Biology subjects

Clokie, M. R.

Publications and source records attributed to Clokie, M. R..

6 recordsLinked to original sources

bioRxiv2026

Isolation and characterisation of Lytic Jumbo Klebsiella phage BMPCR_005026

Background: Klebsiella pneumoniae is a key causative agent of multidrug resistant nosocomial infections. Bacteriophages offer a promising alternative treatment, but the diversity of Klebsiella species requires the characterisation of a broad range of phages, particularly the poorly characterised jumbo phages. Materials and Methods: Phage BMCPR_005026 was isolated from sewage against Klebsiella pneumoniae. Whole genome sequencing, transmission electron microscopy and host range analysis against a diverse set of 40 clinically relevant Klebsiella strains were used to characterise the phage. Results: The virion had a myovirus morphology and genomic analysis placed it within an undefined family in Caudoviricetes where it forms a new species within the genus Alcyoneusvirus. BMCPR_005026 could form plaques on 3 of the 40 Klebsiella strains tested (7.5%) and formed halos. Conclusion: BMCPR_005026 represents a new species of phage within the genus Alcyoneusvirus with activity against 3 Klebsiella KL-types.

microbiology↗

bioRxiv2026

Large scale antibiotic-phage synergy studies reveal key combinations for urinary tract infection and urosepsis treatments

The growing problem of AMR infections in healthcare has prompted the search for alternative treatments, with increasing interest in bacteriophages. However, most bacteriophage-antibiotic interactions are incompletely understood, and the benefits of combining them remains context dependent. In this study, we screened thousands of phage-antibiotic combinations to assess interaction outcomes in clinical E. coli and K. pneumoniae isolates. By integrating bacteriophages into an existing, scalable clinical MIC determination platform, we identified shifts in antibiotic MIC and susceptibility, revealing patterns of additivity and antagonism. Overall, interactions showed a species-specific profile; additive interactions predominated, particularly for E. coli. Hierarchical clustering highlighted frequent positive interactions between {beta}-lactams and Tequatroviruses. Notably, closely related phages sometimes displayed divergent phenotypes, indicating that interaction outcomes cannot be inferred solely from taxonomic relatedness or genomic similarity. Taken together, these results establish a foundation for rational, evidence-based development of phage-antibiotic therapies to restore and broaden treatment options against multidrug-resistant infections.

microbiology↗

bioRxiv2025

Characterisation of novel bacteriophages against the cattle pathogen Moraxella bovis

BackgroundInfectious bovine keratoconjunctivitis is the most important cattle ocular disease worldwide. The infection is primarily caused by Moraxella bovis and is a highly contagious disease that significantly affects cattle welfare. Currently, antibiotic medication is the primary treatment for infectious bovine keratoconjunctivitis. However, with rising concerns over antibiotic resistance, we propose developing a more targeted therapeutic strategy using bacteriophages (phages). Materials and MethodsWe have isolated the first known Moraxella bovis phages, characterised them according to their genome sequence, local virulence index and with transmission electron microscopy. The host ranges were assessed using 41 clinical M. bovis strains isolated from infected cows. ResultsFour phages were isolated and characterised. Comparative analysis identified a high degree of genomic similarity between the phages MB15, MB16, MB26 and MB43. MB43 was the most distinct, with the smallest host range phenotype. ConclusionsThe isolated phages show therapeutic potential for further development against Moraxella infections.

microbiology↗

bioRxiv2025

Bacteriophage diversity declines with COPD severity in the respiratory microbiome

Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterised the lung virome by re-analysing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. Whilst viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Phages infecting anaerobic oral bacteria showed disproportionately lower abundance--Porphyromonas phages were 40-fold less abundant despite only 4-fold lower bacterial abundance--whilst pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonised patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognised feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.

microbiology↗

bioRxiv2020

Analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolates of bacteria

Antimicrobial resistance (AMR) is a major problem globally. The main bacterial organisms associated with urinary tract infection (UTI) associated sepsis are E. coli and Klebsiella along with Enterobacter species. These all have AMR strains known as ESBL (Extended Spectrum Beta-Lactamase), which are featured on the WHO priority pathogens list as critical for research. Bacteriophages (phages) as viruses that can infect and kill bacteria, could provide an effective tool to tackle these AMR strains. There is currently no gold standard for developing a phage cocktail. Here we describe a novel approach to develop an effective phage cocktail against a set of ESBL-producing E. coli and Klebsiella largely isolated from patients in UK hospitals. By comparing different measures of phage efficacy, we show which are the most robust, and suggest an efficient screening cascade that could be used to develop phage cocktails to target other AMR bacterial species. A target panel of 38 ESBL-producing clinical strains isolated from urine samples was collated and used to test phage efficacy. After an initial screening of 68 phages, six were identified and tested against these 38 strains to determine their clinical coverage and killing efficiency. To achieve this, we assessed four different methods to assess phage virulence across these bacterial isolates. These were the Direct Spot Test (DST), the Efficiency of Plating (EOP) assay, the planktonic killing assay and the biofilm assay. The final ESBL cocktail of six phages could effectively kill 23/38 strains (61%) for Klebsiella 13/19 (68%) and for E. coli 10/19 (53%) based on the planktonic killing assay data. The ESBL E. coli collection had six isolates from the prevalent UTI-associated ST131 sequence type, five of which were targeted effectively by the final cocktail. Of the four methods used to assess phage virulence, the data suggests that planktonic killing assays are as effective as the much more time-consuming EOPs and data for the two assays correlates well. This suggests that planktonic killing is a good proxy to determine which phages should be used in a cocktail. This assay when combined with the virulence index also allows phage synergy to inform cocktail design.

microbiology↗

bioRxiv2020

Rapid discovery of novel prophages using biological feature engineering and machine learning

Prophages are phages that are integrated into bacterial genomes and which are key to understanding many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity, yet this remains the paradigm and thus many phages remain unidentified. We present a novel, fast and generalizing machine learning method based on feature space to facilitate novel prophage discovery. To validate the approach, we reanalyzed publicly available marine viromes and single-cell genomes using our feature-based approaches and found consistently more phages than were detected using current state-of-the-art tools while being notably faster. This demonstrates that our approach significantly enhances bacteriophage discovery and thus provides a new starting point for exploring new biologies.

bioinformatics↗