PhD Y. Pannekoek publications


Publications PhD Y. Pannekoek

Assistant Professor
Main activities
Education, Research
Molecular Microbiology of Bacterial Meningitis and Chlamydia infections.
Focus of research

We study the molecular epidemiology and population structure of the main pathogens causing meningitis, Neisseria meningitidis and Streptococcus pneumoniae, and of Chlamydia species causing respiratory infections and sexual transmitted disease. In addition, we study the pathogenesis of meningococcal and invasive pneumococcal disease. We are particularly interested in the bacterial stress response and its regulation by small RNAs (ribo-regulation) in conjunction with alternative sigma factors like sigmaE.
In collaborative studies with Dr. D. van de Beek (Department of Neurology, AMC) we investigate clinical aspects of bacterial meningitis as well correlation between clinical features, outcome and host and bacterial factors.


  • Jelocnik Martina, Polkinghorne Adam, Pannekoek Yvonne Multilocus Sequence Typing (MLST) of Chlamydialesin: Methods in Molecular Biology. Humana Press Inc.; 2019. p. 69-86


  • Versteeg Bart, Bruisten Sylvia M., Pannekoek Yvonne, Jolley Keith A., Maiden Martin C. J., van der Ende Arie, Harrison Odile B. Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease BMC genomics 2018;19 (1):130 [PubMed]


  • Li Min, Jelocnik Martina, Yang Feng, Gong Jianseng, Kaltenboeck Bernhard, Polkinghorne Adam, Feng Zhixin, Pannekoek Yvonne, Borel Nicole, Song Chunlian, Jiang Ping, Li Jing, Zhang Jilei, Wang Yaoyao, Wang Jiawei, Zhou Xin, Wang Chengming Asymptomatic infections with highly polymorphic Chlamydia suis are ubiquitous in pigs BMC veterinary research 2017;13 (1):370 [PubMed]
  • Guo Weina, Jelocnik Martina, Li Jing, Sachse Konrad, Polkinghorne Adam, Pannekoek Yvonne, Kaltenboeck Bernhard, Gong Jiansen, You Jinfeng, Wang Chengming From genomes to genotypes: molecular epidemiological analysis of Chlamydia gallinacea reveals a high level of genetic diversity for this newly emerging chlamydial pathogen BMC genomics 2017;18 (1):949 [PubMed]
  • Pannekoek Yvonne, Huis In 't Veld Robert A. G., Schipper Kim, Bovenkerk Sandra, Kramer Gertjan, Brouwer Matthijs C., van de Beek Diederik, Speijer Dave, van der Ende Arie Neisseria meningitidis Uses Sibling Small Regulatory RNAs To Switch from Cataplerotic to Anaplerotic Metabolism mBio 2017;8 (2):e02293-16 [PubMed]
  • Pannekoek Yvonne, Huis In 't Veld Robert, Schipper Kim, Bovenkerk Sandra, Kramer Gertjan, Speijer Dave, van der Ende Arie Regulation of Neisseria meningitidis cytochrome bc1 components by NrrF, a Fur-controlled small noncoding RNA FEBS open bio 2017;7 (9):1302-1315 [PubMed]
  • Huis In 't Veld Robert A. G. Riboregulation in Neisseria meningitidis 2017. 279p. ISBN 9789462997745. [UvA Dissertations Online] University of Amsterdam. (Supervisor: de Jong M. D.; Co-supervisors: van der Ende A., Pannekoek Y.)
  • Wyllie Anne L., Pannekoek Yvonne, Bovenkerk Sandra, van Engelsdorp Gastelaars Jody, Ferwerda Bart, van de Beek Diederik, Sanders Elisabeth A. M., Trzciński Krzysztof, van der Ende Arie Sequencing of the variable region of rpsB to discriminate between Streptococcus pneumoniae and other streptococcal species Open biology 2017;7 (9):170074 [PubMed]
  • Ferrando Maria Laura, Willemse Niels, Zaccaria Edoardo, Pannekoek Yvonne, van der Ende Arie, Schultsz Constance Streptococcal Adhesin P (SadP) contributes to Streptococcus suis adhesion to the human intestinal epithelium PLoS ONE 2017;12 (4):e0175639 [PubMed]
  • Huis In 't Veld Robert A. G., Kramer Gertjan, van der Ende Arie, Speijer Dave, Pannekoek Yvonne The Hfq regulon of Neisseria meningitidis FEBS open bio 2017;7 (6):777-788 [PubMed]


  • Willemse N., Howell K. J., Weinert L. A., Heuvelink A., Pannekoek Y., Wagenaar J. A., Smith H. E., van der Ende A., Schultsz C. An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis Scientific reports 2016;6:28984 [PubMed]
  • Versteeg Bart, Bruisten Sylvia M., van der Ende Arie, Pannekoek Yvonne Does typing of Chlamydia trachomatis using housekeeping multilocus sequence typing reveal different sexual networks among heterosexuals and men who have sex with men? BMC infectious diseases 2016;16 (1):162 [PubMed]
  • Pannekoek Yvonne, Qi-Long Qin, Zhang Yu-Zhong, van der Ende Arie Genus delineation of Chlamydiales by analysis of the percentage of conserved proteins justifies the reunifying of the genera Chlamydia and Chlamydophila into one single genus Chlamydia Pathogens and disease 2016;74 (6):ftw071 [PubMed]


  • Siarkou Victoria I., Vorimore Fabien, Vicari Nadia, Magnino Simone, Rodolakis Annie, Pannekoek Yvonne, Sachse Konrad, Longbottom David, Laroucau Karine Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA PLoS ONE 2015;10 (5):e0126433 [PubMed]
  • Ferrando Maria Laura, de Greeff Astrid, van Rooijen Willemien J. M., Stockhofe-Zurwieden Norbert, Nielsen Jens, Wichgers Schreur Paul J., Pannekoek Yvonne, Heuvelink Annet, van der Ende Arie, Smith Hilde, Schultsz Constance Host-pathogen Interaction at the Intestinal Mucosa Correlates With Zoonotic Potential of Streptococcus suis Journal of infectious diseases 2015;212 (1):95-105 [PubMed]
  • van Samkar A., Brouwer M. C., Pannekoek Y., van der Ende A., van de Beek D. Streptococcus gallolyticus meningitis in adults: report of five cases and review of the literature Clinical microbiology and infection 2015;21 (12):1077-1083 [PubMed]


  • Jelocnik Martina, Walker Evelyn, Pannekoek Yvonne, Ellem Judy, Timms Peter, Polkinghorne Adam Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST) Veterinary microbiology 2014;174 (1-2):214-222 [PubMed]
  • Piet Jurgen R., Geldhoff Madelijn, van Schaik Barbera D. C., Brouwer Matthijs C., Valls Seron Mercedes, Jakobs Marja E., Schipper Kim, Pannekoek Yvonne, Zwinderman Aeilko H., van der Poll Tom, van Kampen Antoine H. C., Baas Frank, van der Ende Arie, van de Beek Diederik Streptococcus pneumoniae arginine synthesis genes promote growth and virulence in pneumococcal meningitis Journal of infectious diseases 2014;209 (11):1781-1791 [PubMed]
  • Pannekoek Yvonne, Speijer Dave, van der Ende Arie The Regulatory Small RNAs of Neisseriain: John K. Davies, Charlene M. Kahler, editors. Pathogenic Neisseria: Genomics, Molecular Biology and Disease Intervention. S.l.: Caister Academic Press; 2014. p. 41-58, ISBN 9781908230478


  • van Lent Sarah, Piet Jurgen R., Beeckman Delphine, van der Ende Arie, van Nieuwerburgh Filip, Bavoil Patrik, Myers Garry, Vanrompay Daisy, Pannekoek Yvonne Full Genome Sequences of All Nine Chlamydia psittaci Genotype Reference Strains Journal of bacteriology 2012;194 (24):6930-6931 [PubMed]
  • Pannekoek Yvonne, van der Ende Arie Identification and functional characterization of sRNAs in Neisseria meningitidis Methods in molecular biology (Clifton, N.J.) 2012;799:73-89 [PubMed]


  • Pannekoek Y., van der Ende A. Chlamydia psittaci infection in nongastrointestinal MALT lymphomas and their precursor lesions American journal of clinical pathology 2011;136 (3):480; author reply 481 [PubMed]
  • Huis In 't Veld Robert Antonius Gerhardus, Willemsen Antonius Marcellinus, van Kampen Antonius Hubertus Cornelis, Bradley Edward John, Baas Frank, Pannekoek Yvonne, van der Ende Arie Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis PLoS ONE 2011;6 (12):e29002 [PubMed]
  • Piet J. R., Huis in 't Veld R. A. G., van Schaik B. D. C., van Kampen A. H. C., Baas F., van de Beek D., Pannekoek Y., van der Ende A. Genome sequence of Neisseria meningitidis serogroup B strain H44/76 Journal of bacteriology 2011;193 (9):2371-2372 [PubMed]
  • Ruettger Anke, Feige Jens, Slickers Peter, Schubert Evelyn, Morré Servaas A., Pannekoek Yvonne, Herrmann Björn, de Vries Henry J. C., Ehricht Ralf, Sachse Konrad Genotyping of Chlamydia trachomatis strains from culture and clinical samples using an ompA-based DNA microarray assay Molecular and cellular probes 2011;25 (1):19-27 [PubMed]


  • Hopman Carla Th P., Speijer Dave, van der Ende Arie, Pannekoek Yvonne Identification of a novel anti-sigmaE factor in Neisseria meningitidis BMC microbiology 2010;10 (1):164 [PubMed]
  • Pannekoek Yvonne, Dickx Veerle, Beeckman Delphine S. A., Jolley Keith A., Keijzers Wendy C., Vretou Evangelia, Maiden Martin C. J., Vanrompay Daisy, van der Ende Arie Multi Locus Sequence Typing of Chlamydia Reveals an Association between Chlamydia psittaci Genotypes and Host Species PLoS ONE 2010;5 (12):e14179 [PubMed]


  • Pannekoek Y., Visser C., Duim B., Heddema E. R. Chlamydophila psittaci infections in The Netherlands Drugs of today (Barcelona, Spain) 2009;45 (Suppl. B):151-157 [PubMed]
  • Pannekoek Yvonne, Huis In 't Veld Robert, Hopman Carla Th P., Langerak Ankie A. J., Speijer Dave, van der Ende Arie Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis FEMS microbiology letters 2009;294 (2):216-224 [PubMed]


  • Ponsioen Cyriel Y., Pannekoek Yvonne, Vergani Diego, Cheeseman Paul, Mieli-Vergani Giorgina Chlamydia infection as risk factor for pediatric biliary tract disease European journal of gastroenterology & hepatology 2008;20 (4):365-366 [PubMed]
  • Verminnen Kristel, Duquenne Barbara, de Keukeleire David, Duim Birgitta, Pannekoek Yvonne, Braeckman Lutgart, Vanrompay Daisy Evaluation of a Chlamydophila psittaci infection diagnostic platform for zoonotic risk assessment Journal of clinical microbiology 2008;46 (1):281-285 [PubMed]
  • Pannekoek Yvonne, Morelli Giovanna, Kusecek Barica, Morré Servaas A., Ossewaarde Jacobus M., Langerak Ankie A., van der Ende Arie Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis BMC microbiology 2008;8:42 [PubMed]


  • Heddema Edou R. Psittacosis. Molecular tools for detection and typing of Chlamydophila psittaci 2007. 104p. ISBN 9789787383896. [UvA Dissertations Online] University of Amsterdam. (Supervisor: Vandenbroucke-Grauls Christina M. J. E.; Co-supervisors: Pannekoek Yvonne, Visser Caroline E.)


  • Morré S. A., Spaargaren J., Ossewaarde J. M., Land J. A., Bax C. J., Dörr P. J., Oostvogel P. M., Vanrompay D., Savelkoul P. H. M., Pannekoek Y., van Bergen J. E. A. M., Fennema H. S. A., de Vries H. J., Crusius J. B. A., Peña A. S., Ito J. I., Lyons J. M. Description of the ICTI consortium: an integrated approach to the study of Chlamydia trachomatis infection Drugs of today (Barcelona, Spain) 2006;42 (Suppl. A):107-114 [PubMed]
  • Heddema E. R., Beld M. G. H. M., de Wever B., Langerak A. A. J., Pannekoek Y., Duim B. Development of an internally controlled real-time PCR assay for detection of Chlamydophila psittaci in the LightCycler 2.0 system Clinical microbiology and infection 2006;12 (6):571-575 [PubMed]
  • Heddema Edou R., van Hannen Erik J., Duim Birgitta, Vandenbroucke-Grauls Christina M. J. E., Pannekoek Yvonne Genotyping of Chlamydophila psittaci in human samples Emerging infectious diseases 2006;12 (12):1989-1990 [PubMed]
  • Pannekoek Y., van der Ende A. Inclusion proteins of Chlamydiaceae Drugs of today (Barcelona, Spain) 2006;42 (Suppl. A):65-73 [PubMed]
  • Morré Servaas A., Pannekoek Y., Ossewaarde J. M. More than 25 years of urogenital Chlamydia trachomatis research in the Netherlands Drugs of today (Barcelona, Spain) 2006;42 (Suppl. A):5-24 [PubMed]
  • Mulder Marijn M. S., Heddema Edou R., Pannekoek Yvonne, Faridpooya Koorosh, Oud Monique E. C. M., Schilder-Tol Esther, Saeed Peerooz, Pals Steven T. No evidence for an association of ocular adnexal lymphoma with Chlamydia psittaci in a cohort of patients from the Netherlands Leukemia research 2006;30 (10):1305-1307 [PubMed]


  • Pannekoek Yvonne, Spaargaren Joke, Langerak Ankie A. J., Merks Judith, Morré Servaas A., van der Ende Arie Interrelationship between Polymorphisms of incA, fusogenic properties of Chlamydia trachomatis strains, and clinical manifestations in patients in the Netherlands Journal of clinical microbiology 2005;43 (5):2441-2443 [PubMed]
  • Pannekoek Yvonne, Heurgué-Hamard Valérie, Langerak Ankie A. J., Speijer Dave, Buckingham Richard H., van der Ende Arie The N-5-glutamine S-adenosyl-L-methionine-dependent methyltransferase PrmC/HemK in Chlamydia trachomatis methylates class 1 release factors Journal of bacteriology 2005;187 (2):507-511 [PubMed]


  • van Passel Mark, Bart Aldert, Pannekoek Yvonne, van der Ende Arie Phylogenetic validation of horizontal gene transfer? Nature genetics 2004;36 (10):1028 [PubMed]


  • Pannekoek Yvonne, Westenberg Steven M., Eijk Paul P., Repping Sjoerd, van der Veen Fulco, van der Ende Arie, Dankert Jacob Assessment of Chlamydia trachomatis infection of semen specimens by ligase chain reaction Journal of medical microbiology 2003;52 (Part 9):777-779 [PubMed]


  • Ponsioen Cyriel Y., Defoer Jacqueline, ten Kate Fiebo J. W., Weverling Gerrit J., Tytgat Guido N. J., Pannekoek Yvonne, Wertheim-Dillen Pauline M. E. A survey of infectious agents as risk factors for primary sclerosing cholangitis: are Chlamydia species involved? European journal of gastroenterology & hepatology 2002;14 (6):641-648 [PubMed]


  • Ringrose J. H., Muijsers A. O., Pannekoek Y., Yard B. A., Boog C. J., van Alphen L., Dankert J., Feltkamp T. E. Influence of infection of cells with bacteria associated with reactive arthritis on the peptide repertoire presented by HLA-B27 Journal of medical microbiology 2001;50 (4):385-389 [PubMed]
  • Bart A., Pannekoek Y., Dankert J., van der Ende A. NmeSI restriction-modification system identified by representational difference analysis of a hypervirulent Neisseria meningitidis strain Infection and immunity 2001;69 (3):1816-1820 [PubMed]
  • Pannekoek Y., van der Ende A., Eijk P. P., van Marle J., de Witte M. A., Ossewaarde J. M., van den Brule A. J., Morré S. A., Dankert J. Normal IncA expression and fusogenicity of inclusions in Chlamydia trachomatis isolates with the incA I47T mutation Infection and immunity 2001;69 (7):4654-4656 [PubMed]


  • Accurate detection of male subclinical genital tract infection via cervical culture and DNA hybridization assay of the female partner International journal of andrology 2000;23 (1):43-45 [PubMed]
  • Cytokine concentrations in seminal plasma from subfertile men are not indicative of the presence of Ureaplasma urealyticum or Mycoplasma hominis in the lower genital tract Journal of medical microbiology 2000;49 (8):697-700 [PubMed]
  • PCR assessment of Chlamydia trachomatis infection of semen specimens processed for artificial insemination Journal of clinical microbiology 2000;38 (10):3763-3767 [PubMed]


  • Value of detecting leukocytospermia in the diagnosis of genital tract infection in subfertile men Fertility and sterility 1998;70 (2):315-319 [PubMed]


  • Type III secretion genes identify a putative virulence locus of Chlamydia Molecular microbiology 1997;25 (2):351-359 [PubMed]


  • Construction of recombinant neisserial Hsp60 proteins and mapping of antigenic domains Molecular microbiology 1995;15 (2):277-285 [PubMed]


  • Immunogenicity of the meningococcal stress protein MSP63 during natural infection Clinical and experimental immunology 1993;93 (3):377-381 [PubMed]


  • Identification and characterization of a cross-reactive and a unique B-cell epitope on the hsp60 homologue from Neisseria gonorrhoeae FEMS microbiology letters 1992;78 (1):23-29 [PubMed]
  • Identification and molecular analysis of a 63-kilodalton stress protein from Neisseria gonorrhoeae Journal of bacteriology 1992;174 (21):6928-6937 [PubMed]