A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick Identification
<i>Chlamydia</i> (<i>C</i>.) <i>psittaci</i> is the causative agent of avian chlamydiosis and human psittacosis. In this study, we extracted single-nucleotide polymorphisms (SNPs) from the whole genome sequences of 55 <i>C. psittaci</i> strains and ide...
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| Format: | Article |
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MDPI AG
2021-03-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/3/625 |
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| author | Fabien Vorimore Rachid Aaziz Bertille de Barbeyrac Olivia Peuchant Monika Szymańska-Czerwińska Björn Herrmann Christiane Schnee Karine Laroucau |
| author_facet | Fabien Vorimore Rachid Aaziz Bertille de Barbeyrac Olivia Peuchant Monika Szymańska-Czerwińska Björn Herrmann Christiane Schnee Karine Laroucau |
| author_sort | Fabien Vorimore |
| collection | DOAJ |
| description | <i>Chlamydia</i> (<i>C</i>.) <i>psittaci</i> is the causative agent of avian chlamydiosis and human psittacosis. In this study, we extracted single-nucleotide polymorphisms (SNPs) from the whole genome sequences of 55 <i>C. psittaci</i> strains and identified eight major lineages, most of which are host-related. A combined PCR/high-resolution melting (HRM) assay was developed to screen for eight phylogenetically informative SNPs related to the identified <i>C. psittaci</i> lineages. The PCR-HRM method was validated on 11 available reference strains and with a set of 118 field isolates. Overall, PCR-HRM clustering was consistent with previous genotyping data obtained by <i>omp</i>A and/or MLST analysis. The method was then applied to 28 <i>C. psittaci</i>-positive samples from animal or human cases. As expected, PCR-HRM typing results from human samples identified genotypes linked to ducks and pigeons, a common source of human exposure, but also to the poorly described Mat116-like genotype. The new genotyping method does not require time-consuming sequencing and allows a quick identification of the source of infection. |
| first_indexed | 2024-03-10T13:09:11Z |
| format | Article |
| id | doaj.art-f019b81d0d944eaf8ac1c107115e4e95 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T13:09:11Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-f019b81d0d944eaf8ac1c107115e4e952023-11-21T10:56:46ZengMDPI AGMicroorganisms2076-26072021-03-019362510.3390/microorganisms9030625A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick IdentificationFabien Vorimore0Rachid Aaziz1Bertille de Barbeyrac2Olivia Peuchant3Monika Szymańska-Czerwińska4Björn Herrmann5Christiane Schnee6Karine Laroucau7Laboratory for Animal Health, Bacterial Zoonosis Unit, ANSES Maisons-Alfort, Paris-Est University, 94706 Paris, FranceLaboratory for Animal Health, Bacterial Zoonosis Unit, ANSES Maisons-Alfort, Paris-Est University, 94706 Paris, FranceMycoplasma and Chlamydia Infections in Humans, University of Bordeaux, 33076 Bordeaux, FranceMycoplasma and Chlamydia Infections in Humans, University of Bordeaux, 33076 Bordeaux, FranceDepartment of Cattle and Sheep Diseases, National Veterinary Research Institute, 24100 Pulawy, PolandDepartment of Clinical Microbiology, Uppsala University Hospital, 75185 Uppsala, SwedenInstitute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), 07743 Jena, GermanyLaboratory for Animal Health, Bacterial Zoonosis Unit, ANSES Maisons-Alfort, Paris-Est University, 94706 Paris, France<i>Chlamydia</i> (<i>C</i>.) <i>psittaci</i> is the causative agent of avian chlamydiosis and human psittacosis. In this study, we extracted single-nucleotide polymorphisms (SNPs) from the whole genome sequences of 55 <i>C. psittaci</i> strains and identified eight major lineages, most of which are host-related. A combined PCR/high-resolution melting (HRM) assay was developed to screen for eight phylogenetically informative SNPs related to the identified <i>C. psittaci</i> lineages. The PCR-HRM method was validated on 11 available reference strains and with a set of 118 field isolates. Overall, PCR-HRM clustering was consistent with previous genotyping data obtained by <i>omp</i>A and/or MLST analysis. The method was then applied to 28 <i>C. psittaci</i>-positive samples from animal or human cases. As expected, PCR-HRM typing results from human samples identified genotypes linked to ducks and pigeons, a common source of human exposure, but also to the poorly described Mat116-like genotype. The new genotyping method does not require time-consuming sequencing and allows a quick identification of the source of infection.https://www.mdpi.com/2076-2607/9/3/625<i>Chlamydia psittaci</i>SNPPCR-high-resolution melting (HRM)psittacosisavian chlamydiosisgenotyping |
| spellingShingle | Fabien Vorimore Rachid Aaziz Bertille de Barbeyrac Olivia Peuchant Monika Szymańska-Czerwińska Björn Herrmann Christiane Schnee Karine Laroucau A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick Identification Microorganisms <i>Chlamydia psittaci</i> SNP PCR-high-resolution melting (HRM) psittacosis avian chlamydiosis genotyping |
| title | A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick Identification |
| title_full | A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick Identification |
| title_fullStr | A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick Identification |
| title_full_unstemmed | A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick Identification |
| title_short | A New SNP-Based Genotyping Method for <i>C. psittaci</i>: Application to Field Samples for Quick Identification |
| title_sort | new snp based genotyping method for i c psittaci i application to field samples for quick identification |
| topic | <i>Chlamydia psittaci</i> SNP PCR-high-resolution melting (HRM) psittacosis avian chlamydiosis genotyping |
| url | https://www.mdpi.com/2076-2607/9/3/625 |
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