All Stories

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

    Article • Journal of Infection, November 2024, Elsevier

    Dr Ben Pascoe

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

    Article • EClinicalMedicine, October 2024, Elsevier

    Dr Ben Pascoe

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

    Article • Journal of Medical Microbiology, September 2024, Society for General Microbiology

    Dr Ben Pascoe

  4. Global Variation in Escherichia coli mcr-1 Genes and Plasmids from Animal and Human Genomes Following Colistin Usage Restrictions in Livestock

    Article • Antibiotics, August 2024, MDPI AG

    Dr Ben Pascoe

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

    Article • Microbial Genomics, July 2024, Society for General Microbiology

    Dr Ben Pascoe

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

    Article • npj Vaccines, June 2024, Springer Science + Business Media

    Dr Ben Pascoe

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

    Article • mBio, April 2024, ASM Journals

    Dr Ben Pascoe

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

    Article • PLoS Neglected Tropical Diseases, March 2024, PLOS

    Dr Ben Pascoe

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

    Article • Journal of Medical Microbiology, January 2024, Society for General Microbiology

    Dr Ben Pascoe

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

    Article • Journal of Global Antimicrobial Resistance, January 2024, Elsevier

    Dr Ben Pascoe

  11. Recombination-mediated dissemination of Methicillin-resistant S. aureus clonal complex 1 in the Egyptian health care settings

    Article • Annals of Clinical Microbiology and Antimicrobials, December 2023, Springer Science + Business Media

    Dr Ben Pascoe, Dr. Eman Badr

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

    Article • Nature Communications, December 2023, Springer Science + Business Media

    Dr. Roberto Herrera-Goepfert, Dr Ben Pascoe

  13. C-SOP-1001: High Molecular Weight DNA (HMW DNA) Extraction from Bacteria using NEB Monarch HMW DNA extraction kit v1

    Article • November 2023, ZappyLab, Inc.

    Dr Ben Pascoe

  14. Genomic tailoring of autogenous poultry vaccines to reduceCampylobacterfrom farm to fork

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  15. C-SOP-201: Genomic DNA Quantification using a Qubit Fluorometer v1

    Article • November 2023, ZappyLab, Inc.

    Dr Ben Pascoe

  16. Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations

    Article • Microbial Genomics, October 2023, Society for General Microbiology

    Dr Ben Pascoe

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

    Article • Microbial Genomics, October 2023, Society for General Microbiology

    Dr Ben Pascoe

  18. Urbanization spreads antimicrobial resistant enteric pathogens in wild bird microbiomes

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  19. Investigation of swine caecal microbiomes in the northern region of Thailand

    Article • July 2023, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  20. Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study

    Article • Heliyon, July 2023, Elsevier

    Dr Ben Pascoe

  21. Contrasting genes conferring short and long-term biofilm adaptation inListeria

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  22. 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

    Article • Veterinary Integrative Sciences, May 2023, Chiang Mai University

    Dr Ben Pascoe

  23. Author Correction: Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

    Article • Nature Communications, March 2023, Springer Science + Business Media

    Dr Ben Pascoe

  24. Colistin resistance and resistance determinants are mobile amongSalmonella entericaisolates from diseased and healthy pigs in Thailand

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  25. Machine Learning the Source Campylobacter Infection in the United States of America

    Article • January 2023, Elsevier

    Dr Ben Pascoe

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

    Article • Nature Communications, November 2022, Springer Science + Business Media

    Dr Ben Pascoe

  27. Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs

    Article • Microbial Genomics, November 2022, Society for General Microbiology

    Dr Ben Pascoe

  28. Multiple hypervirulent methicillin-sensitiveStaphylococcus aureuslineages contribute towards poor patient outcomes in orthopedic device-related infections

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  29. Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity

    Article • Microbiology Spectrum, August 2022, ASM Journals

    Dr Ben Pascoe

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

    Article • Frontiers in Microbiology, August 2022, Frontiers

    Dr Ben Pascoe

  31. Assessing the pathogenic potential of less common Salmonella enterica serotypes circulating in the Thai pork production chain

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  32. Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance

    Article • Microbial Genomics, June 2022, Society for General Microbiology

    Dr Ben Pascoe

  33. Stereoselective metabolism of chloramphenicol by bacteria isolated from wastewater, and the importance of stereochemistry in environmental risk assessments for antibiotics

    Article • Water Research, June 2022, Elsevier

    Dr Ben Pascoe

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

    Article • Molecular Ecology, May 2022, Wiley

    Dr Ben Pascoe

  35. Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

    Article • eLife, February 2022, eLife

    Dr Ben Pascoe

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

    Article • Veterinary Integrative Sciences, February 2022, Chiang Mai University

    Dr Ben Pascoe

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

    Article • December 2021, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

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

    Article • International Journal of Food Microbiology, November 2021, Elsevier

    Dr Ben Pascoe

  39. High-resolution sweep metagenomics using fast probabilistic inference

    Article • Wellcome Open Research, October 2021, Faculty of 1000, Ltd.

    Dr Ben Pascoe

  40. Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages

    Article • PLoS Genetics, September 2021, PLOS

    Dr Ben Pascoe

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

    Article • September 2021, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  42. Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans

    Article • Communications Biology, August 2021, Springer Science + Business Media

    Dr Ben Pascoe

  43. Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  44. Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates

    Article • PLoS Pathogens, June 2021, PLOS

    Dr Ben Pascoe

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

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

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

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

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

    Article • PeerJ, May 2021, PeerJ

    Dr Ben Pascoe

  48. Stereoselective Bacterial Metabolism of Antibiotics in Environmental Bacteria – A Novel Biochemical Workflow

    Article • Frontiers in Microbiology, April 2021, Frontiers

    Dr Ben Pascoe

  49. Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli

    Article • Nature Communications, March 2021, Springer Science + Business Media

    Dr Ben Pascoe

  50. Cross-species evolutionary rewiring in the enteric bacteriumCampylobacter

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  51. Genome evolution and the emergence of pathogenicity in avian Escherichia coli

    Article • Nature Communications, February 2021, Springer Science + Business Media

    Dr Ben Pascoe

  52. Antimicrobial resistantSalmonellaspp. circulating in antibiotic-free organic pig farms of northern-Thailand

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  53. Multiple clones of colistin-resistant Salmonella enterica carrying mcr-1 plasmids in meat products and patients in Northern Thailand

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

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

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  55. Stress-resistance associated with multi-host transmission and enhanced biofilm formation at 42 °C among hyper-aerotolerant generalist Campylobacter jejuni

    Article • Food Microbiology, December 2020, Elsevier

    Dr Ben Pascoe

  56. Genome-wide identification of host-segregating SNPs for source attribution of clinical Campylobacter coli isolates

    Article • Applied and Environmental Microbiology, October 2020, ASM Journals

    Dr Ben Pascoe

  57. A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas

    Article • The ISME Journal, September 2020, Springer Science + Business Media

    Dr Ben Pascoe

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

    Article • PeerJ, August 2020, PeerJ

    Dr Ben Pascoe

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

    Article • PLoS Neglected Tropical Diseases, August 2020, PLOS

    Dr Ben Pascoe

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

    Article • Proceedings of the National Academy of Sciences, May 2020, Proceedings of the National Academy of Sciences

    Dr Ben Pascoe

  61. Genomic epidemiology of Campylobacter jejuni associated with asymptomatic paediatric infection in the Peruvian Amazon

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  62. Hydrocarbon seepage in the deep seabed links subsurface and seafloor biospheres

    Article • Proceedings of the National Academy of Sciences, April 2020, Proceedings of the National Academy of Sciences

    Dr Ben Pascoe

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

    Article • Journal of Global Antimicrobial Resistance, April 2020, Elsevier

    Dr Ben Pascoe

  64. High-resolution sweep metagenomics using fast probabilistic inference

    Article • Wellcome Open Research, January 2020, Faculty of 1000, Ltd.

    Dr Ben Pascoe

  65. Genetic diversity of composite enterotoxigenic Staphylococcus epidermidis pathogenicity islands

    Article • Genome Biology and Evolution, November 2019, Oxford University Press (OUP)

    Dr Ben Pascoe

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

    Article • Environmental Microbiology, August 2019, Wiley

    Dr Ben Pascoe

  67. Domestication of Campylobacter jejuni NCTC 11168

    Article • Microbial Genomics, July 2019, Society for General Microbiology

    Dr Ben Pascoe

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

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

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

    Article • International Journal of Food Microbiology, May 2019, Elsevier

    Dr Ben Pascoe

  70. Domestication of Campylobacter jejuni NCTC 11168

    Article • April 2019, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  71. DNA extraction: Campylobacter v1

    Article • January 2019, ZappyLab, Inc.

    Dr Ben Pascoe

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

    Article • Veterinary Record Open, January 2019, BMJ

    Dr Ben Pascoe

  73. Disease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis

    Article • Nature Communications, November 2018, Springer Science + Business Media

    Dr Ben Pascoe

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

    Article • Microbial Genomics, October 2018, Society for General Microbiology

    Dr Ben Pascoe

  75. A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk

    Article • BMC Biology, August 2018, Springer Science + Business Media

    Dr Ben Pascoe

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

    Article • Microbial Genomics, July 2018, Society for General Microbiology

    Dr Ben Pascoe

  77. Epistasis analysis uncovers hidden antibiotic resistance-associated fitness costs hampering the evolution of MRSA

    Article • July 2018, Springer Science + Business Media

    Dr Ben Pascoe

  78. High Resolution Whole Genome Multilocus Sequence Typing (wgMLST) Schemes for Salmonella enterica Weltevreden Epidemiologic Investigations

    Article • Microbiology and Biotechnology Letters, June 2018, Korean Society for Microbiology and Biotechnology

    Dr Ben Pascoe

  79. High-resolution sweep metagenomics using ultrafast read mapping and inference

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  80. The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species

    Article • Frontiers in Microbiology, March 2018, Frontiers

    Dr Ben Pascoe

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

    Article • Molecular Ecology, March 2018, Wiley

    Dr Ben Pascoe

  82. Convergent amino acid signatures in polyphyletic Campylobacter jejuni sub-populations suggest human niche tropism

    Article • Genome Biology and Evolution, February 2018, Oxford University Press (OUP)

    Dr Ben Pascoe

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

    Article • Scientific Reports, January 2018, Nature

    Dr Ben Pascoe

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

    Article • FEMS Microbiology Letters, December 2017, Oxford University Press (OUP)

    Dr Ben Pascoe

  85. Genome Comparison of Erythromycin Resistant Campylobacter from Turkeys Identifies Hosts and Pathways for Horizontal Spread of erm(B) Genes

    Article • Frontiers in Microbiology, November 2017, Frontiers

    Dr Ben Pascoe

  86. Comparative Genomics Study of Staphylococcus epidermidis Isolates from Orthopedic-Device-Related Infections Correlated with Patient Outcome

    Article • Journal of Clinical Microbiology, August 2017, ASM Journals

    Dr Ben Pascoe, Dr Thomas Fintan Moriarty

  87. Local genes for local bacteria: Evidence of allopatry in the genomes of transatlanticCampylobacterpopulations

    Article • Molecular Ecology, June 2017, Wiley

    Dr Ben Pascoe

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

    Article • June 2017, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

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

    Article • May 2017, PeerJ

    Dr Ben Pascoe

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

    Article • May 2017, PeerJ

    Dr Ben Pascoe

  91. Recombination-mediated host-adaptation by avian Staphylococcus aureus

    Article • Genome Biology and Evolution, February 2017, Oxford University Press (OUP)

    Dr Ben Pascoe

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

    Article • Scientific Reports, February 2017, Nature

    Dr Ben Pascoe

  93. Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni

    Article • Applied and Environmental Microbiology, January 2017, ASM Journals

    Dr Ben Pascoe

  94. Genome‐wide association of functional traits linked with C ampylobacter jejuni survival from farm to fork

    Article • Environmental Microbiology, January 2017, Wiley

    Dr Ben Pascoe

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

    Article • December 2016, PeerJ

    Dr Ben Pascoe

  96. Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

    Article • PLoS Genetics, September 2016, PLOS

    Dr Ben Pascoe, Professor Ulrich Dobrindt

  97. Bayesian identification of bacterial strains from sequencing data

    Article • Microbial Genomics, August 2016, Society for General Microbiology

    Dr Ben Pascoe

  98. Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides

    Article • Journal of Bacteriology, August 2016, ASM Journals

    Dr Ben Pascoe, Alejandra A Culebro

  99. Genetic features of livestock-associated Staphylococcus aureus ST9 isolates from Chinese pigs that carry the lsa(E) gene for quinupristin/dalfopristin resistance

    Article • International Journal of Medical Microbiology, August 2016, Elsevier

    Dr Ben Pascoe, Dr Jianzhong Zhang

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

    Article • July 2016, PeerJ

    Dr Ben Pascoe

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

    Article • July 2016, PeerJ

    Dr Ben Pascoe

  102. From Escherich to the Escherichia coli genome

    Article • The Lancet Infectious Diseases, June 2016, Elsevier

    Dr Ben Pascoe

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

    Article • April 2016, Cold Spring Harbor Laboratory Press

    Dr Ben Pascoe

  104. Correction: Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples

    Article • PLoS ONE, April 2016, PLOS

    Dr Ben Pascoe

  105. Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples

    Article • PLoS ONE, March 2016, PLOS

    Dr Ben Pascoe

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

    Article • Genome Announcements, January 2016, ASM Journals

    Dr Ben Pascoe

  107. Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds inCampylobacter jejuni

    Article • Environmental Microbiology, October 2015, Wiley

    Dr Ben Pascoe

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

    Article • The ISME Journal, August 2015, Nature

    Dr Ben Pascoe

  109. Persistent Staphylococcus aureus Isolates from Two Independent Cases of Bacteremia Display Increased Bacterial Fitness and Novel Immune Evasion Phenotypes

    Article • Infection and Immunity, June 2015, ASM Journals

    Dr Ben Pascoe

  110. Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis

    Article • Genome Biology and Evolution, April 2015, Oxford University Press (OUP)

    Dr Ben Pascoe

  111. Evidence of land-sea transfer of the zoonotic pathogenCampylobacterto a wildlife marine sentinel species

    Article • Molecular Ecology, December 2014, Wiley

    Dr Ben Pascoe

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

    Article • PLoS ONE, March 2014, PLOS

    Dr Ben Pascoe

  113. Dormant Cells of Staphylococcus aureus Are Resuscitated by Spent Culture Supernatant

    Article • PLoS ONE, February 2014, PLOS

    Dr Ben Pascoe

  114. Progressive genome‐wide introgression in agriculturalCampylobacter coli

    Article • Molecular Ecology, December 2012, Wiley

    Professor Julian Parkhill, Dr Ben Pascoe

  115. Staphylococcus epidermidis in Biomaterial-Associated Infections

    Article • August 2012, Springer Science + Business Media

    Dr Ben Pascoe

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

    Article • Journal of Bacteriology, November 2009, ASM Journals

    Dr Ben Pascoe

  117. Zinc-Responsive Regulation of Alternative Ribosomal Protein Genes in Streptomyces coelicolor Involves Zur and σR

    Article • Journal of Bacteriology, March 2007, ASM Journals

    Dr Ben Pascoe