All Outputs (26)

Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics. (2024)
Journal Article
Krishnamurthi, R., González-Tortuero, E., Plahe, G., Goodhead, I. B., Fothergill, J. L., James, C. E., & Allison, H. E. (in press). Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics. Journal of Visualized Experiments, 10.3791/64945. https://doi.org/10.3791/64945

Temperate phages are found integrated as prophages in the majority of bacterial genomes. Some prophages are cryptic and fixed in the bacterial chromosome, but others are active and can be triggered into a replicative form either spontaneously or by e... Read More about Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics..

Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages (2022)
Journal Article
Gonzalez Tortuero, E., Krishnamurthi, R., Goodhead, I., Allison, H., & James, C. (2022). Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages. Access Microbiology, 4(5), https://doi.org/10.1099/acmi.ac2021.po0318

Pseudomonas aeruginosais an important opportunistic pathogen, causing nosocomial infections. The Liverpool Epidemic Strain (LES), a major cause of mortality and morbidity in cystic fibrosis patients, harbours five prophages associated with increased... Read More about Improving phage genome annotation to understand phage biology: the case of Pseudomonas aeruginosa LES prophages.

Comparative analysis of gene prediction tools for viral genome annotation (2021)
Journal Article
Gonzalez-Tortuero, E., Krishnamurthi, R., Allison, H., Goodhead, I., & James, C. Comparative analysis of gene prediction tools for viral genome annotation. https://doi.org/10.1101/2021.12.11.472104. Manuscript submitted for publication

The number of newly available viral genomes and metagenomes has increased exponentially since the development of high throughput sequencing platforms and genome analysis tools. Bioinformatic annotation pipelines are largely based on open reading fram... Read More about Comparative analysis of gene prediction tools for viral genome annotation.

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda (2021)
Journal Article
Ackers-Johnson, G., Kibombo, D., Kusiima, B., Nsubuga, M., Kigozi, E., Kajumbula, H., …James, C. (2021). Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda. Microbiology, 167(5), 001000. https://doi.org/10.1099/mic.0.001000

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based i... Read More about Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda.

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda (2020)
Journal Article
Goodhead, I., Ackers, H., Birtles, R., & James, C. (2020). Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda. bioRxiv, https://doi.org/10.1101/2020.11.20.371203

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based i... Read More about Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda.

Ram locus is a key regulator to trigger multidrug resistance in Enterobacter aerogenes (2018)
Journal Article
Molitor, A., James, C., Fanning, S., Pages, J., & Davin-Regli, A. (2018). Ram locus is a key regulator to trigger multidrug resistance in Enterobacter aerogenes. Journal of Medical Microbiology, 67(2), 148-159. https://doi.org/10.1099/jmm.0.000667

Purpose: Several genetic regulators belonging to AraC family are involved in the emergence of MDR isolates of E. aerogenes due to alterations in membrane permeability. Compared with the genetic regulator Mar, RamA may be more relevant towards the eme... Read More about Ram locus is a key regulator to trigger multidrug resistance in Enterobacter aerogenes.

Campylobacter jejuni transcriptome changes during loss of culturability in water (2017)
Journal Article
Bronowski, C., Mustafa, K., Goodhead, I., James, C., Nelson, C., Lucaci, A., …Winstanley, C. (2017). Campylobacter jejuni transcriptome changes during loss of culturability in water. PLoS ONE, 12(11), e0188936. https://doi.org/10.1371/journal.pone.0188936

Background: Water serves as a potential reservoir for Campylobacter, the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different st... Read More about Campylobacter jejuni transcriptome changes during loss of culturability in water.

50 important research questions in microbial ecology (2017)
Journal Article
Antwis, R., Griffiths, S., Harrison, X., Aranega-Bou, P., Arce, A., Bettridge, A., …Sutherland, W. (2017). 50 important research questions in microbial ecology. FEMS Microbiology Ecology, 93(5), https://doi.org/10.1093/femsec/fix044

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth... Read More about 50 important research questions in microbial ecology.

Evolutionary diversification of Pseudomonas aeruginosa in an artificial sputum model (2017)
Journal Article
Davies, E., James, C., Brockhurst, M., & Winstanley, C. (2017). Evolutionary diversification of Pseudomonas aeruginosa in an artificial sputum model. BMC Microbiology, 17(3), https://doi.org/10.1186/s12866-016-0916-z

Background During chronic lung infections of cystic fibrosis patients Pseudomonas aeruginosa populations undergo extensive evolutionary diversification. However, the selective drivers of this evolutionary process are poorly understood. To test the e... Read More about Evolutionary diversification of Pseudomonas aeruginosa in an artificial sputum model.

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms (2016)
Journal Article
Davies, E., James, C., Williams, D., O'Brien, S., Fothergill, J., Haldenby, S., …Brockhurst, M. (2016). Temperate phages both mediate and drive adaptive evolution in pathogen biofilms. Proceedings of the National Academy of Sciences, 113(29), 8266-8271. https://doi.org/10.1073/pnas.1520056113

Temperate phages drive genomic diversification in bacterial pathogens. Phage-derived sequences are more common in pathogenic than non-pathogenic taxa, and are associated with changes in pathogen virulence. High abundance and mobilisation of temper... Read More about Temperate phages both mediate and drive adaptive evolution in pathogen biofilms.

Temperate phages enhance pathogen fitness in chronic lung infection (2016)
Journal Article
Davies, E. V., James, C. E., Kukavica-Ibrulj, I., Levesque, R. C., Brockhurst, M. A., & Winstanley, C. (2016). Temperate phages enhance pathogen fitness in chronic lung infection. ISME Journal, 10(10), 2553-2555. https://doi.org/10.1038/ismej.2016.51

The Liverpool Epidemic Strain (LES) is a polylysogenic, transmissible strain of Pseudomonas aeruginosa, capable of superinfecting existing P. aeruginosa respiratory infections in individuals with cystic fibrosis (CF). The LES phages are highly active... Read More about Temperate phages enhance pathogen fitness in chronic lung infection.

The role of temperate bacteriophages in bacterial infection (2016)
Journal Article
Davies, E., Winstanley, C., Fothergill, J., & James, C. (2016). The role of temperate bacteriophages in bacterial infection. FEMS Microbiology Letters, 363(5), fnw015. https://doi.org/10.1093/femsle/fnw015

Bacteriophages are viruses that infect bacteria. There are an estimated 1031 phage on the planet, making them the most abundant form of life. We are rapidly approaching the centenary of their identification, and yet still have only a limited understa... Read More about The role of temperate bacteriophages in bacterial infection.

Polylysogeny magnifies competitiveness of a bacterial pathogen in vivo (2014)
Journal Article
Burns, N., James, C., & Harrison, E. (2015). Polylysogeny magnifies competitiveness of a bacterial pathogen in vivo. Evolutionary Applications, 8(4), 346-351. https://doi.org/10.1111/eva.12243

The rise of next generation sequencing is revealing a hidden diversity of temperate phages within the microbial community. While a handful of these phages have been well characterized, for the vast majority, the role of phage carriage, and especially... Read More about Polylysogeny magnifies competitiveness of a bacterial pathogen in vivo.

Lytic activity by temperate phages of Pseudomonas aeruginosa in long-term cystic fibrosis chronic lung infections (2014)
Journal Article
James, C. E., Davies, E. V., Fothergill, J. L., Walshaw, M. J., Beale, C. M., Brockhurst, M. A., & Winstanley, C. (2015). Lytic activity by temperate phages of Pseudomonas aeruginosa in long-term cystic fibrosis chronic lung infections. ISME Journal, 9(6), 1391-1398. https://doi.org/10.1038/ismej.2014.223

Pseudomonas aeruginosa is the most common bacterial pathogen infecting the lungs of cystic fibrosis (CF) patients. The transmissible Liverpool epidemic strain (LES) harbours multiple inducible prophages (LESϕ2; LESϕ3; LESϕ4; LESϕ5; and LESϕ6), some o... Read More about Lytic activity by temperate phages of Pseudomonas aeruginosa in long-term cystic fibrosis chronic lung infections.

Role of environmental survival in transmission of Campylobacter Jejuni (2014)
Journal Article
Bronowski, C., James, C., & Winstanley, C. (2014). Role of environmental survival in transmission of Campylobacter Jejuni. FEMS Microbiology Letters, 356(1), 8-19. https://doi.org/10.1111/1574-6968.12488

Campylobacter species are the most common cause of bacterial gastroenteritis, with C. jejuni responsible for the majority of these cases. Although it is clear that livestock, and particularly poultry, are the most common source, it is likely that the... Read More about Role of environmental survival in transmission of Campylobacter Jejuni.

Recent advances in studies of polymicrobial interactions in oral biofilms (2013)
Journal Article
James, C. (2013). Recent advances in studies of polymicrobial interactions in oral biofilms. Current Oral Health Reports, 1(1), 59-69. https://doi.org/10.1007/s40496-013-0006-3

The oral cavity supports a complex and finely balanced consortium of microbial species, many of which cooperate within structured biofilms. These communities develop through multitudinous synergistic and antagonistic interspecies relationships. Chang... Read More about Recent advances in studies of polymicrobial interactions in oral biofilms.

Use of artificial sputum medium to test antibiotic efficacy against pseudomonas aeruginosa in conditions more relevant to the cystic fibrosis lung (2012)
Journal Article
Kirchner, S., Fothergill, J., Wright, E., James, C., Mowat, E., & Winstanley, C. (2012). Use of artificial sputum medium to test antibiotic efficacy against pseudomonas aeruginosa in conditions more relevant to the cystic fibrosis lung. Journal of Visualized Experiments, 64, 1-8. https://doi.org/10.3791/3857

There is growing concern about the relevance of in vitro antimicrobial susceptibility tests when applied to isolates of P. aeruginosa from cystic fibrosis (CF) patients. Existing methods rely on single or a few isolates grown aerobically and plankto... Read More about Use of artificial sputum medium to test antibiotic efficacy against pseudomonas aeruginosa in conditions more relevant to the cystic fibrosis lung.

Differential infection properties of three inducible prophages from an epidemic strain of Pseudomonas aeruginosa (2012)
Journal Article
James, C., Fothergill, J., Kalwij, H., Hall, A., Cottell, J., Brockhurst, M., & Winstanley, C. (2012). Differential infection properties of three inducible prophages from an epidemic strain of Pseudomonas aeruginosa. BMC Microbiology, 12(216), 1-10. https://doi.org/10.1186/1471-2180-12-216

Background: Pseudomonas aeruginosa is the most common bacterial pathogen infecting the lungs of patients with cystic fibrosis (CF). The Liverpool Epidemic Strain (LES) is transmissible, capable of superseding other P. aeruginosa populations and is... Read More about Differential infection properties of three inducible prophages from an epidemic strain of Pseudomonas aeruginosa.

The effect of antibiotic treatment on bacteriophage production by a cystic fibrosis epidemic strain of Pseudomonas aeruginosa (2011)
Journal Article
Fothergill, J., Mowat, E., Walshaw, M., Ledson, M., James, C., & Winstanley, C. (2011). The effect of antibiotic treatment on bacteriophage production by a cystic fibrosis epidemic strain of Pseudomonas aeruginosa. Antimicrobial Agents and Chemotherapy, 55(1), 426-428. https://doi.org/10.1128/AAC.01257-10

Phage production in response to antibiotics varied among four isolates of a Pseudomonas aeruginosa cystic fibrosis (CF) epidemic strain. Whereas ciprofloxacin induced higher levels of phage production, other CF-relevant antibiotics led to reduced p... Read More about The effect of antibiotic treatment on bacteriophage production by a cystic fibrosis epidemic strain of Pseudomonas aeruginosa.

How beta-lactam antibiotics enter bacteria: a dialogue with the porins (2009)
Journal Article
James, C., Mahendran, K., Molitor, A., Bolla, J., Bessonov, A., Winterhalter, M., & Pages, J. (2009). How beta-lactam antibiotics enter bacteria: a dialogue with the porins. PLoS ONE, 4(5), e5453. https://doi.org/10.1371/journal.pone.0005453

BACKGROUND:Multi-drug resistant (MDR) infections have become a major concern in hospitals worldwide. This study investigates membrane translocation, which is the first step required for drug action on internal bacterial targets. beta-lactams, a major... Read More about How beta-lactam antibiotics enter bacteria: a dialogue with the porins.