In 2010, researchers reported that the two US-licensed rotavirus vaccines contained DNA or DNA fragments from porcine circovirus (PCV). Although PCV, a common virus among pigs, is not thought to cause illness in humans, these findings raised several safety concerns. In this study, we sought to determine whether viruses, including PCV, could be detected in ileal tissue samples of children vaccinated with one of the two rotavirus vaccines. A broad spectrum, novel DNA detection technology, the Lawrence Livermore Microbial Detection Array (LLMDA), was utilized, and confirmation of viral pathogens using the polymerase chain reaction (PCR) was conducted. The LLMDA technology was recently used to identify PCV from one rotavirus vaccine. Ileal tissue samples were analyzed from 21 subjects, aged 15–62 months. PCV was not detected in any ileal tissue samples by the LLMDA or PCR. LLMDA identified a human rotavirus A from one of the vaccinated subjects, which is likely due to a recent infection from a wild type rotavirus. LLMDA also identified human parechovirus, a common gastroenteritis viral infection, from two subjects. Additionally, LLMDA detected common gastrointestinal bacterial organisms from the Enterobacteriaceae, Bacteroidaceae, and Streptococcaceae families from several subjects. This study provides a survey of viral and bacterial pathogens from pediatric ileal samples, and may shed light on future studies to identify pathogen associations with pediatric vaccinations. 1. Introduction Rotavirus is the most common cause of severe diarrhea among infants and young children . Prior to the introduction of rotavirus vaccines, rotavirus infection was estimated to cause approximately 2.7 million cases of severe gastroenteritis in children, almost 60,000 hospitalizations, and around 37 deaths each year in the USA alone . Three vaccines against rotavirus have been developed: Rotashield (Wyeth-Lederle Vaccines and Pediatrics, ), RotaTeq (Merck, ), and Rotarix (GlaxoSmithKline, ). Rotashield, a rhesus-based tetravalent rotavirus vaccine, was recommended for routine vaccination of US infants in 1999  but was withdrawn from the US market within 1 year of its introduction because of its association with intussusception . RotaTeq, a human-bovine reassortant rotavirus vaccine , was recommended for vaccination of US infants in 2006  with 3 doses administered orally at ages 2, 4, and 6 months . In 2008, Rotarix, a monovalent vaccine based on an attenuated human rotavirus , was licensed in the USA for pediatric use as a 2-dose series and
T. K. Fischer, C. Viboud, U. Parashar et al., “Hospitalizations and deaths from diarrhea and rotavirus among children <5 years of age in the United States, 1993–2003,” The Journal of Infectious Diseases, vol. 195, no. 8, pp. 1117–1125, 2007.
A. Z. Kapikian, Y. Hoshino, R. M. Chanock, and I. Perez-Schael, “Efficacy of a quadrivalent rhesus rotavirus-based human rotavirus vaccine aimed at preventing severe rotavirus diarrhea in infants and young children,” The Journal of Infectious Diseases, vol. 174, supplement 1, pp. S65–S72, 1996.
P. M. Heaton, M. G. Goveia, J. M. Miller, P. Offit, and H. F. Clark, “Development of a pentavalent rotavirus vaccine against prevalent serotypes of rotavirus gastroenteritis,” The Journal of Infectious Diseases, vol. 192, supplement 1, pp. S17–S21, 2005.
CDC, “Prevention of rotavirus gastroenteritis among infants and children. Recommendations of the Advisory Committee on Immunization Practices (ACIP),” Morbidity and Mortality Weekly Report, vol. 55, pp. 1–13, 2006.
B. de Vos, T. Vesikari, A. C. Linhares et al., “A rotavirus vaccine for prophylaxis of infants against rotavirus gastroenteritis,” The Pediatric Infectious Disease Journal, vol. 23, no. 10, pp. S179–S182, 2004.
CDC, “Prevention of rotavirus gastroenteritis among infants and children. Recommendations of the Advisory Committee on Immunization Practices (ACIP),” Morbidity and Mortality Weekly Report, vol. 55, pp. 1–13, 2009.
A. T. Curns, C. A. Steiner, M. Barrett, K. Hunter, E. Wilson, and U. D. Parashar, “Reduction in acute gastroenteritis hospitalizations among US children after introduction of rotavirus vaccine: analysis of hospital discharge data from 18 US States,” The Journal of Infectious Diseases, vol. 201, no. 11, pp. 1617–1624, 2010.
M. O'Ryan, J. Diaz, N. Mamani, M. Navarrete, and C. Vallebuono, “Impact of rotavirus infections on outpatient clinic visits in Chile,” The Pediatric Infectious Disease Journal, vol. 26, no. 1, pp. 41–45, 2007.
M. M. Patel, D. Steele, J. R. Gentsch, J. Wecker, R. I. Glass, and U. D. Parashar, “Real-world impact of rotavirus vaccination,” The Pediatric Infectious Disease Journal, vol. 30, no. 1, pp. S1–S5, 2011.
J. G. Victoria, C. Wang, M. S. Jones et al., “Viral nucleic acids in live-attenuated vaccines: detection of minority variants and an adventitious virus,” Journal of Virology, vol. 84, no. 12, pp. 6033–6040, 2010.
J. A. Ellis, B. M. Wiseman, G. Allan et al., “Analysis of seroconversion to Porcine circovirus 2 among veterinarians from the United States and Canada,” Journal of the American Veterinary Medical Association, vol. 217, no. 11, pp. 1645–1646, 2000.
G. M. Allan, F. Mcneilly, I. Mcnair et al., “Absence of evidence for Porcine circovirus type 2 in cattle and humans, and lack of seroconversion or lesions in experimentally infected sheep,” Archives of Virology, vol. 145, no. 4, pp. 853–857, 2000.
K. Hattermann, C. Roedner, C. Schmitt, T. Finsterbusch, T. Steinfeldt, and A. Mankertz, “Infection studies on human cell lines with Porcine circovirus type 1 and Porcine circovirus type 2,” Xenotransplantation, vol. 11, no. 3, pp. 284–294, 2004.
D. C. Payne, S. Humiston, D. Opel et al., “A multi-center, qualitative assessment of pediatrician and maternal perspectives on rotavirus vaccines and the detection of Porcine circovirus,” BMC Pediatrics, vol. 11, article 83, 2011.
L. Erlandsson, M. W. Rosenstierne, K. McLoughlin, C. Jaing, and A. Fomsgaard, “The microbial detection array combined with random Phi29-amplification used as a diagnostic tool for virus detection in clinical samples,” PLoS ONE, vol. 6, no. 8, Article ID e22631, 2011.
D. Hysom, P. Naraghi-Arani, M. Elsheikh, A. C. Carrillo, P. L. Williams, and S. N. Gardner, “Skip the alignment: degenerate, multiplex primer and probe design using k-mer matching instead of alignments,” PLoS ONE, vol. 7, no. 4, Article ID e34560, 2012.
C. S. Ranucci, T. Tagmyer, and P. Duncan, “Adventitious agent risk assessment case study: evaluation of RotaTeq for the presence of Porcine circovirus,” PDA Journal of Pharmaceutical Science and Technology, vol. 65, no. 6, pp. 589–598, 2011.
D. C. Payne, M. Wikswo, and U. D. Parashar, “Manual for the surveillance of vaccine-preventable diseases,” in Rotavirus, S. W. Roush, L. McIntyre, and L. M. Baldy, Eds., chapter 13, Centers for Disease Control and Prevention, Atlanta, Ga, USA, 5th edition, 2012.
H. Antunes, A. Afonso, M. Iturriza et al., “G2P the most prevalent rotavirus genotype in 2007 winter season in an European non-vaccinated population,” Journal of Clinical Virology, vol. 45, no. 1, pp. 76–78, 2009.
Z. Burián, H. Szabó, G. Székely et al., “Detection and follow-up of torque teno midi virus (“small anelloviruses”) in nasopharyngeal aspirates and three other human body fluids in children,” Archives of Virology, vol. 156, no. 9, pp. 1537–1541, 2011.