Vaccine 22 (2004) 3367–3374 Defining the genome content of live plague vaccines by use of whole-genome DNA microarray Dongsheng Zhou 1 , Yanping Han 1 , Erhei Dai, Yajun Song, Decui Pei, Junhui Zhai, Zongmin Du, Jin Wang, Zhaobiao Guo, Ruifu Yang ∗ Laboratory of Analytical Microbiology, National Center for Biomedical Analysis, Army Center for Microbial Detection and Research, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing 100071, PR China Received 14 October 2003; received in revised form 26 February 2004; accepted 27 February 2004 Available online 28 March 2004 Abstract Yersinia pestis whole-genome DNA microarrays were developed to perform genomic comparison of a collection of live plague vaccines. By using the genomic DNA to probe the DNA microarrays, we detected dozens of deletions and amplifications of the genomic regions in the 19 vaccine strains analyzed. The revealed genomic differences within the vaccine strains of different origins provide us an unprecedented opportunity to understand the molecular background of the variability of the immunogenic and protective potency of plague live vaccine. The whole-genome DNA microarray also provides an ideal tool to perform the pre-evaluation of a vaccine strain for its high throughput to determine the genomic features essential or unallowable for the live vaccines. © 2004 Elsevier Ltd. All rights reserved. Keywords: Yersinia pestis; Live plague vaccines; DNA microarray 1. Introduction Plague, one of the most devastating diseases of human history, is caused by Yersinia pestis. Endemic areas for this disease widely exist in Asia, Africa and America, where the occasional epizootics of animal plague pose great threats to public health [1]. Plague has been classified as a reemerging disease by the Word Health Organiza- tion due to the worldwide increasing incidence of human plague. Cases of bubonic plague can be well controlled by timely antibiotic treatment. However, the pneumonic or septicemic plague is difficult to be treated with antibi- otic therapy. The recent isolation of a multiple antibiotic resistant strain of Y. pestis indicates that the longer term potential for the use of antibiotics to treat plague is less certain [2]. The public health threat posed by plague is thought to be only reliably encountered by use of the effec- tive vaccines. Both live attenuated and killed whole cells vaccines have been used in human [3–5]. The sub-unit vaccines based on the F1 and V antigens take promis- ∗ Corresponding author. Tel.: +86-10-66948595; fax: +86-10-83820748. E-mail address: yangrf@nic.bmi.ac.cn (R. Yang). 1 Zhou D. and Han Y. contributed equally to this work. ing for their efficacy against both bubonic and pneumonic plague when tested recently in animal models of the disease [4,5]. The large-scale genome sequencing effort and the abil- ity to immobilize thousands of DNA fragments on a solid surface, such as coated glass slide, have led to the devel- opment of DNA microarray technology. While the DNA microarray-based comparative genome analysis on many strains of several pathogenic species has contributed to our understanding of bacterial diversity, evolution and pathogen- esis [6,7]. Behr et al. described the DNA microarray-based genomic comparison of Mycobacterium tuberculosis with closely related Mycobacterium bovis, and with Baccile Calmette-Guérin (BCG) strains that were produced by serial in vitro passages of M. bovis [8]. The microarray proce- dure was used successfully to analyze the deletions and amplification mutations found in Salmonella mutagenicity assay strains (Ames test) [9]. The Escherichia coli K-12 MC4100, an MG1655 derivant, has provided an important host in early gene expression study, while Peters et al. used a whole-genome array based on the genome sequence of strain MG1655 as a tool to identify the deletions in MC4100 [10]. The DNA microarray technology represents an ideal methodology to compare or define the contents of the closely related genomes. 0264-410X/$ – see front matter © 2004 Elsevier Ltd. All rights reserved. doi:10.1016/j.vaccine.2004.02.035