Biology subjects

Imkamp, F.

Publications and source records attributed to Imkamp, F..

3 recordsLinked to original sources

bioRxiv2024

Chlamydia trachomatis genomes from rectal samples: description of new clade comprising ompA-genotype L4 from Argentina

Whole genome analysis has provided us with insights into the evolution of Chlamydia trachomatis and recently into circulating strains which cause lymphogranuloma venereum (LGV). A large LGV outbreak of a new ompA-genotype, L2b, was first reported in Europe in the early 2000s, primarily affecting men who have sex with men (MSM), and then expanded globally. More recent work shows this outbreak diversifying into variants of described ompA-genotypes, with the same L2b genomic backbone. This study extends the investigation of LGV cases to Argentina and Finland. In 2017, an LGV outbreak was described in Argentina characterized by distinct genomic features shown by both ompA-genotyping and MLST analysis. We have obtained whole genome sequences from cultured isolates and clinical samples via SureSelect (Agilent) target enrichment. Based on ompA and phylogenetic analyses, we describe further diversity within the ompA-genotype L2b clade, illustrating the transmission dynamics in both Argentina and Finland. A key finding is that of a novel clade of Argentinian samples, characterised by a proposed new ompA-genotype L4. Additionally, we present the genome sequence of a non-LGV strain associated with anorectal proctitis. These findings contribute to the investigation of LGV evolution, particularly with the presence of the novel L4 lineage, and provide insights into genomic diversity and transmission dynamics of C. trachomatis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/624510v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@3bd641org.highwire.dtl.DTLVardef@6f6866org.highwire.dtl.DTLVardef@2f1b6eorg.highwire.dtl.DTLVardef@b2137a_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementThe phylogeny of C. trachomatis has been described in several publications and has been clear for a decade. The evolution of this STI in the intervening years also informs a great deal about the transmission opportunities and selective pressures that the intracellular bacterium is under. Through genome sequencing, also directly from clinical samples, we provide the first LGV genomes from Argentina and Finland, and describe further evidence of global circulation of the ompA-genotype L2b lineage. We describe a fully novel lineage of LGV C. trachomatis, from Argentina, proposed as ompA-genotype L4. We also find evidence of a strain causing proctitis from the urogenital lineage. Together, these provide significant new findings in the investigation of C. trachomatis. Data summaryAll illumina sequence data, with human read data removed using Hostile (1) and KrakenTools (https://github.com/jenniferlu717/KrakenTools), is deposited with the European Nucleotide Archive (ENA) under project number PRJEB72167.

microbiology↗

bioRxiv2024

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

Rates of bacterial sexually transmitted infections (STIs) are rising and accessing their genomes provides information on strain evolution, circulating strains, and encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP), globally the most common bacterial STIs. Mycoplasma genitalium (MG) is also a bacterial STI which is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole genome sequences, and evaluated four approaches using clinical samples from Argentina (39), Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies (ONT), which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP, and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT positive samples; from 36% of NG positive samples, and from 60% of TP positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. This data can be utilized to examine circulating strains, genotypic resistance, and guide public health strategies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/624631v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@578aeborg.highwire.dtl.DTLVardef@16185f9org.highwire.dtl.DTLVardef@1a2ae87org.highwire.dtl.DTLVardef@1703fa7_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementGenome data on circulating sexually transmitted infections (STIs) is important to better understand transmission networks, antimicrobial resistance and to guide treatment decisions. For many bacterial STIs, this information is difficult to obtain, as the bacteria are fastidious, in some cases intracellular, and often recalcitrant to culture. We have developed and tested a target enrichment STI panel of baits to capture whole genomes of Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, and Mycoplasma genitalium with approximately 50% success in genome sequencing for the first three pathogens. We compare this against other sequencing and enrichment methods, which did not provide sufficient data for genome analysis. This panel approach shows potential for clinical samples carrying these pathogens and can potentially also be developed for further pathogen groups. Data summaryAll illumina sequence data, with human read data removed using Hostile (1) and KrakenTools (https://github.com/jenniferlu717/KrakenTools), is deposited with the European Nucleotide Archive (ENA) under project number PRJEB72167.

microbiology↗

bioRxiv2024

Multifocal cutaneous neoplastic vascular proliferations in a rainbow boa (Epicrates cenchria) collection with boid inclusion body disease

Reports on neoplastic processes in snakes are sparse regardless of their location, origin or behavior. Here, we describe the occurrence of multifocal cutaneous neoplastic processes consistent with hemangioma and hemangioendothelioma, with a differential diagnosis of angiomatosis, in a colony of native Brazilian rainbow boas (Epicrates cenchria) which also included animals affected by boid inclusion body disease (BIBD). Thirteen snakes were affected; seven of these had been introduced from other Brazilian sites years earlier, the others had been bred in house but were not offspring of knowingly affected animals. The breeding regime allowed contact between all female and male animals over the years. The cutaneous lesions were first observed over eight years ago, with additional cases detected during the three following years, but no new cases in the last five years. Two affected animals were subjected to a post mortem examination and were found to suffer from peliosis hepatis as one of the additional pathological changes. BIBD was confirmed in five of the eight examined animals, by histology, immunohistology for reptarenavirus nucleoprotein, and multiplex RT-PCR targeting the reptarenavirus S segment. Reptarenavirus infection was also detected in cells in the cutaneous neoplastic processes. PCRs for Bartonella henselae and B. quintana as well as bacterial DNA in general, performed on a pool of six skin lesions, yielded negative results, ruling out ongoing bacterial infection, like bacillary angiomatosis in humans, of the lesions. The results hint towards an association of reptarenavirus infection and BIBD with neoplastic processes which is worth further investigations.

pathology↗