Additional file 1. Results of the suspension array with sera from mice infected with various Chlamydia species. Pooled sera from mice experimentally infected with Chlamydia, and two pools from naive mice, were tested with bead sets loaded with antigens as indicated. Results for C. psittaci, C. gallinacea, and the last naive mouse are also presented in Figure 1. The results are given in MFI, values above the cutoffs are highlighted in red. For beads with the negative control (NC) compound, values given are the average MFI of three parallel runs; the standard deviations are also given (SD). Serum-specific cutoffs were calculated as three times the average signal on NC beads from three parallel runs (3*avNC). Abbreviations: p, purified peptide; Cga, Cps, Cab, and Cav resp. C. gallinacea, C. psittaci, C. abortus, C. avium. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values.

Additional file 1. Results of the suspension array with sera from mice infected with various Chlamydia species. Pooled sera from mice experimentally infected with Chlamydia, and two pools from naive mice, were tested with bead sets loaded with antigens as indicated. Results for C. psittaci, C. gallinacea, and the last naive mouse are also presented in Figure 1. The results are given in MFI, values above the cutoffs are highlighted in red. For beads with the negative control (NC) compound, values given are the average MFI of three parallel runs; the standard deviations are also given (SD). Serum-specific cutoffs were calculated as three times the average signal on NC beads from three parallel runs (3*avNC). Abbreviations: p, purified peptide; Cga, Cps, Cab, and Cav resp. C. gallinacea, C. psittaci, C. abortus, C. avium. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values.

Additional file 2. Results of the suspension array with sera from chickens infected with C. psittaci and the available PCR data. Sera from three chickens experimentally infected with C. psittaci 6BC were tested with a fixed panel of beads carrying the antigens indicated in the first column. Results are given in MFI. Values above the cutoffs (3 times the signal on NC beads) are highlighted in red. The same results are presented in Figure 2, but there MFIs were normalized by subtracting 3xavNC to enable visualisation of data for multiple sera in one graph. Abbreviations: dpi, days post-infection; for other abbreviations see Additional file 1. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values. Ct values for the three chickens exposed to C. psittaci 6BC are given for 4 and 21 dpi for swabs and tissue samples as indicated. Ct values that are regarded positive are marked red.

Additional file 2. Results of the suspension array with sera from chickens infected with C. psittaci and the available PCR data. Sera from three chickens experimentally infected with C. psittaci 6BC were tested with a fixed panel of beads carrying the antigens indicated in the first column. Results are given in MFI. Values above the cutoffs (3 times the signal on NC beads) are highlighted in red. The same results are presented in Figure 2, but there MFIs were normalized by subtracting 3xavNC to enable visualisation of data for multiple sera in one graph. Abbreviations: dpi, days post-infection; for other abbreviations see Additional file 1. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values. Ct values for the three chickens exposed to C. psittaci 6BC are given for 4 and 21 dpi for swabs and tissue samples as indicated. Ct values that are regarded positive are marked red.

Additional file 4. Results of the suspension array with sera from chickens infected with C. gallinacea. Sera from 8 chickens experimentally infected with C. gallinacea NL_G47 were tested with a fixed panel of beads loaded with antigens as indicated in the first column. These data were also used for Figure 3, but there MFIs were normalized by subtracting 3xavNC. Here, results are given in MFI, values above the cutoffs are highlighted in red. For abbreviations see Additional files 1 and 2. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values.

Additional file 4. Results of the suspension array with sera from chickens infected with C. gallinacea. Sera from 8 chickens experimentally infected with C. gallinacea NL_G47 were tested with a fixed panel of beads loaded with antigens as indicated in the first column. These data were also used for Figure 3, but there MFIs were normalized by subtracting 3xavNC. Here, results are given in MFI, values above the cutoffs are highlighted in red. For abbreviations see Additional files 1 and 2. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values.

Additional file 6. Results of the suspension array with 120 chicken field sera. Sera from 120 chickens, 20 each from two farms of three farm types, were tested with a fixed panel of beads, loaded with antigens as indicated in the first column. These data were also used for Table 4 and Figure 4. The results are given in MFI, values above the cutoffs are highlighted in red. For a description of cutoffs and abbreviations see Additional file 1. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values.

Additional file 6. Results of the suspension array with 120 chicken field sera. Sera from 120 chickens, 20 each from two farms of three farm types, were tested with a fixed panel of beads, loaded with antigens as indicated in the first column. These data were also used for Table 4 and Figure 4. The results are given in MFI, values above the cutoffs are highlighted in red. For a description of cutoffs and abbreviations see Additional file 1. NB in the manuscript normalized data are used for which the cutoffs were subtracted from the acquired MFI values.

Additional file 8. Seroreactivity of C. psittaci and C. abortus derived peptides with sera from immunized chickens. In addition to observations on seroreactivity of peptides derived from C. gallinacea and C. psittaci, immunizations were performed with bacterins of home-grown C. psittaci and various commercial Chlamydia preparations (Virion/Serion); material of C. avium was not available. At the start of the experiment all chickens showed no signals exceeding the cutoffs, except chicken 145 (n = 1) and 172 (n = 2), where the signals by serum from chicken 172 were relatively high (> 1000). In the final bleeds of chickens immunized with C. psittaci bacterins, antibodies were present against a subset of C. psittaci peptides. Two out of four of these chickens also showed reactivity to one C. abortus peptide, one chicken showed a very low cross-reactivity toward a C. gallinacea peptide. The immunization with C. abortus bacterin in one chicken resulted in high signals on two C. abortus peptides. This suggests that chickens are capable of an immune response to at least a subset of the C. abortus peptides. Both C. abortus-immunized chickens showed also high signals on two C. avium peptides in the final bleeds: this cross-reactivity was not observed in infected mice (Figure 1, Additional file 1) and also not in field samples (no coincidence of signals against C. abortus and C. avium peptides, Figure 4). Chickens immunized with bacterins of two other species (C. pneumoniae and C. trachomatis) only in one case gave a modest signal with one C. psittaci peptide. In addition, chicken sera from the same experiment as the C. psittaci sera used for Figure 2, that were immunized after an ineffective infection, resulted in a specific immune response to most C. psittaci peptides. The panel recognized is broader than what is seen upon an infection experiment (Figure 2, Additional file 2). Taken together these results provide some additional evidence for seroreactivity of a subset of peptides in chicken sera. Observed cross-reactivities may suggest that the immune response upon immunization is different from that upon an infection: signals are high, more peptides are recognized, and even some very significant cross-reactivity is observed (with C. avium peptides).

Additional file 8. Seroreactivity of C. psittaci and C. abortus derived peptides with sera from immunized chickens. In addition to observations on seroreactivity of peptides derived from C. gallinacea and C. psittaci, immunizations were performed with bacterins of home-grown C. psittaci and various commercial Chlamydia preparations (Virion/Serion); material of C. avium was not available. At the start of the experiment all chickens showed no signals exceeding the cutoffs, except chicken 145 (n = 1) and 172 (n = 2), where the signals by serum from chicken 172 were relatively high (> 1000). In the final bleeds of chickens immunized with C. psittaci bacterins, antibodies were present against a subset of C. psittaci peptides. Two out of four of these chickens also showed reactivity to one C. abortus peptide, one chicken showed a very low cross-reactivity toward a C. gallinacea peptide. The immunization with C. abortus bacterin in one chicken resulted in high signals on two C. abortus peptides. This suggests that chickens are capable of an immune response to at least a subset of the C. abortus peptides. Both C. abortus-immunized chickens showed also high signals on two C. avium peptides in the final bleeds: this cross-reactivity was not observed in infected mice (Figure 1, Additional file 1) and also not in field samples (no coincidence of signals against C. abortus and C. avium peptides, Figure 4). Chickens immunized with bacterins of two other species (C. pneumoniae and C. trachomatis) only in one case gave a modest signal with one C. psittaci peptide. In addition, chicken sera from the same experiment as the C. psittaci sera used for Figure 2, that were immunized after an ineffective infection, resulted in a specific immune response to most C. psittaci peptides. The panel recognized is broader than what is seen upon an infection experiment (Figure 2, Additional file 2). Taken together these results provide some additional evidence for seroreactivity of a subset of peptides in chicken sera. Observed cross-reactivities may suggest that the immune response upon immunization is different from that upon an infection: signals are high, more peptides are recognized, and even some very significant cross-reactivity is observed (with C. avium peptides).