Dr. Y. Pannekoek publications


Publications Dr. Y. Pannekoek

Scientific staff member (UD)
Main activities
Research, Teaching
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.


  • Versteeg B, Bruisten SM, Pannekoek Y, Jolley KA, Maiden MCJ, van der Ende A, Harrison OB, 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]


  • Ferrando ML, Willemse N, Zaccaria E, Pannekoek Y, van der Ende A, Schultsz C, Streptococcal Adhesin P (SadP) contributes to Streptococcus suis adhesion to the human intestinal epithelium. PLOS ONE 2017;12 (4):e0175639 [PubMed]
  • Guo W, Jelocnik M, Li J, Sachse K, Polkinghorne A, Pannekoek Y, Kaltenboeck B, Gong J, You J, Wang C, 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]
  • Huis In 't Veld RAG. Riboregulation in Neisseria meningitidis. S.l.: s.n.; 2017. 279p. ISBN 978-94-6299-774-5 [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): de Jong MD; copromotor(s): van der Ende A, Pannekoek Y)
  • Huis In 't Veld RAG, Kramer G, van der Ende A, Speijer D, Pannekoek Y, The Hfq regulon of Neisseria meningitidis. FEBS OPEN BIO 2017;7 (6):777-788 [PubMed]
  • Li M, Jelocnik M, Yang F, Gong J, Kaltenboeck B, Polkinghorne A, Feng Z, Pannekoek Y, Borel N, Song C, Jiang P, Li J, Zhang J, Wang Y, Wang J, Zhou X, Wang C, Asymptomatic infections with highly polymorphic Chlamydia suis are ubiquitous in pigs. BMC VET RES 2017;13 (1):370 [PubMed]
  • Pannekoek Y, Huis In 't Veld RAG, Schipper K, Bovenkerk S, Kramer G, Brouwer MC, van de Beek D, Speijer D, van der Ende A, Neisseria meningitidis Uses Sibling Small Regulatory RNAs To Switch from Cataplerotic to Anaplerotic Metabolism. MBIO 2017;8 (2):e02293-16 [PubMed]
  • Pannekoek Y, Huis In 't Veld R, Schipper K, Bovenkerk S, Kramer G, Speijer D, van der Ende A, Regulation of Neisseria meningitidis cytochrome bc1 components by NrrF, a Fur-controlled small noncoding RNA. FEBS OPEN BIO 2017;7 (9):1302-1315 [PubMed]
  • Wyllie AL, Pannekoek Y, Bovenkerk S, van Engelsdorp Gastelaars J, Ferwerda B, van de Beek D, Sanders EAM, Trzciński K, van der Ende A, Streptococcus pneumoniae and other streptococcal species. OPEN BIOL 2017;7 (9):170074 [PubMed]


  • Pannekoek Y, Qi-Long Q, Zhang YZ, van der Ende A, 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. PATHOG DIS 2016;74 (6):ftw071 [PubMed]
  • Versteeg B, Bruisten SM, van der Ende A, Pannekoek Y, Does typing of Chlamydia trachomatis using housekeeping multilocus sequence typing reveal different sexual networks among heterosexuals and men who have sex with men?. BMC INFECT DIS 2016;16 (1):162 [PubMed]
  • Willemse N, Howell KJ, Weinert LA, Heuvelink A, Pannekoek Y, Wagenaar JA, Smith HE, van der Ende A, Schultsz C, An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis. SCI REP-UK 2016;6:28984 [PubMed]


  • Ferrando ML, de Greeff A, van Rooijen WJM, Stockhofe-Zurwieden N, Nielsen J, Wichgers Schreur PJ, Pannekoek Y, Heuvelink A, van der Ende A, Smith H, Schultsz C, Host-pathogen Interaction at the Intestinal Mucosa Correlates With Zoonotic Potential of Streptococcus suis. J INFECT DIS 2015;212 (1):95-105 [PubMed]
  • Siarkou VI, Vorimore F, Vicari N, Magnino S, Rodolakis A, Pannekoek Y, Sachse K, Longbottom D, Laroucau K, Diversification and Distribution of Ruminant Chlamydia abortus Clones Assessed by MLST and MLVA. PLOS ONE 2015;10 (5):e0126433 [PubMed]
  • van Samkar A, Brouwer MC, Pannekoek Y, van der Ende A, van de Beek D, Streptococcus gallolyticus meningitis in adults: report of five cases and review of the literature. CLIN MICROBIOL INFEC 2015;21 (12):1077-1083 [PubMed]


  • Jelocnik M, Walker E, Pannekoek Y, Ellem J, Timms P, Polkinghorne A, Evaluation of the relationship between Chlamydia pecorum sequence types and disease using a species-specific multi-locus sequence typing scheme (MLST). VET MICROBIOL 2014;174 (1-2):214-222 [PubMed]
  • Pannekoek Y, Speijer D, van der Ende A. The Regulatory Small RNAs of Neisseria in: Davies JK, Kahler CM, editors. Pathogenic Neisseria: Genomics, Molecular Biology and Disease Intervention. S.l.: Caister Academic Press; 2014., p. 41-58
  • Piet JR, Geldhoff M, van Schaik BDC, Brouwer MC, Valls Seron M , Jakobs ME, Schipper K, Pannekoek Y, Zwinderman AH, van der Poll T, van Kampen AHC, Baas F, van der Ende A, van de Beek D, Streptococcus pneumoniae arginine synthesis genes promote growth and virulence in pneumococcal meningitis. J INFECT DIS 2014;209 (11):1781-1791 [PubMed]


  • Pannekoek Y, van der Ende A, Identification and functional characterization of sRNAs in Neisseria meningitidis. METHODS MOL BIOL 2012;799:73-89 [PubMed]
  • van Lent S, Piet JR, Beeckman D, van der Ende A, van Nieuwerburgh F, Bavoil P, Myers G, Vanrompay D, Pannekoek Y, Full Genome Sequences of All Nine Chlamydia psittaci Genotype Reference Strains. J BACTERIOL 2012;194 (24):6930-6931 [PubMed]


  • Huis In 't Veld RAG, Willemsen AM, van Kampen AHC, Bradley EJ, Baas F, Pannekoek Y, van der Ende A, Deep sequencing whole transcriptome exploration of the σE regulon in Neisseria meningitidis. PLOS ONE 2011;6 (12):e29002 [PubMed]
  • Pannekoek Y, van der Ende A, Chlamydia psittaci infection in nongastrointestinal MALT lymphomas and their precursor lesions. AM J CLIN PATHOL 2011;136 (3):480; author reply 481 [PubMed]
  • Piet JR, Huis in 't Veld RAG, van Schaik BDC, van Kampen AHC, Baas F, van de Beek D, Pannekoek Y, van der Ende A, Genome sequence of Neisseria meningitidis serogroup B strain H44/76. J BACTERIOL 2011;193 (9):2371-2372 [PubMed]
  • Ruettger A, Feige J, Slickers P, Schubert E, Morré SA, Pannekoek Y, Herrmann B, de Vries HJC, Ehricht R, Sachse K, Genotyping of Chlamydia trachomatis strains from culture and clinical samples using an ompA-based DNA microarray assay. MOL CELL PROBE 2011;25 (1):19-27 [PubMed]


  • Hopman CTP, Speijer D, van der Ende A, Pannekoek Y, Identification of a novel anti-sigmaE factor in Neisseria meningitidis. BMC MICROBIOL 2010;10 (1):164 [PubMed]
  • Pannekoek Y, Dickx V, Beeckman DSA, Jolley KA, Keijzers WC, Vretou E, Maiden MCJ, Vanrompay D, van der Ende A, 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, Huis In 't Veld R, Hopman CTP, Langerak AAJ, Speijer D, van der Ende A, Molecular characterization and identification of proteins regulated by Hfq in Neisseria meningitidis. FEMS MICROBIOL LETT 2009;294 (2):216-224 [PubMed]
  • Pannekoek Y, Visser C, Duim B, Heddema ER, Chlamydophila psittaci infections in The Netherlands. DRUG TODAY 2009;45 (Suppl. B):151-157 [PubMed]


  • Pannekoek Y, Morelli G, Kusecek B, Morré SA, Ossewaarde JM, Langerak AA, van der Ende A, Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis. BMC MICROBIOL 2008;8:42 [PubMed]
  • Ponsioen CY, Pannekoek Y, Vergani D, Cheeseman P, Mieli-Vergani G, Chlamydia infection as risk factor for pediatric biliary tract disease. EUR J GASTROEN HEPAT 2008;20 (4):365-366 [PubMed]
  • Verminnen K, Duquenne B, de Keukeleire D, Duim B, Pannekoek Y, Braeckman L, Vanrompay D, Evaluation of a Chlamydophila psittaci infection diagnostic platform for zoonotic risk assessment. J CLIN MICROBIOL 2008;46 (1):281-285 [PubMed]


  • Heddema ER. Psittacosis. Molecular tools for detection and typing of Chlamydophila psittaci. s.l.: s.n.; 2007. 104p. ISBN 97873838970 [UvA Dissertations Online] Proefschrift Universiteit van Amsterdam. (Promotor(s): Vandenbroucke-Grauls CMJE; copromotor(s): Pannekoek Y, Visser CE)


  • Heddema ER, Beld MGHM, de Wever B, Langerak AAJ, Pannekoek Y, Duim B, Development of an internally controlled real-time PCR assay for detection of Chlamydophila psittaci in the LightCycler 2.0 system. CLIN MICROBIOL INFEC 2006;12 (6):571-575 [PubMed]
  • Heddema ER, van Hannen EJ, Duim B, Vandenbroucke-Grauls CMJE, Pannekoek Y, Genotyping of Chlamydophila psittaci in human samples. EMERG INFECT DIS 2006;12 (12):1989-1990 [PubMed]
  • Morré SA, Pannekoek Y, Ossewaarde JM, More than 25 years of urogenital Chlamydia trachomatis research in the Netherlands. DRUG TODAY 2006;42 (Suppl. A):5-24 [PubMed]
  • Morré SA, Spaargaren J, Ossewaarde JM, Land JA, Bax CJ, Dörr PJ, Oostvogel PM, Vanrompay D, Savelkoul PHM, Pannekoek Y, van Bergen JEAM, Fennema HSA, de Vries HJ, Crusius JBA, Peña AS, Ito JI, Lyons JM, Description of the ICTI consortium: an integrated approach to the study of Chlamydia trachomatis infection. DRUG TODAY 2006;42 (Suppl. A):107-114 [PubMed]
  • Mulder MMS, Heddema ER, Pannekoek Y, Faridpooya K, Oud MECM, Schilder-Tol E, Saeed P, Pals ST, No evidence for an association of ocular adnexal lymphoma with Chlamydia psittaci in a cohort of patients from the Netherlands. LEUKEMIA RES 2006;30 (10):1305-1307 [PubMed]
  • Pannekoek Y, van der Ende A, Inclusion proteins of Chlamydiaceae. DRUG TODAY 2006;42 (Suppl. A):65-73 [PubMed]


  • Pannekoek Y, Heurgué-Hamard V, Langerak AAJ, Speijer D, Buckingham RH, van der Ende A, The N-5-glutamine S-adenosyl-L-methionine-dependent methyltransferase PrmC/HemK in Chlamydia trachomatis methylates class 1 release factors. J BACTERIOL 2005;187 (2):507-511 [PubMed]
  • Pannekoek Y, Spaargaren J, Langerak AAJ, Merks J, Morré SA, van der Ende A, Interrelationship between Polymorphisms of incA, fusogenic properties of Chlamydia trachomatis strains, and clinical manifestations in patients in the Netherlands. J CLIN MICROBIOL 2005;43 (5):2441-2443 [PubMed]


  • van Passel M, Bart A, Pannekoek Y, van der Ende A, Phylogenetic validation of horizontal gene transfer?. NAT GENET 2004;36 (10):1028 [PubMed]


  • Pannekoek Y, Westenberg SM, Eijk PP, Repping S, van der Veen F, van der Ende A, Dankert J, Assessment of Chlamydia trachomatis infection of semen specimens by ligase chain reaction. J MED MICROBIOL 2003;52 (Part 9):777-779 [PubMed]


  • Ponsioen CY, Defoer J, ten Kate FJW, Weverling GJ, Tytgat GNJ, Pannekoek Y, Wertheim-Dillen PME, A survey of infectious agents as risk factors for primary sclerosing cholangitis: are Chlamydia species involved?. EUR J GASTROEN HEPAT 2002;14 (6):641-648 [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. INFECT IMMUN 2001;69 (3):1816-1820 [PubMed]
  • Pannekoek Y, van der Ende A, Eijk PP, van Marle J, de Witte MA, Ossewaarde JM, van den Brule AJ, Morré SA, Dankert J, Normal IncA expression and fusogenicity of inclusions in Chlamydia trachomatis isolates with the incA I47T mutation. INFECT IMMUN 2001;69 (7):4654-4656 [PubMed]
  • Ringrose JH, Muijsers AO, Pannekoek Y, Yard BA, Boog CJ, van Alphen L, Dankert J, Feltkamp TE, Influence of infection of cells with bacteria associated with reactive arthritis on the peptide repertoire presented by HLA-B27. J MED MICROBIOL 2001;50 (4):385-389 [PubMed]


  • Pannekoek Y, Trum JW, Bleker OP, van der Veen F, Spanjaard L, Dankert J, 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. J MED MICROBIOL 2000;49 (8):697-700 [PubMed]
  • Pannekoek Y, Westenberg SM, de Vries J, Repping S, Spanjaard L, Eijk PP, van der Ende A, Dankert J, PCR assessment of Chlamydia trachomatis infection of semen specimens processed for artificial insemination. J CLIN MICROBIOL 2000;38 (10):3763-3767 [PubMed]
  • Trum JW, Pannekoek Y, Spanjaard L, Bleker OP, van der Veen F, Accurate detection of male subclinical genital tract infection via cervical culture and DNA hybridization assay of the female partner. INT J ANDROL 2000;23 (1):43-45 [PubMed]


  • Trum JW, Mol BW, Pannekoek Y, Spanjaard L, Wertheim P, Bleker OP, van der Veen F, Value of detecting leukocytospermia in the diagnosis of genital tract infection in subfertile men. FERTIL STERIL 1998;70 (2):315-319 [PubMed]


  • Hsia RC, Pannekoek Y, Ingerowski E, Bavoil PM, Type III secretion genes identify a putative virulence locus of Chlamydia. MOL MICROBIOL 1997;25 (2):351-359 [PubMed]


  • Pannekoek Y, Dankert J, van Putten JP, Construction of recombinant neisserial Hsp60 proteins and mapping of antigenic domains. MOL MICROBIOL 1995;15 (2):277-285 [PubMed]


  • Pannekoek Y, Schuurman IG, Dankert J, van Putten JP, Immunogenicity of the meningococcal stress protein MSP63 during natural infection. CLIN EXP IMMUNOL 1993;93 (3):377-381 [PubMed]


  • Pannekoek Y, Dankert J, van Putten JP, Identification and characterization of a cross-reactive and a unique B-cell epitope on the hsp60 homologue from Neisseria gonorrhoeae. FEMS MICROBIOL LETT 1992;78 (1):23-29 [PubMed]
  • Pannekoek Y, van Putten JP, Dankert J, Identification and molecular analysis of a 63-kilodalton stress protein from Neisseria gonorrhoeae. J BACTERIOL 1992;174 (21):6928-6937 [PubMed]