Biology subjects

Jenjaroenpun, P.

Publications and source records attributed to Jenjaroenpun, P..

8 recordsLinked to original sources

bioRxiv2025

Emergence of zoonotic and multi-drug resistant Streptococcus suis

BackgroundStreptococcus suis is an emerging zoonotic porcine pathogen and a leading cause of adult bacterial meningitis in Southeast Asia, associated with raw pork consumption. Most zoonotic S. suis infections globally are by strains from lineage CC1 carrying a serotype 2 capsule. However, in Thailand, [~]40% of the reported zoonotic infections are caused by two endemic lineages, CC104 and CC233 which also have a serotype 2 capsule. In this study, we aimed to identify the drivers of the emergence and recent evolution of these two lineages. MethodsWe sequenced the whole genomes of 141 Thai S. suis zoonotic and porcine strains isolated over a 15-year period and combined them with a curated global dataset of 2761 published S. suis genomes. Using comparative genomics, Bayesian evolutionary models and multivariate analysis we investigated the emergence of zoonotic potential and multi-drug resistance in CC104 and CC233. FindingsWe estimated recent emergence dates for both CC104 (1990; 95% posterior: 1987-1992) and CC233 (2002; 95% posterior: 2000-2004). Both lineages acquired a serotype capsule 2 from CC1 through a capsule locus switching event, prior to their emergence. Both have also experienced multiple antimicrobial resistance (AMR) acquisition events, with some strains carrying 12 determinants encoding resistance against eight classes of antibiotics. Most importantly, CC104 and CC233 lineages are the first zoonotic lineages to have acquired increased resistance to penicillin and ceftriaxone, which form the standard therapy to treat S. suis infections in humans. InterpretationHorizontal transfer of multiple genomic regions can cause rapid emergence of novel multi-drug-resistant zoonotic S. suis lineages. As S. suis is mainly controlled and treated through the use of antibiotics in both pigs and humans, these findings highlight the urgent need for improved and enhanced surveillance, infection control, and treatments.

microbiology↗

bioRxiv2024

CAIM: Coverage-based Analysis for Identification of Microbiome

Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers. Key Points- Metagenomic coverage is an important index to obtain highly accurate species identification by reducing false positives from whole shotgun metagenomic data. - Comparative analyses of CAIM and other bioinformatics tools for species identification on many mock community whole shotgun metagenomic datasets generated by short-read and long-read sequencing and synthetic datasets were performed, showing that CAIM has a very good performance compared with the other tools. - Using the metagenomic coverage approach through CAIM improves the predictive power of species biomarkers identified from in stool samples of colorectal cancer and primary liver datasets.

bioinformatics↗

bioRxiv2024

Long Read Sequencing reveals transgene concatemerization and backbone integration following AAV-driven electroporation of CRISPR RNP complexes in mouse zygotes

Over the last decade CRISPR gene editing has been successfully used to streamline the generation of animal models for biomedical purposes. However, one limitation to its use is the potential occurrence of on-target mutations that may be detrimental or otherwise unintended. These bystander mutations are often undetected using conventional genotyping methods. The use of Adeno-Associated Viruses (AAVs) to bring donor templates in zygotes is currently being deployed by transgenic cores around the world to generate knock-ins with large transgenes. Thanks to a high level of efficiency and the relative ease to establish this technique, it recently became a method of choice for transgenic laboratories. However, a thorough analysis of the editing outcomes following this method is yet to be developed. To this end, we generated three different types of integration using AAVs in two different murine genes (i.e., Ace2 and Foxg1) and employed Oxford Nanopore Technologies long read sequencing to analyze the outcomes. Using a workflow that includes Cas9 enrichment and adaptive sampling, we showed that unintended on-target mutations (sometimes reported using other workflows) can occur when using AAVs. This work highlights the importance of in-depth validation of the mutant lines generated and informs the uptake of this new method.

bioengineering↗

bioRxiv2022

Accurate Identification of Extrachromosomal Circular DNA from Long-read Sequences.

Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in a range of eukaryotic species and cell type including cancer where eccDNA with oncogenes appear to drive tumorigenesis. Most studies of eccDNA employ short-read sequencing to identify for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA identification. An alternative is the long-read sequencing technologies that can potentially be used to construct complete eccDNA. We present a software suite, Construction-based Rolling-circle amplification for eccDNA Sequence Identification and Location (CReSIL) 2.0, to identify and characterize eccDNA from long-read sequences. CReSILs performance in the identification of eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSILs capability in many of the long-read sequencing datasets. This includes datasets enriched for eccDNA as well as whole genome datasets from many cells that contained large eccDNA. CReSIL suite software will be a versatile tool to deeply investigate eccDNA in biological samples.

bioinformatics↗

bioRxiv2020

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

genomics↗

bioRxiv2019

Fragile X Mental Retardation Protein regulates R-loop formation and prevents global chromosome fragility

Fragile X syndrome (FXS) is the most prevalent inherited intellectual disability caused by mutations in the Fragile X Mental Retardation 1 (FMR1) gene. The protein product of FMR1, FMRP, is known as a translational repressor whose nuclear function is not understood. Here we report that FMRP is a genome maintenance protein. We show that FX cells exhibit elevated level of chromosome breaks, both spontaneous and replication stress-induced. We demonstrate that FMRP is required for abating R-loop accumulation, thereby preventing chromosome breakage. Through mapping FMRP-bound chromatin loci in normal cells and correlating with FX-specific chromosome breaks, we identified novel FXS-susceptible genes. We show that FX cells have reduced expression of the uridine diphosphoglucuronosyl transferase 1 family enzymes, suggesting defective xenobiotics glucuronidation and consequential neurotoxicity in FXS.

genomics↗

bioRxiv2018

Decoding the Epitranscriptional Landscape from Native RNA Sequences

Sequencing of native RNA and corresponding cDNA was performed using Oxford Nanopore Technology. The % Error of Specific Bases (%ESB) was higher for native RNA than for cDNA, which enabled detection of ribonucleotide modification sites. Based on %ESB differences of the two templates, a bioinformatic tool ELIGOS was developed and applied to rRNAs of E. coli, yeast and human cells. ELIGOS captured 91%, 95%, [~]75%, respectively, of the known variety of RNA methylation sites in these rRNAs. Yeast transcriptomes from different growth conditions were also compared, which identified an association between metabolic adaptation and inferred RNA modifications. ELIGOS was further applied to human transcriptome datasets, which identified the well-known DRACH motif containing N6-methyadenine being located close to 3-untranslated regions of mRNA. Moreover, the RNA G-quadruplex motif was uncovered by ELIGOS. In summary, we have developed an experimental method coupled with bioinformatic software to uncover native RNA modifications and secondary-structures within transcripts.

genetics↗

bioRxiv2018

Rapid Sequencing of Multiple RNA Viruses in their Native Form

Long-read nanopore sequencing by a MinION device offers the unique possibility to directly sequence native RNA. We combined an enzymatic poly-A tailing reaction with the native RNA sequencing to (i) sequence complex population of single-stranded (ss)RNA viruses in parallel, (ii) detect genome, subgenomic mRNA/mRNA simultaneously, (iii) detect a complex transcriptomic architecture without the need for assembly, (iv) enable real-time detection. Using this protocol, positive-ssRNA, negative-ssRNA, with/without a poly(A)-tail, segmented/non-segmented genomes were mixed and sequenced in parallel. Mapping of the generated sequences on the reference genomes showed 100% length recovery with up to 97 % identity. This work provides a proof of principle and the validity of this strategy, opening up a wide range of applications to study RNA viruses.

genomics↗