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publications

Latest work

93 publications | H-index 36 | i10-index 65 | citations 3,893


ORCiD - ResearchGate - loop - publons - dimensions

*indicates joint authorship 

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preprints

Bosquez JM, Pascoe B, Parker CT, Cooper KK (2025)

Strain specific virulence signatures of Campylobacter jejuni associated with watery versus bloody diarrhea in a neonatal pig model

bioRxiv doi: 10.1101/2025.04.25.650680

Bosquez JM, Parker CT, Pascoe B, Cooper KK (2025)

Growth rates and metabolic traits differentiate Campylobacter jejuni strains by diarrheal manifestation

bioRxiv doi: 10.1101/2025.04.24.650550

Parker CT,  Kathariou S, Miller WG, Huynh S, Pascoe B, Cooper KK (2025)

American black bear (Ursus americanus) as a potential host for Campylobacter jejuni

bioRxiv doi: 10.1101/2025.04.14.648838

Prasertsee T, Chotinun S, Pascoe B*, Patchanee P* (2025) 

MLST-based molecular insights into Salmonella contamination and antimicrobial resistance in antibiotic-free indigenous broiler farms.  

Research Square preprint doi: TBC

2025

Buddhasiri S, Tadee Pa, Kittiwan N, Pascoe B*, Patchanee P* (2025)

Comparative gut microbiota and antibiotic resistance profiles of Thai indigenous Pradu Hang Dam and commercial chickens

Scientific Reports (accepted)

Post V*, Pascoe B*, Mourkas E, Calland JK, Hitchings MD, Erichsen C, Fischer J, Morgenstern M, Richards RG, Sheppard SK**, Moriarty TF** (2025) 

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

Microbial Genomics 11(4): 00132; medRxiv doi: 10.1101/2022.10.21.22280349 

Garcias B, Monteith W, Vidal A, Aguirre L, Pascoe B, Kobras CM, Hitchings MD, Sheppard SK, Martin M, Darwich L (2025)

Characterisation of Antibiotic Determinants and Heavy Metal Resistance Genes in Escherichia coli from Pigs in Catalonia

Microbial Genomics 11(3): 001371

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 (2025)

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 16 (2): e02054-24

2024

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

2023

Elsayed SW, Elghaish RA, Saif NA, Mouftah SF, Badr E, Naga IS, Shata AH, Pascoe B, Sheppard SK, Elhadidy M (2023) 

Recombination-Mediated Adaptation of Methicillin-resistant S. aureus Clonal Complex 1 in the Egyptian Health Care Settings

Annals of Clinical Microbiology and Antimicrobials 22: 109

Thorell K*, Muñoz-Ramírez ZM*, Wang D, Sandoval-Motta S, Agostini RB, Ghirotto S, Torres RC, HpGP Research Network, Falush D, Camargo MC, Rabkin CS (2023) [consortium member]

The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Nature Communications 14: 8184

Abrudan MI, Shamanna V, Prasanna A, Underwood A, Argimón S, Nagaraj G, Di Gregorio S, Govindan V, Vasanth A, Dharmavaram S, Kekre M, Aanensen DM, Ravikumar KL the NIHR Global Health Research Unit consortium. (2023) [consortium member] 

Novel multidrug-resistant sublineages of Staphylococcus aureus clonal complex 22 discovered in India 

mSphere 8(5): e00185-23

Zang X, Pascoe B, Mourkas E, Kong K, Jiao X, Sheppard SK and Huang J (2023)

Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations

Microbial Genomics 9 (10): 001121

Monteith W*, Pascoe B*, Mourkas E, Clark J, Hakim M, Hitchings MD, McCarthy N, Yahara K, Asakura H, Sheppard SK (2023)

Contrasting genes conferring short and long-term biofilm adaptation in Listeria

Microbial Genomics 9 (10): 001114; bioRxiv doi: 10.1101/2023.06.22.546149

Woodall CA*, Hammond A*, Cleary DW, Preston A, Muir P, Pascoe B, Sheppard SK, Hay AD (2023) 

Oral and gut microbiome biomarkers of susceptibility to respiratory tract infection in adults: a longitudinal cohort feasibility study

Heliyon 9 (8): e18610 doi: 10.1016/j.heliyon.2023.e18610 medRxiv doi: 10.1101/2021.12.21.21268189

Buawiratlert T, Tadee Pa, Chotinun S, Chuammitri P, Kheowsri S, Suddee W, Kittiwan N, Eiamsam-ang T, Pascoe B, Patchanee P (2023)

Prevalence and Antimicrobial-Resistant Patterns of Non-typhoidal Salmonella in Good Agricultural Practice Certified Broiler Farms and Poultry Slaughterhouses in an Intensive Farming Area in Upper Northern Part of Thailand

Veterinary Integrative Sciences 21 (3) doi: 10.12982/VIS.2023.057

Prasertsee T, Pascoe B*, Patchanee P* (2023)

Colistin resistance and resistance determinants are mobile among Salmonella enterica isolates from diseased and healthy pigs in Thailand

bioRxiv doi: 10.1101/2023.01.31.526471

2022

Kittiwan N, Calland JK, Mourkas E, Hitchings MD, Murray S, Tadee Ph, Tadee Pa, Duangsonk K, Méric G, Sheppard SK, Patchanee P*, Pascoe B* (2022) 

Non-serotype 2 isolates from healthy pigs are a potential zoonotic reservoir of Streptococcus suis genetic diversity and antimicrobial resistance 

Microbial Genomics doi: 10.1099/mgen.0.000882; bioRxiv doi: 10.1101/2021.06.17.447897

Thorpe HA*, Tourrette E*, Yahara K*, Vale FF, Liu S, Oleastro M, Alarcon T,  Perets TT, Latifi-Navid S, Yamaoka Y, Martinez-Gonzalez B, Karayiannis I, Karamitros T, Sgouras DN, Elamin W, Pascoe B, Sheppard SK, Ronkainen J, Aro P, Engstrand L, Agreus L, Suerbaum S, Thorell K, Falush D (2022)

Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

Nature Communications 13 (1), 1-11

Tucker K, Mageiros L, Carstens A, Bröcker L, Archer E, Smith K, Mourkas E, Pascoe B, Nel D, Meric G, Sheppard SK, Kasprzyk-Hordern B, Botes M, Feil EJ, Wolfaardt G (2022)

Spatiotemporal investigation of antibiotic resistance in the urban water cycle influenced by environmental and anthropogenic activity

Microbiology Spectrum 10 (5), e02473-22

Mouftah SF*, Pascoe B*, Calland JK, Mourkas E, Tonkin N, Lefevré C, Deuker D, Smith S, Wickenden H, Hitchings MD, Sheppard SK, Elhadidy M (2022) 

Local accessory gene sharing drives lineage-specific acquisition of antimicrobial resistance in Egyptian Campylobacter spp. 

Microbial Genomics 8(6):834; doi: 10.1099/mgen.0.000834; bioRxiv doi: 10.1101/2021.09.24.461243 

Eiamsam-Ang T, Tadee Pa, Pascoe B*, Patchanee P* (2022)

Genome-based analysis of infrequent Salmonella serotypes through the Thai pork production chain

Frontiers in Microbiology 3283

White H, Vos M, Sheppard SK, Pascoe B, Raymond B (2022) 

Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades

Molecular Ecology (13):3584-3597; doi: 10.1111/mec.16490

Elder FCT, Pascoe B, Wells S, Sheppard SK, Snape J, Gaze WH, Feil EJ, Kasprzyk-Hordern B (2022) Stereospecific metabolism of chloramphenicol by bacteria isolated wastewater, and the importance of stereochemistry in environmental risk assessments for antibiotics

Water Research 217:118415; doi: 10.1016/j.watres.2022.118415

Kittiwan N, Tadee Pa, Tadee Ph, Buawiratlert T, Eiamsam-ang T, Boonma O, Rojanasthien S, Pascoe B, Patchanee P (2022)

Identification of Streptococcus suis carriage in healthy pigs in Chiang Mai, Thailand

Veterinary Integrative Sciences 20 (2), 363-376

Mourkas E, Yahara K, Bayliss SC, Calland JK, Johansson H, Mageiros L, Muñoz-Ramirez ZY, Futcher G, Méric G, Hitchings MD, Sandoval-Motta S, Torres J, Jolley KA, Maidem MCJ, Ellström P, Waldenström J, Pascoe B & Sheppard SK* (2022) 

Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

eLife 11:e73552

Post V*, Pascoe B*, Mourkas E, Calland JK, Hitchings MD, Erichsen C, Fischer J, Morgenstern M, Richards RG, Sheppard SK**, Moriarty TF** (2022) 

Multiple hyper-virulent methicillin-sensitive Staphylococcus aureus lineages contribute towards poor patient outcomes in orthopaedic device-related infections

medRxiv doi: 10.1101/2022.10.21.22280349 

2021

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 

2020

Jehanne Q, Pascoe B, Bénéjat L, Ducournau A, Buissonnière A, Mourkas E, Mégraud F, Bessède E, Sheppard SK & Lehours P. (2020) 

Determination of Campylobacter coli host-segregating SNPs and their use for source attribution of clinical isolates

Applied Environmental Microbiology doi: 10.1128/AEM.01787-20

Muñoz-Ramirez ZY, Pascoe B, Mendez-Tenorio A, Mourkas E, Sandoval-Motta S, Perez-Perez G, Morgan DR, Dominguez RL, Ortiz-Princz D, Cavazza ME, Rocha G, Queiroz DMM, Catalano M, de la Palma GZ,  Goldman CG, Venegas A, Alarcon T, Oleastro M, Vale FF, Goodman KJ, Torres RC, Berthenet B, Hitchings MD, Blaser MJ, Sheppard SK, Thorell K* & Torres J* (2020) 

A five-hundred year tale of co-evolution, adaptation and virulence: Helicobacter pylori in the Americas 

ISME doi: 10.1038/s41396-020-00758-0 Nature Reviews in Microbiology [Comment] 

Pascoe B, Schiaffino F, Murray S, Méric G, Bayliss SC, Hitchings MD, Mourkas E, Calland JK, Burga R, Peñataro-Yori P, Jolley KA, Cooper KK, Parker CT, Paredes-Olortegui M, Kosek M & Sheppard SK. (2020)

Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon

PloS NTD 14(8):e0008533; doi: 10.1371/journal.pntd.0008533; medRxiv doi: 10.1101/2020.04.26.20075689

Mourkas E, Taylor AJ, Méric G, Bayliss SC, Pascoe B, Mageiros L, Calland JK, Hitchings MD, Ridley A, Vidal A, Forbes KJ, Strachan NJC, Parker CT, Parkhill J, Jolley KA, Cody AJ, Maiden MCJ, Kelly DJ*, Sheppard SK* (2020)

Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni

PNAS 117 (20) 11018-11028; doi: 10.1073/pnas.1917168117

Patchanee P, Tanamai P, Tadee Ph, Hitchings MD, Calland JK, Sheppard SK, Meunsene D, Pascoe B* & Tadee Pa* (2020)

Whole-genome characterisation of multidrug resistant monophasic variants of Salmonella Typhimurium from pig production in Thailand

PeerJ 8:e9700; doi:10.7717/peerj.9700

Nguyen LTT, Nguyen KNT, Le PNTA, Cafini F, Pascoe B, Sheppard SK, Nguyen TB, Hoang TPN, Nguyen TV, Pham TTK, Morikawa K, Nguyen DQ, Duong HX. (2020)

The emergence of plasmid-borne, cfr-mediated linezolid resistant-staphylococci in Vietnam

Journal of Global Antimicrobial Resistance 22: 462-465; doi: 10.1016/j.jgar.2020.04.008

2019

Banaszkiewicz S, Calland JK, Mourkas E, Sheppard SK, Pascoe B & Bania J. (2019)

Genetic diversity of composite enterotoxigenic Staphylococcus epidermidis pathogenicity islands

Genome Biology and Evolution 11 (12) 3498–3509; doi.org/10.1093/gbe/evz259

Mourkas E*, Florez-Cuadrado D*, Pascoe B, Calland JK, Bayliss SC, Mageiros L, Méric G, Hitchings MD, Quesada A, Porrero C, Ugarte-Ruiz M, Gutierrez-Fernandez J, Dominguez L, Sheppard SK. (2019)

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

Environmental Microbiology 21 (12) 4597-4613; doi:10.1111/1462-2920.14760

Bliss L, Pascoe B, Sheppard SK. (2019) 

Hermes: an ensemble machine learning architecture for protein secondary structure prediction

bioRxiv doi: 10.1101/640656

Pascoe B*, Williams LK*, Calland JK, Méric, G, Hitchings MD, Dyer M, Ryder J, Shaw S, Lopes BS, Chintoan-Uta C, Allan E, Vidal A, Fearnley C, Everest P, Pachebat JA, Cogan TA, Stevens MP, Humphrey TJ, Wilkinson TS, Cody AJ, Colles FM, Jolley KA, Maiden MCJ, Strachan N, Pearson BM, Linton D, Wren BW, Parkhill J, Kelly DJ, van Vliet AHM, Forbes KJ, Sheppard SK. (2019)

Domestication of Campylobacter jejuni NCTC 11168

Microbial Genomics 10.1099/mgen.0.000279; bioRxiv doi: 10.1101/591701

Prasertsee T, Chuammitri P, Deeudom M, Chokesajjawatee N, Santiyanont P, Tadee Pa, Nuangmek A, Tadee Ph, Sheppard SK, Pascoe B*, Patchanee P.* (2019)

Core genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain

IJFM doi: 10.1016/j.ijfoodmicro.2019.05.022

Royden A, Ormandy E, Pinchbeck G, Pascoe B, Hitchings MD, Sheppard SK, Williams NJ. (2019)

Prevalence of faecal carriage of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in veterinary hospital staff and students

Veterinary Record Open 6: e000307; doi: 10.1136/vetreco-2018-000307

2018

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

2017

Post, V., Morgenstern, M., Harris, LG., Mageiros, L., Hitchings, MD., Méric, G., Pascoe, B., Sheppard, SK., Richards, GR., Moriarty, TF. (2017) 

Phenotypic and genotypic characterisation of Staphylococcus epidermidis from orthopaedic device-related infections correlated with patient outcome 

Orthopaedic Proceedings 99-B (22): 65

Florez-Cuadrado, D., Ugarte-Ruiz, M., Méric, G., Quesada, A., Concepción Porrero, M., Pascoe, B., Sáez-Llorente, JL., Orozco, GL., Domínguez, L. & Sheppard, SK. (2017) 

Genome comparison of erythromycin resistant Campylobacter from turkey identifies hosts and pathways for horizontal spread of erm(B) genes 

Frontiers in Microbiology 8: 2240; DOI: 10.3389/fmicb.2017.02240

Post, V., Harris, LG., Morgenstern, M., Mageiros, L., Hitchings, MD., Méric, G., Pascoe, B., Sheppard, SK., Richards, GR. & Moriarty, TF. (2017) 

A comparative genomics study of Staphylococcus epidermidis from orthopedic device-related infections correlated with patient outcome 

Journal of Clinical Microbiology 55 (10): 3089-3103; (doi:10.1128/JCM.00881-17)

Pascoe, B.; Méric, G., Yahara, K., Wimalarathna, H., Murray, S., Hitchings, MD., Sproston, EL., Carrillo, CD., Taboada, EN., Cooper, KK., Huynh, S., Cody, A., Jolley, KA., Maiden, MCJ., McCarthy, N., Didelot, X., Parker, CT. and Sheppard, SK. (2017) 

Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations 

Molecular Ecology 26 (17): 4497-4508; DOI: 10.1111/mec.14176 [PeerJ preprint doi: 10.7287/peerj.preprints.2638v1]

Thépault, A., Méric, G., Rivoal, K., Pascoe, B., Mageiros, L., Touzain, F., Rose, V., Béven, V., Chemaly, M., Sheppard, SK. (2017) 

Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni 

Applied Environmental Microbiology 83 (7): e03085-16; doi: 10.1128/AEM.03085-16

Murray, S.*; Pascoe, B.*; Méric, G., Mageiros, L., Yahara, K., Hitchings, MD., Friedmann, Y., Gormley, FJ; Wendlandt, S; Schwarz, S.; Lamble S, Bray JE, Bowden, R.; Jolley KA, Maiden, MCJ., Corander, J.; Fitzgerald, JR.; Sheppard, SK. (2017) 

Recombination-mediated host-adaptation by avian Staphylococcus aureus. 

Genome Biology & Evolution 9 (4): 830-842; DOI: 10.1093/gbe/evx037 

Vale, FF., Nunes, A., Oleastro, M., Gomes, JP., Sampaio, D., Rocha, R., Vítor, J., Engstrand, L., Pascoe, B., Berthenet, E., Sheppard, SK., Hitchings, MD., Mégraud, F., Vadivelu, J., Lehours, P. (2017) 

Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins 

Scientific Reports 7:42471; DOI: 10.1038/srep42471 

Yahara, K., Méric, G., Taylor, AJ., de Vries, SPW., Murray, S., Pascoe, B., Mageiros, L., Torralbo, A., Vidal, A., Ridley, A., Komukai, S., Wimalarathna, H., Cody, AJ., Colles, FM., McCarthy, N., Harris, D., Bray, JE., Jolley, KA., Maiden, MCJ., Bentley, SD., Parkhill, J., Bayliss, CD., Grant, A., Maskell, D., Didelot, X., Kelly, DJ., Sheppard, SK. (2016) 

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork. 

Environmental Microbiology 19(1):361-380; doi:10.1111/1462-2920.13628 [PeerJ preprint: doi.org/10.7287] 

2016

Yan, X., Li, Z., Chlebowicz, MA., Tao, X., Ni, M., Hu, Y., Li, Z., Grundmann, H., Murray, S., Pascoe, B., Sheppard, SK., Bo, X., van Dijl, JM., Du, P., Zhang, M., You, Y., Yu, X., Meng, F., Wang, S., and Zhang, J. (2016)  

Livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs carry the lsa(E) gene and are quinupristin/ dalfopristin resistant 

IJMM doi:10.1016/j.ijmm.2016.08.001

Culebro, A., Revez, J., Pascoe, B., Friedmann, Y., Hitchings, MD., Stupak, J., Sheppard, SK., Li, J., Rossi, M. (2016) 

Genetic and chemical differentiation of Campylobacter coli and Campylobacter jejuni lipooligosaccharide pathways 

JBact doi: 10.1128/JB.00347-16 [BioRxiv: dx.doi.org/10.1101/050328]

van Vliet, AHM; Pearson, BM; Williams, NJ; Pascoe, B, Méric, G; Ashton, P; Jenkins, C; Sheppard, SK; Crossman, LC; Wain J. (2016) 

Generating tools for the molecular epidemiology of Campylobacter coli by next generation genome sequencing. 

FSA Report October 2016 

McNally, A., Oren, Y., Kelly, D., Pascoe, B., Dunn, S., Sreecharan, T., Vehkala, M., Välimäki, N., Prentice, M., Ashour, A.; Avram, O., Pupko, T., Dobrindt, U., Literak, I., Guenther, S., Schaufer, K., Wieler, L., Zhiyoung, Z., Sheppard, S.; McInerney, J., Corander, J. (2016) 

Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. 

Plos Genetics 12 (9): e1006280 **Top 50 most downloaded PLoS Genetics papers 2016**

Sankar, A., Malone, B., Bayliss, S., Pascoe, B., Méric, G., Hitchings, MD., Sheppard, SK., Feil, EJ., Corander, J. & Honkela, A. (2016) 

Bayesian identification of bacterial strains from sequencing data. 

Microbial Genomics doi: 10.1099/mgen.0.000075 [arXiv:1511.06546]

Méric, G., Hitchings, MD., Pascoe, B. & Sheppard, SK. (2016) 

From Escherich to the Escherichia coli genome: how a commensal bacterium shaped the history of modern microbiology. 

Lancet Infectious Diseases 16 (6): 634-636

Harris, LG., Murray, S., Pascoe, B., Bray, JE., Méric, G., Mageiros, L., Wilkinson, TS., Jeeves, RE., Rohde, H., Schwarz, S., de Lancastre, H., Miragaia, M., Rolo, J., Bowden, R., Jolley, KA., Maiden, MCJ., Mack, D. & Sheppard, SK. (2016). 

Biofilm morphotypes and population structure among Staphylococcus epidermidis from commensal and clinical samples. 

PLoS ONE 11(3): e0151240

Dearlove B, Cody A, Pascoe B, Méric G, Wilson D, Sheppard SK (2016) 

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. 

The ISME Journal 10 (3): 721-9 [arXiv:1504.01607]

Jackson, E., Ogrodzki, P., Pascoe, B., Sheppard, SK. & Forsythe, S. (2016) 

Draft Genome Sequence of an Enterobacter Species Associated with Illnesses and Powdered Infant Formula. 

Genome Announcement 4(1): e01479-15

2007-2015

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

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