Genomic scale analysis of Pasteurella multocida gene expression during growth within the natural chicken host

Little is known about the genomic-scale transcriptional responses of bacteria during natural infections. We used whole-genome microarray analysis to assess the transcriptional state of the gram-negative pathogen Pasteurella multocida, the causative agent of fowl cholera, during infection in the natural chicken host. We compared the expression profiles of bacteria harvested from the blood of septicemic chickens experiencing late-stage fowl cholera with those from bacteria grown in rich medium. Independent analysis of bacterial expression profiles from the infection of three individual chickens indicated that 40 genes were differentially expressed in all three individuals, 126 were differentially expressed in two of the three individuals, and another 372 were differentially expressed in one individual. Real-time reverse transcription-PCR assays were used to confirm the expression ratios for a number of genes. Of the 40 genes differentially expressed in all three individuals, 17 were up-regulated and 23 were down-regulated in the host compared with those grown in rich medium. The majority (10 of 17) of the up-regulated genes were involved in amino acid transport and metabolism and energy production and conversion, clearly indicating how P. multocida alters its biosynthetic and energy production pathways to cope with the host environment. In contrast, the majority (15 of 23) of down-regulated genes were of unknown or poorly characterized functions. There were clear differences in gene expression between the bacteria isolated from each of the three chickens, a finding consistent with individual host variation being an important factor in determining pathogen gene expression. Interestingly, bacteria from only two of the three infected animals had a gene expression profile highly similar to that observed during growth under iron-limiting conditions, suggesting that severe iron starvation may not always occur during P. multocida infection.