publications

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

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 

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

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

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