* indicates joint authorship
Google scholar


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 [Preprint]; Sequence data [1][2]; Supplementary material [figShare]; Twitter [thread]

Hepner S, Kuleshov K, Tooming-Kunderud A, Alig N, Gofton A, Casjens S, Rollins RE, Dangel A, Mourkas E, Sheppard SK, Wieser A, Hübner J, Sing A, Fingerle V, Margos G (2023) A high fidelity approach to assembling the complex Borrelia genome. Research Square doi: 10.21203/ [preprint]

Post V*, Pascoe B*, Mourkas E, Calland JK, Hitchings MD, Erichsen C, Fischer J, Morgenstern M, Richards RG, Sheppard SK**, Moriarty TF** (2022) Multiple hypervirulent methicillin-sensitive Staphylococcus aureus lineages contribute towards poor patient outcomes in orthopaedic device-related infections. medRxiv doi: 10.1101/2022.10.21.22280349 [Preprint]; Sequence data [SRA]; [collection]; Supplementary material [figshare], StaphDB [BIGSdb]; Genealogy [microreact]; Twitter [thread]




Thorpe HA*, Tourrette E*, Yahara K*, Vale FM, 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 (In press) [TBC]; bioRxiv doi: 10.1101/2021.06.05.447065 [Preprint]; Twitter [thread]

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 [Publisher]; bioRxiv doi: 10.1101/2021.06.17.447897 [Preprint]; Sequence data [NCBI]; Supplementary material [figshare]; Genealogy [microreact]; Twitter [thread]

Tucker K, Mageiros L, Carstens A, Bröcker L, Archer E, Smith K, Mourkas E, Pascoe B, Nel D, Méric G, Sheppard SK, Kasprzyk-Hordern B, Botes M, Feil EJ, and Wolfaardt G (2022) Spatiotemporal investigation of antibiotic resistance in the urban water cycle influenced by environmental and anthropogenic activity. Microbiology Spectrum e0247322; doi: 10.1128/spectrum.02473-22 [Publisher]

Xu L, Zang J, Cong W, Holton E, Jiang L, Sheppard SK, Wang Y, Wang N, Weeks J, Fu C, Jiang Q, Lambert H, Kasprzyk-Horden B (2022) Assessment of community-wide antimicrobials usage in Eastern China using wastewater-based epidemiology. Water Research 222:118942; doi: 10.1016/j.watres.2022.118942 [Publisher]

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 13:968695; doi: 10.3389/fmicb.2022.968695 [Publisher]; bioRxiv doi: 10.1101/2022.06.27.497844 [preprint]; Sequence data [1][2]

Cai S, Wang N, Xu L, Yan F, Jiang Q, Zhao X, Wang W, Wang H, Cong W, Sheppard SK, Weeks J, Kasprzyk-Horden B, Fu C, Lambert H (2022) Impacts of Antibiotic Residues in the Environment on Bacterial Resistance and Human Health in Eastern China: An Interdisciplinary Mixed-Methods Study Protocol. Int J Environ Res Public Health 19(13): 8145 [Publisher]

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 [Publisher]; bioRxiv doi: 10.1101/2021.09.24.461243 [Preprint]; Sequence data [SRA]; Supplementary material [figshare]; Twitter [thread]

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 [Publisher]

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 [Publisher]

Kittiwan N, Tadee Pa, Tadee Ph, Buawiratlert T, Elamsam-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; doi: 10.12982/VIS.2022.027 [Publisher]

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 [Publisher]; bioRxiv doi: 10.1101/2021.08.24.457495 [Preprint]; Supplementary material [figshare]; Twitter [thread]

Sheppard SK (2022) Strain wars and the evolution of opportunistic pathogens. Current Opinion in Microbiology 67:102138. doi:10.1016/j.mib.2022.01.009 [Publisher]


Woodall CA*, Hammond A*, Cleary DW, Preston P, Muir P, Pascoe BSheppard SK, Hay AD (2021) Oral and gut microbiome biomarkers of susceptibility to respiratory tract infection in adults: a longitudinal cohort feasibility study. medRxiv doi: 10.1101/2021.12.21.21268189 [Preprint]

Heinz E, Holt, KE, Meehan CJ, Sheppard SK (2021) Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics. Microbial Genomics doi: 10.1099/mgen.0.000722 [Publisher]

Arning N, Sheppard SK, Sion C. Bayliss, Clifton DA & Wilson DJ (2021) Machine learning to predict the source of campylobacteriosis using whole genome data. PLoS Genetics 17(10): e1009436 [Publisher]; bioRxiv doi: 10.1101/2021.02.23.432443 [Preprint]

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 [Publisher] bioRxiv doi: 10.1101/2020.12.02.407999 [Preprint]; Sequence data [NCBI]; Supplementary material [figShare] Twitter [thread]

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 [Publisher]; bioRxiv doi: 10.1101/332544 [Preprint] mSWEEP [GitHub]

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 [Publisher]; Sequence data [SRA]; Supplementary material [figshare]; Genealogy [microreact]; Twitter [@benizao][@mgrover_gi]; Reddit [r/IBSresearch]

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 [Publisher]; bioRxiv 10.1101/2020.12.02.407528 [Preprint]

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 [Publisher] bioRxiv doi: 10.1101/2020.12.08.415869 [Preprint]; Sequence data [NCBI]

Meunsene D, Eiamsam-ang T, Patchanee P, Pascoe B, Tadee Ph, Tadee P. (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 [Publisher]

Kobras CM, Fenton AK*, Sheppard SK* (2021) Next-generation microbiology: from comparative genomics to gene function. Genome Biology 22:123; doi: 10.1186/s13059-021-02344-9 [Publisher]

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 [Publisher]; Sequence data [NCBI]; Supplementary material [figShare]; Twitter [thread]

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 [Publisher] Sequence data [SRA]

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 [Publisher]; bioRxiv doi: 10.1101/2020.12.16.419408 [Preprint]

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/ [Publisher] Sequence data [SRA]


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. AEM doi: 10.1128/AEM.01787-20 [Publisher]

Ferraresso J, Lawton B, Bayliss SC, Sheppard SK, Cardazzo B, Gaze W, Buckling A, Vos M. (2020) Determining the prevalence, identity and possible origin of bacterial pathogens in soil. Environmental Microbiology doi: 10.1111/1462-2920.15243 [Publisher]

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 [Publisher] 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 [Publisher] medRxiv doi: 10.1101/2020.04.26.20075689 [Preprint], Sequence data [SRA], Supplementary material [figShare], Genealogies [1][2].

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 [Publisher]; Sequence data [SRA]; Supplementary material [figShare]

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 [Publisher]; Sequence data [SRA]; Supplementary material [FigShare]; Genealogy [microreact]

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 [Publisher] Sequence data [SRA] Context for Vietnamese isolates [microreact]


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; [Publisher] Supplementary material [Figshare] Genomes [StaphDb] Genealogy [Microreact]

Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ. (2019) PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience 8:10, doi:10.1093/gigascience/giz119 [Publisher] bioRxiv doi: 10.1101/598391 [Preprint] Pirate [GitHub]

Cowley LA, Dallman TJ, Jenkins C, Sheppard SK. (2019) Phage Predation Shapes the Population Structure of Shiga-Toxigenic Escherichia coli O157:H7 in the UK: An Evolutionary Perspective. Frontiers in Mircobiology doi: [Publisher]

Espadinha D, Sobral R, Mendes CI, Méric G, Sheppard SK, Carriço JA, De Lencastre H, Miragaia M. (2019) Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages. Frontiers in Microbiology doi: 10.3389/fmicb.2019.01971 [Publisher]

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 [Publisher] Sequence data [SRA]

Bliss L, Pascoe B, Sheppard SK. (2019) Hermes: an ensemble machine learning architecture for protein secondary structure prediction. bioRxiv doi: 10.1101/640656 [Preprint] Hermes [GitHub]

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 [Publisher]; bioRxiv doi: 10.1101/591701 [Preprint] Supplementary data [Figshare] Genealogy [Microreact] Sequence data [SRA] European nucleotide archive [ENA]

Prasertsee T, Chuammitri P, Deeudom M, Chokesajjawatee N, Santiyanont P, Tadee Pa, Nuangmek A, Tadee PhSheppard 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 [Publisher]

Berthenet E, Thépault A, Chemaly M, Rivoal K, Buissonnière A, Bénéjat L, Bessède E, Mégraud F, Sheppard SK, Lehours P. (2019) Source attribution of Campylobacter jejuni shows variable importance of chicken and ruminants reservoirs in non-invasive and invasive French clinical isolates. Scientific Reports 9: 8098 [Publisher]

Colclough A, Corander J, Sheppard SK, Bayliss SC, Vos M (2019) Patterns of cross‐resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials. Evolutionary Applications doi: 10.1111/eva.12762 [Publisher]

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


Méric G*Mageiros L*, Pensar J, Laabei M, Yahara KPascoe B, Kittiwan N, Tadee P, Post V, Lamble S, Bowden R, Bray JE, Morgenstern M, Jolley KA, Maiden MCJ, Feil EJ, Didelot X, Miragaia M, de Lencastre H, Moriarty TF, Rohde H, Massey R, Mack D, Corander J, Sheppard SK. (2018) Disease-causing genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nature Communications 9:5034; doi: 10.1038/s41467-018-07368-7 [Publisher] Genomes on BIGSdb [link] Raw sequence data [link]

Aidley J, Wanford JJ, Green LR, Sheppard SK, Bayliss CD. (2018) PhasomeIt: an ‘omics’ approach to cataloguing the breadth of phase variation in the genus Campylobacter. Microbial Genomics 4; doi: 10.1099/mgen.0.000228 [Publisher] PhasomeIt [GitHub] Dataset [Figshare]

Dunn SJ, Pascoe B, Turton J, Flemming V, Diggle M, Sheppard SK, McNally M, Manning G. (2018) Genomic epidemiology of clinical Campylobacter spp. at a single health trust site. Microbial Genomics 4; doi: 10.1099/mgen.0.000227 [Publisher]

Berthenet EYahara K, Thorell K, Pascoe BMéric 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) Helicobacter pylori genome-wide association study shows promise for predicting gastic cancer risk. BMC Biology 16:84 [Publisher]

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 4; doi:10.1099/mgen.0.000201 [Publisher] Aquaculture pathogen database [link] Microreact [link]

Sproston EL*, Wimalarathna HML*, Sheppard SK. (2018) Trends in fluoroquinolone resistance in Campylobacter. Microbial Genomics 4; doi:10.1099/mgen.0.000198 [Publisher]

Sheppard SK, Guttman DS, Fitzgerald JR. (2018) Population genomics of bacterial host adaptation. Nature Reviews Genetics (19) 549–565 (doi: 10.1038/s41576-018-0032-z) [Publisher]

Yokoyama M, Stevens ELaabei M, Bacon L, Heesom K, Bayliss SCOoi NO’Neill AJMurray EWilliams PLubben AReeksting S, Méric GPascoe BSheppard SKRecker M, Hurst LD, Massey RC. (2018) Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA. Genome Biology 19:94 (doi: 10.1186/s13059-018-1469-2) [PublisherbioRxiv doi: 10.1101/148825 [Preprint]

Thépault A, Rose V, Quesne S, Poezevara T, Béven V, Hirchaud E, Touzain F, Lucas P, Méric G, Mageiros L, Sheppard SK, Chemaly M, Rivoal K. (2018) Ruminant and chicken: important sources of campylobacteriosis in France despite a variation of source attribution in 2009 and 2015. Scientific Reports 8:9305 [Publisher]

Tadee P, Boonkhot P, Hitchings MD, Pascoe B, Sheppard SK, Patchanee P. (2018) High Resolution Whole Genome Multilocus Sequence Typing (wgMLST) Schemes for Salmonella enterica Weltevreden Epidemiologic Investigations. Microbiology and Biotechnology Letters 46(2): 162-170 [Publisher]

Atterby C*, Mourkas E*, Méric G, Pascoe B, Waldenstrom J, Sheppard SK, Olsen B, Jarhult JD, Ellstrom P. (2018) The potential of isolation source to predict colonization in avian hosts: a case study in Campylobacter jejuni strains from three bird species. Frontiers in Microbiology 9:51. [Publisher]

Thorpe HA, Bayliss SC, Sheppard SK, Feil EJ. (2018) Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria. GigaScience giy015. [PublisherbioRxiv (doi:10.1101/179515) [Preprint]

Méric G, Mageiros L, Pascoe B, 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 [Publisher].

Méric G, McNally A, Pessia A, Mourkas E, Pascoe B, Mageiros L, Vehkala M, Corander J, Sheppard SK. (2018) Convergent amino acid signatures in paraphyletic Campylobacter jejuni sub-populations suggest human niche tropism. Genome Biology and Evolution 10 (3), 763-774 [Publisher].

Kirk KF, Méric G, Nielsen HL, Pascoe BSheppard 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 (1), 1902 [Publisher].

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP. (2018) Weak Epistasis May Drive Adaptation in Recombining Bacteria. Genetics 300662.2017 [Publisher].

Rossi G, Silva HO, Aguilar EG, Pascoe B, Méric G, Mourkas E, Hitchings MD, Mathias LA, Ruiz VLA, Fukumasu H, Sheppard SK, Vical AMC. (2018) Comparative genomic survey of Bacillus cereus sensu stricto isolates from the dairy production chain in Brazil. FEMS Microbiology Letters 365 (3), fnx283 [Publisher].


Florez-Cuadrado D, Ugarte-Ruiz M, Méric G, Quesada A, Porrero MC, Pascoe B, Saez-Llorente JL, Lopez-Orozco G, Dominguez 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) [Publisher].

Eriksson P, Mourkas E, González-Acuna D, Björn Olsen, Ellström P. (2017) Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species. Infection Ecology & Epidemiology 7 (1), 1386536 [Publisher].

Zhou S-M, Muhammad RA, Sheppard SK, Howe R, Lyons RA, Brophy S. (2017) Mining electronic health records to identify predictive factors associated with hospital admission for Campylobacter infections. The Lancet 399 (S99): [Publisher]

Petrovska L, Tang Y, Jansen van Rensburg MJ, Cawthraw S, Nunez J, Sheppard SK, Ellis RJ, Whatmore AM, Crawshaw TR, Irvine RM. (2017) Genome Reduction for Niche Association in Campylobacter hepaticus, A Cause of Spotty Liver Disease in Poultry. Frontiers in Cellular and Infection Microbiology 7:354 [PubMed].

Woodcock DJ, Krusche P, Strachan NJC, Forbes KJ, Cohan FM, Méric G, Sheppard SK. (2017) Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter. Scientific Reports 7, article number: 9650. [Publisher].

Post V, Harris LG, Morgenstern M, Mageiros L, Hitchings MD, Méric G, Pascoe B, Sheppard SK, Richards RG, Moriarty TF. (2017) Comparative genomics study of Staphylococcus epidermidis from orthopedic device-related infections correlated with patient outcome. Journal of Clinical Microbiology 55 (10), 3089-3103 [Publisher].

Pascoe B, Meric G, Yahara K, Wimaralathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MC, McCarthy ND, Didelot X, Parker C, 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) [Publisher].

Murray S*, Pascoe B*, Méric G, Mageiros L, Yahara K, Hitchings MD, Friedmann Y, Gormley FJ, Mack D, Bray JE, Lamble S, Bowden R, Jolley KA, Maiden MCJ, Wendlandt S, Schwarz S, Corander J, Fitzgerald JR, Sheppard SK. (2016) Recombination-mediated host-adaptation by avian Staphylococcus aureus. Genome Biology and Evolution 9(4):830-842 [Publisher].

Thorell K*, Yahara K*, Berthenet E, Lawson DJ, Kato I, Tenorio Mendez A, Rizzato C, Mercedes Bravo M, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D. (2017) Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. PLoS Genetics 13(4): e1006730 [Publisher][Press release].

Esson D, Gupta S, Bailey D, Wigley P, Wedley A, Matherd AE, Méric G, Mastroeni P, Sheppard SK, Thomson NR, Parkhill J, Maskell D, Christie G, Grant AJ. (2017) Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape. Microbial Pathogenesis 104:202–211 [Publisher]

Bayliss SC, Verner-Jeffreys DW, Bartie KL, Aanensen DM, Sheppard SK, Adams A, Feil EJ. (2017) The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens. Frontiers in Microbiology [Publisher]

Vale FF, Nunes A, Oleastro M, Gomes JP, Sampaio DA, Rocha R, Vítor JMB, 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 article:42471 [Publisher].

Thepault A, Méric G, Rivoal K, Pascoe B, Mageiros L, Touzain F, Rose V, Beven V, Chemaly M, Sheppard SK. (2017) Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni. Applied and Environmental Microbiology 83(7):e03085-16 [PubMed] [Publisher].

Post V, Harris L, Morgenstern M, Richards RG, Sheppard SK, Moriarty F. (2017) Characterisation of nasal methicillin-resistant Staphylococcus aureus isolated from international human and veterinary surgeons. Journal of Medical Microbiology 66:360-70 [Publisher].

Yahara K*, Méric G*, Taylor AJ, de Vries SP, Murray S, Pascoe B, Mageiros L, Torralbo A, Vidal A, Ridley AM, Komukai S, Wimalarathna H, Cody AJ, Colles FM, McCarthy ND, Harris D, Bray JE, Jolley KA, Maiden MC, Bentley SD, Parkhill J, Bayliss CD, Grant AJ, Maskell D, Didelot X, Kelly DJ, Sheppard SK. (2017) Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork. Environmental Microbiology 19(1):361–380. [Publisher].

Vinatzer B, Weisberg A, Monteil CL, Elmarakeby HA, Sheppard SK, Heath LS. (2017) A proposal for a genome similarity-based taxonomy for plant pathogenic bacteria that is sufficiently precise to reflect phylogeny, host range, and outbreak affiliation applied to Pseudomonas syringae sensu lato as a proof of concept. Phytopathology  Volume 107(1):18-28 [Publisher].


Esson D, Mather AE, Scanlan E, Gupta S, de Vries SPW, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, Mastroeni P, Sheppard SK, Christie G, Thomson NR, Parkhill J, Maskell D, Grant AJ. (2016) Genomic variations leading to alterations in cell morphology of Campylobacter spp. Scientific Reports 6:38303. [Publisher].

Monteil CL, Yahara K, Studholme DJ, Mageiros L, Méric G, Swingle B, Morris CE, Vinatzer BA, Sheppard SK. (2016) Population-genomic insights into emergence, crop-adaptation, and dissemination of Pseudomonas syringae pathogens. Microbial Genomics 2(10): doi:10.1099/mgen.0.000089 [Publisher].

McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO, 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. doi: 10.1371/journal.pgen.1006280 [Publisher]

Connor TR, Loman NJ, Thompson S, Smith A, Southgate J, Poplawski R, Bull MJ, Richardson E, Ismail M, Elwood-Thompson S, Kitchen C, Guest M, Bakke M, Sheppard SK, Pallen MJ. (2016) CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microbial Genomics 2(9): doi:10.1099/mgen.0.000086 [Publisher]

Berthenet ESheppard S, Vale FF. (2016) Recent “omics” advances in Helicobacter pyloriHelicobacter  21(S1):14–18. [Publisher]

Yana X, Li Z, Chlebowiczc MA, Tao X, Ni M, Hu Y, Li Z, Grundmann H, Murray S, Pascoe B, Sheppard SK, Bo X, Maarten van Dijl J, Du P, Zhang M, You Y, Yu X, Meng F, Wang S, Zhang J. (2016) Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance. International Journal of Medical Microbiology 306(8):722–729 [Publisher]

Culebro A, Revez J, Pascoe B, Friedmann Y, Hitchings MD, Stupak J, Sheppard SK, Li J, Rossi M. (2016) Large sequence diversity within biosynthesis locus and common biochemical features of Campylobacter coli lipooligosaccharides. Journal of Bacteriology 198(20):2829-40. [Publisher]

Sankar A, Malone B, Bayliss SC, 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 2(8): doi:10.1099/mgen.0.000075 [Publisher]

Gilbert MJ, Miller WG, Yee E, Zomer AL, van der Graaf-van Bloois L, Fitzgerald C, Forbes KJ, Méric G, Sheppard SK, Wagenaar JA, Duim B. (2016) Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages. Genome Biology and Evolution. 2;8(6):2006-19. [Pubmed]

Méric G, Hitchings MD, Pascoe B, Sheppard SK. (2016) From Escherich to the Escherichia coli genome. The Lancet Infectious Diseases 16(6):634–636. [Publisher]

Mainda G, Lupolova N, Sikakwa L, Bessell PR, Muma JB, Hoyle DV, McAteer SP, Gibbs K, Williams NJ, Sheppard SK, La Ragione RM, Cordoni G, Argyle SA, Wagner S, Chase-Topping ME, Dallman TJ, Stevens MP, Bronsvoort BM, Gally DL. Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle. Scientific Reports. 25(6):26589. [Publisher]

Numminen E, Gutmann MU, Shubin M, Marttinen P, Méric G, van Schaik W, Coque T, Baquero F, Willems R, Sheppard SK, Feil EJ, Hanage WP, Corander J. (2016) The impact of host metapopulation structure on the population genetics of colonizing bacteria. Journal of Theoretical Biology 396:53-62. [Publisher]

Harris LG, Murray S, Pascoe B, Bray J, Meric G, Mageiros L, Wilkinson TS, Jeeves R, Rohde H, Schwarz S, de Lencastre H, Miragaia M, Rolo J, Bowden R, Jolley KA, Maiden MC, Mack D, Sheppard SK. (2016) Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples. PLoS One 11(3):e0151240. [Pubmed]


Jackson E, Ogrodzki P, Pascoe B, Sheppard SK, Forsythe S. (2015) Draft Genome Sequence of an Enterobacter Species Associated with Illnesses and Powdered Infant Formula. Genome Announcements 4(1):e01479-15. [Publisher]

Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MC, Sheppard SK, Falush D. (2015) The landscape of realized homologous recombination in pathogenic bacteria. Molecular Biology and Evolution 33(2):456-71. [Pubmed]

Pascoe B, Méric G, Murray S, Mageiros L, Yahara K, Bowen R, Jones NH, Jeeves RE, Lappin-Scott HM, Asakura H, Sheppard SK. (2015) Enhanced biofilm formation evolves from divergent genetic backgrounds in host generalist Campylobacter jejuni. Environmental Microbiology 17(11):4779-89. [Pubmed]

Dearlove B, Cody A, Pascoe B, Méric G, Wilson D, Sheppard SK. (2015) Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. The ISME Journal 10(3):721-9. [Pubmed]

Facey P, Méric G, Hitchings MD, Pachebat JA, Hegarty MJ, Chen X, Morgan LVA, Hoeppner JE, Whitten MMA, Kirk WDJ, Dyson PJ, Sheppard SK, Del Sol R. (2015) Draft genomes, phylogenetic reconstruction and comparative genomics of two novel cohabiting bacterial symbionts isolated from Frankliniella occidentalis. Genome Biology and Evolution 7(8):2188-2202. [Publisher]

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. [Publisher]

Sheppard SK, Maiden MCJ. (2015) The Evolution of Campylobacter jejuni and Campylobacter coli. Cold Spring Harbor Perspectives in Biology 7(8):a018119. [Pubmed]

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):1313-1328.[Publisher]

Morley L, McNally A, Paszkiewicz K, Corander J, Méric G, Sheppard SK, Blom J, Manning G. (2015) Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex. Applied and Environmental Microbiology 81(11):3641-7. [Pubmed]

Torralbo A, Borge C, Garcia-Bocanegra I, Méric G, Perea A, Carbonero A (2015) Higher resistance of Campylobacter coli compared to Campylobacter jejuni at chicken slaughterhouse. Comparative Immunology, Microbiology and Infectious Diseases 39:47-52. [Publisher]

Searle LJ*, Méric G*, Porcelli I, Sheppard SK, Lucchini S. (2015) Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli. Plos One 10(3):e0117906 [Publisher]

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):208-221. [Pubmed]


Farhat M, Shapiro BJ, Sheppard SK, Colijn C, Murray M. (2014) A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens. Genome Medicine 6:101. [Publisher]

Sheppard SK, Cheng L, Méric G, de Haan CPA, Llarena A-K, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, Strachan NJC, Forbes K, Colles FM, Jolley KA, Bentley SD, Maiden MCJ, Hänninen M-L, Parkhill J, Hanage WP, Corander J. (2014) Cryptic ecology among host generalist Campylobacter jejuni in domestic animals. Molecular Ecology 23(10):2442–2451. [Publisher]

Meric 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. [Publisher]

Yahara K, Didelot X, Ansari MA, Sheppard SK and Falush D. (2014) Efficient inference of recombination hot regions in bacterial genomes. Molecular Biology and Evolution 31(6): 1593–1605. [Pubmed]

Torralbo A, Borge C, Allepuz A, García-Bocanegra I, Sheppard SK, Perea A, Carbonero A. (2014) Prevalence and risk factors of Campylobacter infection in broiler flocks from southern Spain. Preventive Veterinary Medicine 114(2):106-13. [Pubmed]

Sheppard SK, Méric G.(eds.) Campylobacter Ecology and Evolution, Caister Academic Press, April 2014, c.350 pages [Publisher][PDF information][Amazon] ISBN: 978-1-908230-36-2.

Brisse S, Brehony C, Conceição T, Cubero M, Glasner C, Le Gouil M, Renvoisé A, Sheppard S, Weinert L. (2014) Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 Conference. Research in Microbiology 165(2):140-53 [PubMed]


Strachan NJ, Rotariu O, Macrae M, Sheppard SK, Smith-Palmer A, Cowden J, Maiden MC, Forbes KJ. (2013) Operationalising factors that explain the emergence of infectious diseases: a case study of the human campylobacteriosis epidemic. PLoS One 8(11):e79331. [Pubmed]

Wimalarathna HML, Richardson JF, Lawson AJ, Elson R, Meldrum R, Little CL, Maiden MCJ, McCarthy ND, Sheppard SK. (2013) Widespread acquisition of antimicrobial resistance among Campylobacter isolates from UK retail poultry and evidence for clonal expansion of resistant lineages. BMC Microbiology 13:160. [Pubmed]

Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MCJ, Parkhill J, Falush D. (2013) Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. PNAS 110(29):11923-7. [Pubmed]

Roux F, Sproston E, Rotariu O, MacRae M, Sheppard SK, Bessell P, Smith-Palmer A, Cowden J, Maiden MCJ, Forbes KJ, Strachan NJC. (2013) Elucidating the Aetiology of Human Campylobacter coli Infections. PLoS One 8(5):e64504. [Pubmed]

Sheppard SK, Didelot X, Jolley KA, Darling AE, Pascoe B, Meric G, Kelly DJ, Cody A, Colles FM, Strachan NJ, 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 MC, Falush D. (2013) Progressive genome-wide introgression in agricultural Campylobacter coli. Molecular Ecology 22(4):1051-64. [Pubmed]

Read DS, Woodcock DJ, Strachan NJ, Forbes KJ, Colles FM, Maiden MC, Clifton-Hadley F, Ridley A, Vidal A, Rodgers J, Whiteley AS, Sheppard SK. (2013) Evidence for phenotypic plasticity amongst multi-host Campylobacter jejuni and C. coli lineages using ribosomal MLST and Raman spectroscopy. Applied and Environmental Microbiolgy 79(3):965-73. [Pubmed]


Asakura H, Brüggemann H, Sheppard SK, Ekawa T, Meyer TF, Yamamoto S, Igimi S. (2012) Molecular Evidence for the Thriving of Campylobacter jejuni ST-4526 in Japan. PLoS One 7(11):e48394. [Pubmed]

Strachan NJ, Rotariu O, Smith-Palmer A, Cowden J, Sheppard SK, O’Brien SJ, Maiden MC, Macrae M, Bessell PR, Matthews L, Reid SW, Innocent GT, Ogden ID, Forbes KJ. (2013) Identifying the seasonal origins of human campylobacteriosis. Epidemiology & Infection 141(6):1267-75. [Pubmed]

Nichols GL, Richardson JF, Sheppard SK, Lane C, Sarran C. (2012) Campylobacter epidemiology: a descriptive study reviewing 1 million cases in England and Wales between 1989 and 2011. BMJ Open 2(4). [Pubmed]

Didelot X, Meric G, Falush D, Darling AE. (2012) Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli. BMC Genomics 13:256. [Pubmed]

Sheppard SK, Jolley KA, Maiden MCJ. (2012) A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter. Genes 3(2):261-277. [Publisher]

Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony CM, Colles FM, Wimalarathna HM, Harrison OB, Sheppard SK, Cody AJ, Maiden MC. (2012) Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain. Microbiology 158(Pt 4):1005-15. [Pubmed]


Colles FM, Ali JS, Sheppard SK, McCarthy ND, Maiden MC. (2011) Campylobacter populations in wild and domesticated Mallard ducks (Anas platyrhynchos). Environmental Microbiology Reports 3(5):574-580. [Pubmed]

Sproston EL, Ogden ID, MacRae M, Dallas JF, Sheppard SK, Cody AJ, Colles FM, Wilson MJ, Forbes KJ, Strachan NJ. (2011) Temporal variation and host association in the Campylobacter population in a longitudinal ruminant farm study. Applied and Environmental Microbiology 77(18):6579-86. [Pubmed]

Sheppard SK, Colles FM, McCarthy ND, Strachan NJ, Ogden ID, Forbes KJ, Dallas JF, Maiden MC. (2011) Niche segregation and genetic structure of Campylobacter jejuni populations from wild and agricultural host species. Molecular Ecology 20(16):3484-90. [Pubmed]

Sheppard SK, McCarthy ND, Jolley KA, Maiden MC. (2011) Introgression in the genus Campylobacter: generation and spread of mosaic alleles. Microbiology 157(Pt 4):1066-74. [Pubmed]

Hastings R, Colles FM, McCarthy ND, Maiden MC, Sheppard SK. (2011) Campylobacter genotypes from poultry transportation crates indicate a source of contamination and transmission. Journal of Applied Microbiology 110(1):266-76. [Pubmed]


Sheppard SK, Maiden MCJ and Falush D. (2010) Population Genetics of Campylobacter, in Bacterial Population Genetics in Infectious Disease (eds D. A. Robinson, D. Falush and E. J. Feil), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470600122.ch10

Sheppard SK, Dallas JF, Wilson DJ, Strachan NJ, McCarthy ND, Jolley KA, Colles FM, Rotariu O, Ogden ID, Forbes KJ, Maiden MC. (2010) Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland. PLoS One 5(12):e15708. [Pubmed]

Sproston EL, Ogden ID, MacRae M, Forbes KJ, Dallas JF, Sheppard SK, Cody A, Colles F, Wilson MJ, Strachan NJ. (2010) Multi-locus sequence types of Campylobacter carried by flies and slugs acquired from local ruminant faeces. Journal of Applied Microbiology 109(3):829-38. [Pubmed]

Sheppard SK, Colles F, Richardson J, Cody AJ, Elson R, Lawson A, Brick G, Meldrum R, Little CL, Owen RJ, Maiden MC, McCarthy ND. (2010) Host association of Campylobacter genotypes transcends geographic variation. Applied and Environmental Microbiology 76(15):5269-77. [Pubmed]

Raymond B, Wyres KL, Sheppard SK, Ellis RJ, Bonsall MB. (2010) Environmental factors determining the epidemiology and population genetic structure of the Bacillus cereus group in the field. PLoS Pathogens 20;6(5):e1000905. [Pubmed]

Colles FM, McCarthy ND, Sheppard SK, Layton R, Maiden MC. (2010) Comparison of Campylobacter populations isolated from a free-range broiler flock before and after slaughter. International Journal of Food Microbiology 137(2-3):259-64. [Pubmed]

Nielsen LN, Sheppard SK, McCarthy ND, Maiden MC, Ingmer H, Krogfelt KA. (2010) MLST clustering of Campylobacter jejuni isolates from patients with gastroenteritis, reactive arthritis and Guillain-Barré syndrome. Journal of Applied Microbiology 108(2):591-9. [Pubmed]

Cody AJ, Colles FM, Sheppard SK, Maiden MC. (2010) Where does Campylobacter come from? A molecular odyssey. Advances in Experimental Medicine and Biology 659:47-56. [Pubmed]


Ogden ID, Dallas JF, MacRae M, Rotariu O, Reay KW, Leitch M, Thomson AP, Sheppard SK, Maiden M, Forbes KJ, Strachan NJ. (2009) Campylobacter excreted into the environment by animal sources: prevalence, concentration shed, and host association. Foodborne Pathogens and Disease 6(10):1161-70. [Pubmed]

Rotariu O, Dallas JF, Ogden ID, MacRae M, Sheppard SK, Maiden MC, Gormley FJ, Forbes KJ, Strachan NJ. (2009) Spatiotemporal homogeneity of Campylobacter subtypes from cattle and sheep across northeastern and southwestern Scotland. Applied and Environmental Microbiology 75(19):6275-81. [Pubmed]

Sheppard SK, Dallas JF, MacRae M, McCarthy ND, Sproston EL, Gormley FJ, Strachan NJ, Ogden ID, Maiden MC, Forbes KJ. (2009) Campylobacter genotypes from food animals, environmental sources and clinical disease in Scotland 2005/6. International Journal of Food Microbiology 134(1-2):96-103. [Pubmed]

Sheppard SK, Dallas JF, Strachan NJ, MacRae M, McCarthy ND, Wilson DJ, Gormley FJ, Falush D, Ogden ID, Maiden MC, Forbes KJ. (2009) Campylobacter genotyping to determine the source of human infection. Clinical Infectious Diseases 48(8):1072-8. [Pubmed]

Strachan NJ, Gormley FJ, Rotariu O, Ogden ID, Miller G, Dunn GM, Sheppard SK, Dallas JF, Reid TM, Howie H, Maiden MC, Forbes KJ. (2009) Attribution of Campylobacter infections in northeast Scotland to specific sources by use of multilocus sequence typing. Journal of Infectious Diseases 199(8):1205-8. [Pubmed]


Colles FM, Jones TA, McCarthy ND, Sheppard SK, Cody AJ, Dingle KE, Dawkins MS, Maiden MC. (2008) Campylobacter infection of broiler chickens in a free-range environment. Environmental Microbiology 10(8):2042-50. [Pubmed]

Sheppard SK, McCarthy ND, Falush D, Maiden MC. (2008) Convergence of Campylobacter species: implications for bacterial evolution. Science 320(5873):237-9. [Pubmed]


Sheppard SK, Beckman M, Lloyd D. (2007) The effect of temperature on methane dynamics in soil and peat cores: Calculations from membrane inlet mass spectrometry. Canadian Journal of Soil Science 87(1): 11-22 [Publisher]

Harper GL, Sheppard SK, Harwood JD, Read DS, Glen DM, Bruford MW, Symondson WO. (2006) Evaluation of temperature gradient gel electrophoresis for the analysis of prey DNA within the guts of invertebrate predators. Bulletin of Entomological Research 96(3):295-304. [Pubmed]

Read DS, Sheppard SK, Bruford MW, Glen DM, Symondson WO. (2006) Molecular detection of predation by soil micro-arthropods on nematodes. Molecular Ecology 15(7):1963-72. [Pubmed]

Sheppard SK, Harwood JD. (2005) Advances in molecular ecology: tracking trophic links through predator-prey food-webs. Functional Ecology 19(5):751-62. [Publisher]

Sheppard SK, Bell J, Sunderland KD, Fenlon J, Skervin D, Symondson WO. (2005) Detection of secondary predation by PCR analyses of the gut contents of invertebrate generalist predators. Molecular Ecology 14(14):4461-8. [Pubmed]

Sheppard SK, Gray N, Head IM, Lloyd D. (2005) The impact of sludge amendment on gas dynamics in an upland soil: monitored by membrane inlet mass spectrometry. Bioresource Technology 96(10):1103-15. [Pubmed]

Foltan P, Sheppard S, Konvicka M, Symondson WO. (2005) The significance of facultative scavenging in generalist predator nutrition: detecting decayed prey in the guts of predators using PCR. Molecular Ecology 14(13):4147-58. [Pubmed]

Sheppard SK, Henneman ML, Memmott J, Symondson WO. (2004) Infiltration by alien predators into invertebrate food webs in Hawaii: a molecular approach. Molecular Ecology 13(7):2077-88. [Pubmed]

Gray ND, Hastings RC, Sheppard SK, Loughnane P, Lloyd D, McCarthy AJ, Head IM. (2003) Effects of soil improvement treatments on bacterial community structure and soil processes in an upland grassland soil. FEMS Microbiology Letters 46(1):11-22. [Pubmed]

Sheppard SK, Lloyd D. (2002) Effects of soil amendment on gas depth profiles in soil monoliths using direct mass spectrometric measurement. Bioresource Technology 84(1):39-47. [Pubmed]

Sheppard SK, Lloyd D. (2002) Direct mass spectrometric measurement of gases in soil monoliths.Journal of Microbiological Methods 50(2):175-88. [Pubmed]

Sheppard SK, Lloyd D. (2002) Diurnal Oscillations in Gas Production (O2, CO2, CH4, and N2) in Soil Monoliths. Biological Rhythm Research 33(5):577-91. [Publisher]