publications

Post V*, Pascoe B*, Mourkas E, Calland JK, Hitchings MD, Erichsen C, Fischer J, Morgenstern M, Richards RG, Sheppard SK**, Moriarty TF** (2024) 

Methicillin-sensitive Staphylococcus aureus lineages contribute towards poor patient outcomes in orthopaedic device-related infections

Microbial Genomics (Accepted); medRxiv doi: 10.1101/2022.10.21.22280349 

Garcias B, Monteith W, Vidal A, Aguirre L, Pascoe B, Mourkas E, Sheppard SK, Martin M, Darwich L (2024)

Plasmid and Chromosomal Locations of Antibiotic, Biocide and Heavy Metal Resistance Genes in Escherichia coli isolates from Pigs in Catalonia (Spain) 

Microbial Genomics (Accepted)

Cooper KK, Mourkas E, Schiaffino F, Parker CT, Pinedo T, Garcia_Bardales P, Peñataro_Yori P, Paredes_Olortegui M, Manzanares K, Romaina_Cachique L, Silva_Delgado H, Hitchings MD,Huynh, Sheppard SK, Pascoe B and Kosek MN

Sharing of cmeRABC alleles between C. coli and C. jejuni associated with extensive drug resistance in Campylobacter isolates from infants and poultry in the Peruvian Amazon

mBio (Accepted)

Schiaffino F*, Colston JM*, Paredes Olortegui M, Penataro Yori P, Mourkas E, Pascoe B, Lima AAM, Mason CJ, Ahmed T, Kang G, Mduma E, Samie A, Zaidi A, Liu J, Cooper KK, Houpt E, Parker CT, Lee GO, Kosek MN (2024)

The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0–24 months of age in resource-limited settings 

The Lancet Discovery Science [eClinicalMedicine] 76: 102841

Pascoe B, Futcher G, Pensar J, Bayliss SC, Mourkas E, Calland JK, Hitchings MD, Joseph LA, Lane CG, Greenlee T, Arning N, Wilson D, Jolley KA, Corander J, Maiden MCJ, Parker CT, Cooper KK, Rose EB, Bruce BB, Sheppard SK* (2024)

Machine learning to attribute the source of Campylobacter infections in the United States: a retrospective analysis of national surveillance data

Journal of Infection 89(5): 106265; doi: 10.1016/j.jinf.2024.106265; SSRN preprint doi: 10.2139/ssrn.4671846

Prasertsee T, Prachantasena S, Tantitaveewattana P, Chuaythammakit P, Pascoe B*, Patchanee P* (2024)

Assessing antimicrobial resistance profiles of Salmonella enterica in the pork production system

Journal of Medical Microbiology 73 (9): 001894; doi: 10.1099/jmm.0.001894

Mourkas E, Valbenito JO, Marsh H, Hitchings MD, Cooper KK, Parker CT, Székely T, Johansson H, Ellström P, Pascoe B, Waldenström J, Sheppard SK (2024)

Proximity to humans is associated with antimicrobial resistant enteric pathogens in wild bird microbiomes

Current Biology 17 3955-3965; bioRxiv doi: 10.1101/2023.07.11.548564 [Linked opinion piece]

Garcias B, Flores MA, Fernández M, Monteith W, Pascoe B, Sheppard SK, Martín M, Cortey M, Darwich L (2024)

Global variation in Escherichia coli mcr-1 genes and plasmids from animal and human genomes following colistin usage restrictions in livestock. 

Antibiotics 13(8): 759

Vale FF, HpGP Research Network, Roberts RJ, Kobayashi I, Camargo MC, Rabkin CS (2024) [Consortium member]

Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project. 

Gut Microbes 16: 2379440

Shamanna V, Srinivas S, Couto N*, Nagaraj G, Sajankila SP, Krishnappa HG, Kumar KA, Aanensen DM, Lingegowda RK* and the NIHR Global Health Research Unit consortium (2024) [consortium member]

Geographical distribution, disease association and diversity of Klebsiella pneumoniae K/L and O antigens in India: roadmap for vaccine development

Microbial Genomics 10(7): 001271; bioRxiv doi: 10.1101/2024.03.15.585133

Calland JK, Pesonen ME, Mehat J, Pascoe B, Haydon DJ, Lourenco J, Lukasiewicz B, Mourkas E, Hitchings MD, La Ragione R, Hammond P, Wallis T, Corander J*, Sheppard SK* (2024)

Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork

npj Vaccines 9(1): 105; bioRxiv doi: 10.1101/2023.11.09.566360

Taylor AJ, Yahara K, Pascoe B, Ko S, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA, Kobras CM, Bayliss SC, Williams NJ, van Vliet AHM, Parkhill J, Maiden MCJ, Corander J, Hurst LD, Falush D, Keim P, Didelot X, Kelly DJ*, Sheppard SK* (2024) 

Epistasis, core-genome disharmony, and adaptation in recombining bacteria

mBio 15(6): e00581-24, doi: 10.1128/mbio.00581-24; bioRxiv doi: 10.1101/2021.03.15.435406 

Schiaffino F, Parker CT, Garcia Bardales PF, Huynh S, Manzanares Villanueva K, Mourkas E, Pascoe B, Peñataro Yori P, Paredes Olortegui M, Cooper KK, Kosek MN (2024)

Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool

PLoS Neglected Tropical Diseases 18(3): e0012018

Schiaffino F, Parker CT, Paredes-Olortegu M, Pascoe B, Manzanares-Villanueva K, Garcia-Bardales PF, Mourkas E, Huynh S, Peñataro-Yori P, Romaina-Cachique L, Gray HK, Salvatierra G, Silva-Delgado H, Sheppard SK, Cooper KK* & Kosek MN* (2024) 

Genomic resistant determinants of multidrug resistant Campylobacter spp. isolates in Peru

Journal of Global Antimicrobial Resistance 36: 309-318

Eiamsam-ang T, Tadee Pa, Buddhasiri S, Chuammitri P, Kittiwan N, Pascoe B*, Patchanee P* (2024)

Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes

Journal of Medical Microbiology 73 (1):1787; bioRxiv doi: 10.1101/2023.07.03.547425

Calland JK, Pascoe B, Bayliss SC, Mourkas E, Thorpe HA, Berthenet E, Hitchings MD, Feil EJ, Corander J, Blaser MJ, Falush D* & Sheppard SK* (2021) 

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

PLoS Genetics 17(9): e1009829 bioRxiv doi: 10.1101/2020.12.02.407999

Peters S*, Pascoe B*, Wu Z, Bayliss SC, Zeng X, Edogawa S, Edwinson A, Veerabadhran-Gurunathan S, Jawahir S, Calland JK, Mourkas E, Patel R, Wiens T, Decur M, Boxrud D, Smith K, Parker CT, Farrugia G, Zhang Q, Sheppard SK**, Grover M** (2021) 

Campylobacter jejuni genotypes associated with post infection irritable bowel syndrome in humans

Communications Biology 4: 1015

Patchanee P, Chokesajjawatee N, Santiyanount P, Chuammitri P, Deeudom M, Monteith W, Sheppard SK, Pascoe B*, Prasertee T* (2021) 

Characterisation of Salmonella enterica clones carrying mcr-1 plasmids in meat products and patients in Northern Thailand using long read sequencing

IJFM doi: 10.1016/j.ijfoodmicro.2021.109314; bioRxiv doi: 10.1101/2020.12.08.415869

Hwang W, Yong JH, Min KB, Lee K, Pascoe B, Sheppard SK, Yoon SS (2021) 

Genome-Wide Association Study Uncovers Signature Genetic Alterations among Pseudomonas aeruginosa Cystic Fibrosis Isolates 

PLoS Pathogens 17(6):e1009681; bioRxiv doi.org: 10.1101/2020.12.02.407528

Mäklin, T, Kallonen T, David S, Boinett CJ, Pascoe B, Méric G, Aanensen DM, Feil EJ, Baker S, Parkhill J, Sheppard SK, Corander J,  Honkela A. (2021) 

High-resolution sweep metagenomics using fast probabilistic inference

Wellcome Open Research 5:14; doi: 10.12688/wellcomeopenres.15639.1; bioRxiv doi: 10.1101/332544

Mageiros L*, Méric G*, Bayliss SC, Pensar J, Pascoe B, Mourkas E, Calland JK, Yahara K, Murray S, Wilkinson TS, Williams LK, Hitchings MD, Kemmett K, Feil EJ, Jolley KA, Williams NJ, Corander J, Sheppard SK. (2021) 

Genome evolution and emergence of pathogenicity in Avian Escherichia coli

Nature Communications 12 (1): 765; doi: 10.1038/s41467-021-20988-w

Elder FCT, Feil EJ, Pascoe B, Sheppard SK, Snape J, Gaze WH, Kasprzyk-Horden (2021) 

Stereoselective bacterial metabolism of antibiotics in environmental bacteria – a novel biochemical workflow

Frontiers in Microbiology doi: 10.3389/fmicb.2021.562157

Tadee Pa, Patchanee P, Pascoe B, Sheppard SK, Meunsene D, Tadee Ph (2021) 

Occurrence and sequence type of antimicrobial resistant Salmonella spp. circulating in antibiotic-free organic pig farms of northern-Thailand

The Thai Journal of Veterinary Medicine 51(2): 311-319; bioRxiv doi: 10.1101/2020.12.16.419408 

Mouftah S*, Cobo-Diaz JF*, Álvarez-Ordóñez A, Mousa A, Calland JK, Pascoe B, Sheppard SK & Elhadidy M. (2021) 

Stress-resistance is associated with multi‐host transmission and enhanced biofilm formation among hyper-aerotolerant generalist Campylobacter jejuni

Food Microbiology 95:103706; doi: 10.1016/j.fm.2020.103706

Meunsene D, Eiamsam-Ang T, Patchanee P, Pascoe B, Tadee Ph, Tadee Pa (2021)

Molecular evidence for cross boundary spread of Salmonella spp. in meat sold at retail markets in the middle Mekong basin area

PeerJ 9, e11255

Taylor AJ, Yahara K, Pascoe B, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA, Kobras CM, Bayliss SC, Williams NJ, van Vliet AHM, Parkhill J, Maiden MCJ, Corander J, Hurst LD, Falush D, Keim P, Didelot X, Kelly DJ*, Sheppard SK* (2021) 

Cross-species evolutionary rewiring in the enteric bacterium Campylobacter

bioRxiv doi: 10.1101/2021.03.15.435406 

Méric, G.*, Mageiros, M.*, Pensar, J., Laabei, M., Yahara, K., Pascoe, B., Kittiwan, Tadee Ph., N., Lamble, S., Bowden, R., Jolley, KA., Maiden, MCJ., Feil, EJ., Didelot, X., Miragaia, M., de Lencastre, H., Rohde, H., Massey, R., Mack, D., Corander, J. & Sheppard, SK. (2018) 

A pathogen in plain sight: disease-causing genotypes of the commensal skin bacterium Staphylococcus epidermidis

Nature Communications 9:5034; doi: 10.1038/s41467-018-07368-7

Dunn, S., Pascoe, B., Turton J, Fleming V, Diggle M, Sheppard, SK., Manning, G. & McNally, A. (2018)

Genomic Epidemiology of clinical Campylobacter spp. at a single health trust site

Microbial Genomics 4; doi: 10.1099/mgen.0.000227 

Berthenet, E., Yahara, K., Thorell, K., Pascoe, B., Méric, G., Mikhail, JM., Engstrand, L., Enroth, H.,Burette, A., Mégraud, F., Varon, C., Atherton, J., Smith, S., Wilkinson, TS., Hitchings, MD., Falush, D. & Sheppard, SK. (2018)

Predicting gastric cancer risk: small Helicobacter pylori genome-wide association study shows promise

BMC Biology 16:84

Bayliss, SC., Verner-Jeffries D, Ryder D, Suarez R, Ramirez R, Romero J, Pascoe B, Sheppard SK, Godoy M, Feil EJ. (2018)

Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry

Microbial Genomics doi:10.1099/mgen.0.000201

Yokoyama, M., Stevens, E., Laabei, M., Bacon L., Heesom K., Bayliss, S., Ooi, N., O’Neill, A., Murray, E., Williams, P., Lubben, A., Reeksting, S., Méric, G., Pascoe, B., Sheppard, SK., Recker, M., Hurst, L. & Massey, RC. (2018)

Hidden antibiotic resistance fitness costs revealed by GWAS-based epistasis analysis

Genome Biology 19:94 doi: 10.1186/s13059-018-1469-2 [BioRxiv: doi.org/10.1101/148825] 

Tadee, Pa., Boonkhot, P., Hitchings, MD., Pascoe, B., Sheppard, SK. & Patchane, P. (2018)

Whole genome Multilocus Sequence Typing (wgMLST) and acquired antimicrobials resistance genes of pan-susceptible Salmonella Weltevreden from Thai pork production processes

Microbiology and Biotechnology Letters 46(2): 162-170

Atterby, C., Mourkas, E., Méric, G., Pascoe, B., Wang, H., Waldenström, J., Sheppard, SK., Olsen, B., Järhult, J. & Ellström, P. (2018)

The potential of isolation source to predict colonisation in avian hosts: A case study in Campylobacter jejuni strains from three bird species 

Frontiers in Microbiology 9:591 doi: 10.3389/fmicb.2018.00591

Méric, G., Mageiros, M., Pascoe, B., Woodcock D., Mourkas, E., Lamble, S., Bowden, R., Jolley, KA., Raymond, B. & Sheppard, SK. (2018)

Lineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group 

Molecular Ecology 27(7): 1524-1540 doi: 10.1111/mec.14546

Méric, G., McNally, A., Pessia, A., Mourkas, E., Pascoe, B., Mageiros, M., Vehkala, M., Corander, J. & Sheppard, SK. (2018)

Convergent amino acid signatures in paraphyletic Campylobacter jejuni sub-populations suggest human niche tropism

Genome Biology & Evolution 10 (3): 763-774; doi:10.1093/gbe/evy026 

Kirk, KF., Méric, G., Nielsen, HL., Pascoe, B., Sheppard, SK., Thorlacius-Ussing, O. & Nielsen, H. (2018) 

Molecular epidemiology and comparative genomics and typing of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease 

Scientific Reports 8:1902; doi:10.1038/s41598-018-20135-4 

Rossi, GAM., Silva, HO., Aguilar, CEG., Rochetti, A., Pascoe, B., Méric, G., Mourkas, E., Hitchings, MD., Mathias., LA., de Azevedo-Ruiz, VL., Fukumasu, H., Sheppard, SK. & Vidal, AMC. (2018) 

Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil 

FEMS Microbiology Letters 365(3); doi: 10.1093/femsle/fnx283

Pascoe B, Méric G, Murray S, Yahara K, Magerios L, Bowen R, Jones NH, Jeeves RE, Lappin-Scott HM, Asakura H, Sheppard SK (2015) 

Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni. 

Environmental Microbiology 17:(11) 4779–4789

Richards RL, Haigh RD, Pascoe B, Sheppard SK, Price F, Jenkins D, Rajakumar K, Morrissey JA. (2015) 

Persistent Staphylococcus aureus isolates from two independent bacteraemia display increased bacterial fitness and novel immune evasion phenotypes. 

Infection and Immunity 83 (8): 3311-24

Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MCJ, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK (2015) 

Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis. 

Genome Biology and Evolution 7 (5): 1313-28

Baily JL, Méric G, Bayliss S, Foster G, Moss SE, Watson E, Pascoe B, Mikhail J, Pizzi R, Goldstone RJ, Smith DG, Willoughby K, Hall AJ, Sheppard SK*, Dagleish MP* (2015) 

Evidence of land-sea transfer of the zoonotic pathogen Campylobacter to a wildlife marine sentinel species. 

Molecular Ecology 24 (1): 208-21

Méric G, Yahara K, Mageiros L, Pascoe B, Maiden MCJ, Jolley KA, Sheppard SK (2014) 

A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter. 

PLoS ONE 9(3): e92798

Pascoe, B; Dams, L; Wilkinson, TS; Harris, LG; Bodger, O; Mack, D; Davies, AP. (2014) 

Dormant cells of Staphylococcus aureus are resuscitated by spent culture supernatant. 

PLoS One 9 (2): e85998

Sheppard, SK; Didelot, X; Jolley, KA; Darling, AE; Pascoe, B; Méric, G; Kelly, DJ; Cody, A; Colles, FM; Strachan, NJC; Ogden, ID; Forbes, K; French, NP; Carter, P; Miller, WG; McCarthy, ND; Owen, R; Litrup, E; Egholm, M; Affourtit, JP; Bentley, SD; Parkhill, J; Maiden, MCJ & Falush, D (2012) 

Progressive genome-wide introgression in agricultural Campylobacter coli 

Molecular Ecology. 2013 22 (4):1051-64

Mack, D.; Harris, LG.; Jeeves, RE.; Pascoe, B.; Davies, AP.; Wilkinson, TS. (2011) 

Mechanisms of Staphylococcus epidermidis biofilm formation in different types of biomaterial-related infections. 

European Cells & Materials 21 (S2) 21-22 

Kallifidas, D*; Pascoe, B*; Owen, GA; Strain, CM; Hong, HG & Paget, MSB (2010) 

The Zinc-responsive Regulator Zur Controls Expression of the Coelibactin Gene Cluster in Streptomyces coelicolor. 

J Bact 192: (2) 608-611

Owen, GA*; Pascoe, B*; Kallifidas, D & Paget, MSB. (2007) 

Zinc-responsive regulation of alternative ribosomal protein genes in Streptomyces coelicolor involves Zur and σR. 

J Bact 189: (11) 4078-4086