRxiv2026

Antimicrobial resistance at the animal / environment interface: phenotypic detection and persistence of ESBL and carbapenemase producing Enterobacterales in Irish cattle systems

Antimicrobial resistance (AMR) is a critical One Health challenge at the interface of agriculture, the environment and human health. In Ireland, cattle production systems generate large volumes of manure and slurry, which are routinely applied to land. However, data on the prevalence and environmental persistence of clinically important resistance phenotypes remain limited. This study investigated the occurrence, characterisation and persistence of extended-spectrum {beta}-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CPE), as well as fluoroquinolone-resistant bacteria on Irish cattle farms. A total of 450 pooled bovine faecal samples were collected from farms across 25 counties, screened using selective culture, antimicrobial susceptibility testing, and MALDI-TOF MS identification. Carbapenemase activity in presumptive CPE isolates was confirmed using phenotypic and biochemical assays, including MALDI-TOF MBT STAR analysis to demonstrate carbapenem hydrolysis. In parallel, a controlled persistence study evaluated the survival of phenotypically resistant ESBL and CPE bacteria in bovine slurry under simulated seasonal conditions. Overall, 29.6% of farms were positive for ESBL and/or CPE, with ESBL only resistance most prevalent (13.7%), followed by combined ESBL and CPE phenotypes (7.5%). Fluoroquinolone resistance was frequently detected and commonly co-occurred with {beta}-lactam resistance, indicating multidrug resistance. Escherichia coli was the dominant carrier of both ESBL and carbapenemase phenotypes. Persistence experiments demonstrated sustained phenotypic resistance in slurry for up to nine months under simulated winter conditions and up to three months during simulated summer conditions, with resistance becoming undetectable following extended verification. These findings demonstrate that clinically important AMR phenotypes are embedded within Irish cattle production systems and can persist in agricultural waste streams, highlighting slurry as a significant environmental reservoir with implications for environmental dissemination and One Health surveillance.

microbiology↗

bioRxiv2022

Individual Astrocyte Morphology in the Collagenous Lamina Cribrosa Revealed by Multicolor DiOlistic Labeling

Astrocytes in the lamina region of the optic nerve head play vital roles in supporting retinal ganglion cell axon health. In glaucoma, these astrocytes are implicated as early responders to stressors, undergoing characteristic changes in cell function as well as cell morphology. Much of what is currently known about individual lamina astrocyte morphology has been learned from rodent models which lack a defining feature of the human optic nerve head, the collagenous lamina cribrosa (LC). Current methods available for evaluation of collagenous LC astrocyte morphology have significant shortcomings. We aimed to evaluate Multicolor DiOlistic labeling (MuDi) as an approach to reveal individual astrocyte morphologies across the collagenous LC. Gold microcarriers were coated with all combinations of three fluorescent cell membrane dyes, DiI, DiD, and DiO, for a total of seven dye combinations. Microcarriers were delivered to 150m-thick coronal vibratome slices through the LC of pig, sheep, goat, and monkey eyes via MuDi. Labeled tissues were imaged with confocal and second harmonic generation microscopy to visualize dyed cells and LC collagenous beams, respectively. GFAP labeling of DiOlistically-labeled cells with astrocyte morphologies was used to investigate cell identity. 3D models of astrocytes were created from confocal image stacks for quantification of morphological features. DiOlistic labeling revealed fine details of LC astrocyte morphologies including somas, primary branches, higher-order branches, and end-feet. Labeled cells with astrocyte morphologies were GFAP+. Astrocytes were visible across seven distinct color channels, allowing high labeling density while still distinguishing individual cells from their neighbors. MuDi was capable of revealing tens to hundreds of collagenous LC astrocytes, in situ, with a single application. 3D astrocyte models allowed automated quantification of morphological features including branch number, length, thickness, hierarchy, and straightness as well as Sholl analysis. MuDi labeling provides an opportunity to investigate morphologies of collagenous LC astrocytes, providing both qualitative and quantitative detail, in healthy tissues. This approach may open doors for research of glaucoma, where astrocyte morphological alterations are thought to coincide with key functional changes related to disease progression.

bioengineering↗