Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses
Abstract Background Abortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pathogens in equine abortion cases in Australia using metagenomic deep seq...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-08010-5 |
| _version_ | 1818730846587191296 |
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| author | Rumana Akter Charles M. El-Hage Fiona M. Sansom Joan Carrick Joanne M. Devlin Alistair R. Legione |
| author_facet | Rumana Akter Charles M. El-Hage Fiona M. Sansom Joan Carrick Joanne M. Devlin Alistair R. Legione |
| author_sort | Rumana Akter |
| collection | DOAJ |
| description | Abstract Background Abortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pathogens in equine abortion cases in Australia using metagenomic deep sequencing methods. Results After sequencing and analysis, a total of 68 and 86 phyla were detected in the material originating from 49 equine abortion samples and 8 samples from normal deliveries, respectively. Most phyla were present in both groups, with the exception of Chlamydiae that were only present in abortion samples. Around 2886 genera were present in the abortion samples and samples from normal deliveries at a cut off value of 0.001% of relative abundance. Significant differences in species diversity between aborted and normal tissues was observed. Several potential abortigenic pathogens were identified at a high level of relative abundance in a number of the abortion cases, including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus equi subspecies zooepidemicus, Pantoea agglomerans, Acinetobacter lwoffii, Acinetobacter calcoaceticus and Chlamydia psittaci. Conclusions This work revealed the presence of several potentially abortigenic pathogens in aborted specimens. No novel potential abortigenic agents were detected. The ability to screen samples for multiple pathogens that may not have been specifically targeted broadens the frontiers of diagnostic potential. The future use of metagenomic approaches for diagnostic purposes is likely to be facilitated by further improvements in deep sequencing technologies. |
| first_indexed | 2024-12-17T23:08:16Z |
| format | Article |
| id | doaj.art-c71ac7c5a59a44f9aa89cf9bc21666c5 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T23:08:16Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-c71ac7c5a59a44f9aa89cf9bc21666c52022-12-21T21:29:12ZengBMCBMC Genomics1471-21642021-10-0122111410.1186/s12864-021-08010-5Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horsesRumana Akter0Charles M. El-Hage1Fiona M. Sansom2Joan Carrick3Joanne M. Devlin4Alistair R. Legione5Asia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of MelbourneAsia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of MelbourneAsia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of MelbourneEquine Specialist ConsultingAsia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of MelbourneAsia Pacific Centre for Animal Health, The Melbourne Veterinary School, The University of MelbourneAbstract Background Abortion in horses leads to economic and welfare losses to the equine industry. Most cases of equine abortions are sporadic, and the cause is often unknown. This study aimed to detect potential abortigenic pathogens in equine abortion cases in Australia using metagenomic deep sequencing methods. Results After sequencing and analysis, a total of 68 and 86 phyla were detected in the material originating from 49 equine abortion samples and 8 samples from normal deliveries, respectively. Most phyla were present in both groups, with the exception of Chlamydiae that were only present in abortion samples. Around 2886 genera were present in the abortion samples and samples from normal deliveries at a cut off value of 0.001% of relative abundance. Significant differences in species diversity between aborted and normal tissues was observed. Several potential abortigenic pathogens were identified at a high level of relative abundance in a number of the abortion cases, including Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Streptococcus equi subspecies zooepidemicus, Pantoea agglomerans, Acinetobacter lwoffii, Acinetobacter calcoaceticus and Chlamydia psittaci. Conclusions This work revealed the presence of several potentially abortigenic pathogens in aborted specimens. No novel potential abortigenic agents were detected. The ability to screen samples for multiple pathogens that may not have been specifically targeted broadens the frontiers of diagnostic potential. The future use of metagenomic approaches for diagnostic purposes is likely to be facilitated by further improvements in deep sequencing technologies.https://doi.org/10.1186/s12864-021-08010-5AbortionMetagenomicZoonosisAustraliaEquine |
| spellingShingle | Rumana Akter Charles M. El-Hage Fiona M. Sansom Joan Carrick Joanne M. Devlin Alistair R. Legione Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses BMC Genomics Abortion Metagenomic Zoonosis Australia Equine |
| title | Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses |
| title_full | Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses |
| title_fullStr | Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses |
| title_full_unstemmed | Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses |
| title_short | Metagenomic investigation of potential abortigenic pathogens in foetal tissues from Australian horses |
| title_sort | metagenomic investigation of potential abortigenic pathogens in foetal tissues from australian horses |
| topic | Abortion Metagenomic Zoonosis Australia Equine |
| url | https://doi.org/10.1186/s12864-021-08010-5 |
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