To the Editor: We read with interest the report by Wiechmann et al. that, in the investigation of late medieval plague, partial sequencing of the Yersinia pestis pPCP1 plasmid yielded the observation of a 3-T homopolymeric tract which differed from the 5-T homopolymeric tract of the Orientalis Y. pestis CO92 type strain (1). This observation was unexpected because previous data from multispacer sequence typing and glp D gene sequencing yielded only the Orientalis biotype in cases of ancient plague (2).
Using suicide PCR (3), we therefore further investigated pPCP1 in 10 negative control dental pulp specimens and 60 specimens collected from 1 Justinian Orientalis plague site (2), 2 Black Death Orientalis sites, and 2 additional medieval plague sites. All negative controls remained negative; 14 (23%) of 60 plague specimens yielded a PCR product, and 7 interpretable sequences yielded a 3-T homopolymeric tract in all cases.
We further tested a Y. pestis isolate collection comprising 2 Antiqua, 6 Medievalis, and 4 Orientalis strains. No amplification was obtained in DNA-free PCR mix and 5 Y. enterocolitica–negative control isolates, whereas sequencing yielded a 3-T homopolymeric tract in all 12 Y. pestis isolates.
BLAST analysis (http://blast.ncbi.nlm.nih.gov/blast.cgi) indicated that the 5-T homopolymeric tract has been found only once in the Y. pestis CO92 strain (4) and in none of 22 modern and 11 ancient sequences (Table). This 5-T homopolymeric tract is therefore CO92 strain specific and not a marker for the Orientalis biotype. This pPCP1 plasmid sequence, located into a noncoding region of the 3′ extremity of the plasmid, is characterized by several homopolymeric tracts of poly (A) and poly (T), including the 1 herein investigated. Instability of the T-stretches has been reported in bacterial genomes (5) as being hot spots for mutations (5).
Table. Alignment of pPCP1 Yersinis pestis modern and ancient sequences.
| Source and Y. pestis strain | GenBank accession no. | Sequence, 5′ → 3′ |
|---|---|---|
| Complete sequence | ||
| Y. pestis CO92 plasmid pPCP1 | AL109969.1 | 8488_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTTTTGTACGCACCACTGAA_8547 |
| Y. pestis KIM plasmid pPCP1 | AF053945.1 | 8488_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_8547 |
| Y. pestis biovar Microtus str. 91001 plasmid pPCP1 | AE017046.1 | 8487_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_8546 |
| Y. pestis Nepal516 plasmid pPCP | CP000307.1 | 9650_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_9709 |
| Y. pestis Antiqua plasmid pPCP | CP000310.1 | 9661_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_9720 |
| Y. pestis D182038 plasmid pPCP1 | CP001592.1 | 8486_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_8545 |
|
Y. pestis Z176003 plasmid pPCP1 |
CP001596.1 |
8487_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_8546 |
| Modern isolate | ||
| 103813 Y. pestis Nairobi rattus Antiqua | HQ542863 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103814 Y. pestis JHUPRI Antiqua | HQ542864 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103815 Y. pestis 14–47 Medievalis | HQ542865 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103817 Y. pestis 5G5 Medievalis | HQ542866 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103818 Y. pestis 5F1 Medievalis | HQ542867 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103819 Y. pestis 6B4 Medievalis | HQ542868 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103820 Y. pestis 8B7 Medievalis | HQ542869 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103821 Y. pestis 9F11 Medievalis | HQ542870 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103822 Y. pestis 6/69M Orientalis | HQ542871 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| 103823 Y. pestis EV-76 Orientalis | HQ542872 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCAC_114 |
| 103824 Y. pestis algeria 1 Orientalis | HQ542873 | 64_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAA_123 |
| 103825 Y. pestis algeria 2 Orientalis |
HQ542874 |
61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| Ancient strain detected from teeth | ||
| Tooth no. 107 (excavated from Lariey site, France, 17th century) | HQ542875 | 62_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAATGC_123 |
| Tooth no. 515 (excavated from Venice site, Italy, 14th–16th centuries) | HQ542876 | 60_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAATGC_121 |
| Tooth no.1183 (excavated from Bondy site, France, 11th–15th centuries) | HQ542877 | 62_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_121 |
| Tooth no. 1184 (excavated from Bondy site, France, 11th–15th centuries) | HQ542878 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_121 |
| Tooth no. 1190 (excavated from Bondy site, France, 11th–15th centuries) | HQ542879 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| Tooth no. 254 (excavated from Venice site, Italy, 14th–16th centuries) | HQ542880 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
| Tooth no. 1180 (excavated from Bondy site, France, 11th–15th centuries) | HQ542881 | 61_TATATTTTCAAGAAAAGCTGGCTATTTAACATAACGGCAATTT..GTACGCACCACTGAAAT_120 |
Therefore, in our assessment, the data reported for the late medieval Bavaria burial (1) do not support that deaths of persons buried in this site resulted from a non-Orientalis plague. Typing modern or ancient Y. pestis strains should not rely on poly (A) and poly (T) homopolymeric tracts sequencing.
Acknowledgments
This study was funded by Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique 6236.
Footnotes
Suggested citation for this article: Tran T-N-N, Raoult D, Drancourt M. Yersinia pestis DNA sequences in late medieval skeletal finds, Bavaria [letter]. Emerg Infect Dis [serial on the Internet]. 2011 May [date cited]. http://dx.doi.org/10.3201/eid1705.101777
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