An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim

Meriam Guellil* (Corresponding Author), Marcel Keller* (Corresponding Author), Jenna M. Dittmar, Sarah A. Inskip, Craig Cessford, Anu Solnik, Toomas Kivisild, Mait Metspalu, John E. Robb, Christiana L. Scheib* (Corresponding Author)

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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Background The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen's evolutionary history, and no genomes dating prior to 1940 were available. Results We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550 CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill. Conclusions Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases.

Original languageEnglish
Article number22
Number of pages27
JournalGenome Biology
Issue number1
Publication statusPublished - 3 Feb 2022

Bibliographical note

We thank the support of Quinton Carroll, Ben Donnelly-Symes, and colleagues at the Cambridgeshire County Council as well as other members of the After the Plague project: Piers D. Mitchell, Bram Mulder, Tamsin O’Connell, Jay T. Stock, Alice Rose, and Ruoyun Hui. We would also like to thank Corinne Duhig for sharing her previous knowledge of the material and site. Analyses were carried out using the facilities of the High-Performance Computing Center of the University of Tartu.
This work is supported by the Wellcome Trust (Award no. 2000368/Z/15/Z), the European Union through the European Regional Development Funds Project No. 2014-2020.4.01.16-0030 (M.M., C.L.S., M.G., M.K.) and Project No. 2014-2020.4.01.15-0012 (M.M.), and the Estonian Research Council personal research grant (PRG243) (M.M., C.L.S., A.S., T.K.).


  • Haemophilus influenzae
  • Yersinia pestis
  • Plague
  • aDNA
  • Ancient DNA
  • Microbial genomics
  • Osteology
  • Serotype b
  • Pathogen genomics
  • Paleogenomics


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