| 1. |
- Cumlin, Tomas, et al.
(författare)
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From SARS-CoV-2 to Global Preparedness : A Graphical Interface for Standardised High-Throughput Bioinformatics Analysis in Pandemic Scenarios and Surveillance of Drug Resistance
- 2024
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Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 25:12
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Tidskriftsartikel (refereegranskat)abstract
- The COVID-19 pandemic highlighted the need for a rapid, convenient, and scalable diagnostic method for detecting a novel pathogen amidst a global pandemic. While command-line interface tools offer automation for SARS-CoV-2 Oxford Nanopore Technology sequencing data analysis, they are inapplicable to users with limited programming skills. A solution is to establish such automated workflows within a graphical user interface software. We developed two workflows in the software Geneious Prime 2022.1.1, adapted for data obtained from the Midnight and Artic's nCoV-2019 sequencing protocols. Both workflows perform trimming, read mapping, consensus generation, and annotation on SARS-CoV-2 Nanopore sequencing data. Additionally, one workflow includes phylogenetic assignment using the bioinformatic tools pangolin and Nextclade as plugins. The basic workflow was validated in 2020, adhering to the requirements of the European Centre for Disease Prevention and Control for SARS-CoV-2 sequencing and analysis. The enhanced workflow, providing phylogenetic assignment, underwent validation at Uppsala University Hospital by analysing 96 clinical samples. It provided accurate diagnoses matching the original results of the basic workflow while also reducing manual clicks and analysis time. These bioinformatic workflows streamline SARS-CoV-2 Nanopore data analysis in Geneious Prime, saving time and manual work for operators lacking programming knowledge.
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| 2. |
- Herrmann, Björn, 1955-, et al.
(författare)
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SNP-based high-resolution typing of Chlamydia psittaci from humans and wild birds in Sweden : circulation of the Mat116 genotype reveals the transmission mode to humans
- 2024
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Ingår i: Microbes and infection. - : Elsevier. - 1286-4579 .- 1769-714X. ; 26:3
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Tidskriftsartikel (refereegranskat)abstract
- The incidence of Chlamydia psittaci respiratory tract infections in humans has increased in Sweden in recent years. This study aimed to identify the transmission route by genotyping C. psittaci from infected humans and birds.42 human C. psittaci samples and 5 samples from C. psittaci-infected birds were collected. Genotyping was performed using ompA sequencing, Multi-locus sequence typing, and/or SNP-based high-resolution melting-PCR. Epidemiological data was also collected, and a phylogenetic analysis was conducted.Analysis of ompA provided limited resolution, while the SNP-based PCR analysis successfully detected the Mat116 genotype in 3/5 passerine birds and in 26/29 human cases, indicating a high prevalence of this genotype in the human population. These cases were associated with contact with wild birds, mainly through bird feeding during winter or other outdoor exposure. Human cases caused by other genotypes (psittacine and pigeon) were less common and were linked to exposure to caged birds or pigeons.The SNP-genotype Mat116 is rare, but predominated in this study. The use of SNP-based PCR provided a better understanding of the C. psittaci transmission from birds to humans compared to ompA analysis. In Sweden, human psittacosis appears mainly to be transmitted from garden birds during bird feeding in the winter season.
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