The challenge of sequencing Chlamydia trachomatis and other bacterial STI genomes directly from clinical swabs: the optimum solution DOI Creative Commons

Karina Andrea Büttner,

Vera Bregy,

Fanny Wegner

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 23, 2024

Rates of bacterial sexually transmitted infections (STIs) are rising and accessing their genomes provides information on strain evolution, circulating strains, encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) Treponema pallidum (TP), globally the most common STIs. Mycoplasma genitalium (MG) is also a STI which concern due to AMR development. These bacteria fastidious or hard culture, standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts human other microbiota DNA. factors hinder sequencing genomes. We aimed overcome these challenges in obtaining whole genome sequences, evaluated four approaches using clinical from Argentina (39), Switzerland (14), cultured Finland (2) (1). First, direct swab was attempted through Illumina deep metagenomic sequencing, showing extremely low levels target DNA, with under 0.01% sequenced reads being pathogens. Second, host DNA depletion followed by not found produce enrichment very load samples. Third, we tried selective long-read approach new adaptive Oxford Nanopore Technologies (ONT), did improve sufficiently provide genomic information. Finally, novel pan-genome set custom SureSelect probes targeting CT, NG, TP, MG successful. produced 64% CT positive samples; 36% NG samples, 60% TP Additionally, enriched gain partial This first publication date utilize pan panel enrichment. Target enrichment, though costly, proved essential for data can be utilized examine genotypic resistance, guide public health strategies.

Language: Английский

Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses DOI Creative Commons
Sarah Buddle,

Leysa Forrest,

Naomi Akinsuyi

et al.

Genome Medicine, Journal Year: 2024, Volume and Issue: 16(1)

Published: Sept. 9, 2024

Language: Английский

Citations

3
The challenge of sequencing Chlamydia trachomatis and other bacterial STI genomes directly from clinical swabs: the optimum solution DOI Creative Commons

Karina Andrea Büttner,

Vera Bregy,

Fanny Wegner

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 23, 2024

Rates of bacterial sexually transmitted infections (STIs) are rising and accessing their genomes provides information on strain evolution, circulating strains, encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) Treponema pallidum (TP), globally the most common STIs. Mycoplasma genitalium (MG) is also a STI which concern due to AMR development. These bacteria fastidious or hard culture, standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts human other microbiota DNA. factors hinder sequencing genomes. We aimed overcome these challenges in obtaining whole genome sequences, evaluated four approaches using clinical from Argentina (39), Switzerland (14), cultured Finland (2) (1). First, direct swab was attempted through Illumina deep metagenomic sequencing, showing extremely low levels target DNA, with under 0.01% sequenced reads being pathogens. Second, host DNA depletion followed by not found produce enrichment very load samples. Third, we tried selective long-read approach new adaptive Oxford Nanopore Technologies (ONT), did improve sufficiently provide genomic information. Finally, novel pan-genome set custom SureSelect probes targeting CT, NG, TP, MG successful. produced 64% CT positive samples; 36% NG samples, 60% TP Additionally, enriched gain partial This first publication date utilize pan panel enrichment. Target enrichment, though costly, proved essential for data can be utilized examine genotypic resistance, guide public health strategies.

Language: Английский

Citations

2