Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing

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Piroon Jenjaroenpun, Visanu Wanchai, Kikumi D Ono-Moore, Jennifer Laudadio, Laura P James, Sean H Adams, Fred Prior, Intawat Nookaew, David W Ussery, and Thidathip Wongsurawat

Microbiology Resource Announcements. 2020 Dec 17;10(1).

Abstract

Two coding-complete sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were obtained from samples from two patients in Arkansas, in the southeastern corner of the United States. The viral genome was obtained using the ARTIC Network protocol and Oxford Nanopore Technologies sequencing.

Read the publication here: https://mra.asm.org/content/10/1/e01109-20

Genome sequences of antibiotic-resistant Streptococcus suis strains isolated from human patients and diseased and asymptomatic pigs in Thailand

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Suganya Yongkiettrakul, Thidathip Wongsurawat, Piroon Jenjaroenpun, Daniel A. Acheampong, Potjanee Srimanote, Krissana Maneerat, Wonnop Visessanguan, and Intawat Nookaew

Infection, Genetics and Evolution. 2020 Dec 13:104674.

Abstract

Streptococcus suis, a zoonotic bacterial pathogen, has negative economic impacts on both intensive swine production and human health worldwide. Whole-genome sequencing and comparative genomic analysis have been widely used for comprehensive classification and investigation of the genetic basis of several S. suis strains obtained from distinct hosts in different geographic areas, revealing great genetic diversity of this zoonotic pathogen. In this study, whole-genome sequences of antibiotic-resistant S. suis strains isolated from human patients (2 strains), diseased pigs (4 strains), and asymptomatic pigs (3 strains) in Thailand were compared with known genomes of 1186 S. suis strains. Single-nucleotide polymorphism-based phylogenetic analysis indicated that the Thai-isolated S. suis strains have close genetic relatedness to S. suis strains isolated from Canada, China, Denmark, Netherlands, United Kingdom, and United States of America. The genome analysis revealed genes conferring antibiotic resistance (aad(6), ant(6)-Ia, ermB, tet(O), patB, and sat4) and gene clusters (aph(3′)-IIIa and aac(6′)-Ie-aph(2″)-Ia) associated with aminoglycoside, macrolide, and fluoroquinolone resistance in S. suis in Thailand. This work provides additional resources for future genomic epidemiology investigation of S. suis.

Keywords Antibiotic resistance; SNP-based phylogenetics; Streptococcus suis; Whole-genome sequencing

Read the publication here: https://www.sciencedirect.com/science/article/abs/pii/S1567134820305050

Genomic Analysis of Aeromonas veronii C198, a Novel Mcr-3.41-Harboring Isolate from a Patient with Septicemia in Thailand

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Rujirat Hatrongjit, Anusak Kerdsin, Dan Takeuchi, Thidathip Wongsurawat, Piroon Jenjaroenpun, Peechanika Chopjitt, Parichart Boueroy, Yukihiro Akeda, and Shigeyuki Hamada

Pathogens. 2020 Dec;9(12):1031.

Abstract

The resistance of Gram-negative bacteria to colistin, mediated by plasmid-borne mcr genes, is an emerging public health concern. The complete genome sequence (4.55 Mb) of a clinical isolate of Aeromonas veronii biovar veronii obtained from a patient with septicemia was determined using short-read and long-read platforms. This isolate (C198) was found to harbor a novel mcr-3 gene, designated mcr-3.41. Isolate C198 revealed adjacent mcr-3.41 and mcr-3-like genes. It contained one chromosome and two plasmids, both of which encoded a RepB replication protein. Other antimicrobial resistance genes, including blacphA3, blaOXA-12, tetA, rsmA, and adeF, were also present. Isolate C198 was resistant to amoxicillin-clavulanate, ampicillin-sulbactam and tetracycline, and showed intermediate resistance to trimethoprim-sulfamethoxazole. The isolate was susceptible to piperacillin-tazobactam, carbapenem, third-generation cephalosporins, fluoroquinolones, chloramphenicol, and aminoglycosides. Putative virulence genes in the C198 genome encoded type II, III, and VI secretion systems; type IV Aeromonas pili; and type I fimbria, flagella, hemagglutinin, aerolysin, and hemolysins. Multilocus sequence typing revealed a novel sequence type (ST), ST720 for C198. Phylogenetic analysis of the single nucleotide polymorphisms in C198 demonstrated that the strain was closely related to A. veronii 17ISAe. The present study provides insights into the genomic characteristics of human A. veronii isolates.

Keywords Aeromonas veronii; Thailand; colistin; genome; mcr

Read the publication here: https://www.mdpi.com/2076-0817/9/12/1031

ProdMX: Rapid query and analysis of protein functional domain based on compressed sparse matrices

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Visanu Wanchai, Intawat Nookaew, and David W. Ussery

Computational and structural biotechnology journal. 2020 Nov 24.

Abstract

Large-scale protein analysis has been used to characterize large numbers of proteins across numerous species. One of the applications is to use as a high-throughput screening method for pathogenicity of genomes. Unlike sequence homology methods, protein comparison at a functional level provides us with a unique opportunity to classify proteins, based on their functional structures without dealing with sequence complexity of distantly related species. Protein functions can be abstractly described by a set of protein functional domains, such as PfamA domains; a set of genomes can then be mapped to a matrix, with each row representing a genome, and the columns representing the presence or absence of a given functional domain. However, a powerful tool is needed to analyze the large sparse matrices generated by millions of genomes that will become available in the near future. The ProdMX is a tool with user-friendly utilities developed to facilitate high-throughput analysis of proteins with an ability to be included as an effective module in the high-throughput pipeline. The ProdMX employs a compressed sparse matrix algorithm to reduce computational resources and time used to perform the matrix manipulation during functional domain analysis. The ProdMX is a free and publicly available Python package which can be installed with popular package mangers such as PyPI and Conda, or with a standard installer from source code available on the ProdMX GitHub repository at https://github.com/visanuwan/prodmx.

Keywords Proteins; Protein functional domain; Domain architecture; Comparative genomics; Python; Compressed sparse matrix

Read the publication here: https://www.sciencedirect.com/science/article/pii/S2001037020304451

Chest imaging representing a COVID-19 positive rural U.S. population

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Shivang Desai, Ahmad Baghal, Thidathip Wongsurawat, Piroon Jenjaroenpun, Thomas Powell, Shaymaa Al-Shukri, Kim Gates, Phillip Farmer, Michael Rutherford, Geri Blake, Tracy Nolan, Kevin Sexton, William Bennett, Kirk Smith, Shorabuddin Syed, and Fred Prior

Scientific data. 2020 Nov 24;7(1):1-6.

Abstract

As the COVID-19 pandemic unfolds, radiology imaging is playing an increasingly vital role in determining therapeutic options, patient management, and research directions. Publicly available data are essential to drive new research into disease etiology, early detection, and response to therapy. In response to the COVID-19 crisis, the National Cancer Institute (NCI) has extended the Cancer Imaging Archive (TCIA) to include COVID-19 related images. Rural populations are one population at risk for underrepresentation in such public repositories. We have published in TCIA a collection of radiographic and CT imaging studies for patients who tested positive for COVID-19 in the state of Arkansas. A set of clinical data describes each patient including demographics, comorbidities, selected lab data and key radiology findings. These data are cross-linked to SARS-COV-2 cDNA sequence data extracted from clinical isolates from the same population, uploaded to the GenBank repository. We believe this collection will help to address population imbalance in COVID-19 data by providing samples from this normally underrepresented population.

Read the publication here: https://www.nature.com/articles/s41597-020-00741-6

Machine Learning Methods in Drug Discovery

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Lauv Patel, Tripti Shukla, Xiuzhen Huang, David W. Ussery and Shanzhi Wang

Molecules. 2020; 25(22):5277.

Abstract

The advancements of information technology and related processing techniques have created a fertile base for progress in many scientific fields and industries. In the fields of drug discovery and development, machine learning techniques have been used for the development of novel drug candidates. The methods for designing drug targets and novel drug discovery now routinely combine machine learning and deep learning algorithms to enhance the efficiency, efficacy, and quality of developed outputs. The generation and incorporation of big data, through technologies such as high-throughput screening and high through-put computational analysis of databases used for both lead and target discovery, has increased the reliability of the machine learning and deep learning incorporated techniques. The use of these virtual screening and encompassing online information has also been highlighted in developing lead synthesis pathways. In this review, machine learning and deep learning algorithms utilized in drug discovery and associated techniques will be discussed. The applications that produce promising results and methods will be reviewed.

Keywords machine learning; drug discovery; deep learning; in silico screening

Read the publication here: https://www.mdpi.com/1420-3049/25/22/5277

Safety assessment of a nham starter culture Lactobacillus plantarum BCC9546 via whole-genome analysis

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Nipa Chokesajjawatee, Pannita Santiyanont, Kanittha Chantarasakha, Kanokarn Kocharin, Chinae Thammarongtham, Supatcha Lertampaiporn, Tayvich Vorapreeda, Tanawut Srisuk, Thidathip Wongsurawat, Piroon Jenjaroenpun, Intawat Nookaew, and Wonnop Visessanguan

Scientific reports. 2020 Jun 24;10(1):1-2.

Abstract

The safety of microbial cultures utilized for consumption is vital for public health and should be thoroughly assessed. Although general aspects on the safety assessment of microbial cultures have been suggested, no methodological detail nor procedural guideline have been published. Herein, we propose a detailed protocol on microbial strain safety assessment via whole-genome sequence analysis. A starter culture employed in traditional fermented pork production, nham, namely Lactobacillus plantarum BCC9546, was used as an example. The strain’s whole-genome was sequenced through several next-generation sequencing techniques. Incomplete plasmid information from the PacBio sequencing platform and shorter chromosome size from the hybrid Oxford Nanopore-Illumina platform were noted. The methods for 1) unambiguous species identification using 16S rRNA gene and average nucleotide identity, 2) determination of virulence factors and undesirable genes, 3) determination of antimicrobial resistance properties and their possibility of transfer, and 4) determination of antimicrobial drug production capability of the strain were provided in detail. Applicability of the search tools and limitations of databases were discussed. Finally, a procedural guideline for the safety assessment of microbial strains via whole-genome analysis was proposed.

Read the publication here: https://www.nature.com/articles/s41598-020-66857-2

16S rRNA Gene Amplicon Profiling of Baby and Adult Captive Elephants in Thailand

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Sangam Kandel, Supaphen Sripiboon, Piroon Jenjaroenpun, David W. Ussery, Intawat Nookaew, Michael S. Robeson II, Thidathip Wongsurawat

Microbiology Resource Announcements Jun 2020, 9 (24) e00248-20; DOI: 10.1128/MRA.00248-20.

Abstract

Here, we present a 16S rRNA gene amplicon sequence data set and profiles demonstrating the bacterial diversity of baby and adult elephants from four different geographical locations in Thailand. The dominant phyla among baby and adult elephants were Bacteroidetes, Firmicutes, Proteobacteria, Kiritimatiellaeota, Euryarchaeota, and Tenericutes.

Read the publication here: https://mra.asm.org/content/9/24/e00248-20

Complete Genome Sequences of Three Neisseria gonorrhoeae Isolates from Thailand with Multidrug Resistance and Multilocus Sequence Type 1903

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Cherdtrakulkiat T, Wongsurawat T, Jenjaroenpun P, Sutheeworapong S, Leelawiwat W, Hickey AC, Dunne EF, Raengsakulrach B, Tribuddharat C.

Microbiology Resource Announcements. 2020 May 7;9(19).

Abstract

Multilocus sequence typing (MLST) sequence type 1903 (ST1903) is the most common ST of ceftriaxone-resistant Neisseria gonorrhoeae Here, we report three completed genome sequences of MLST ST1903 N. gonorrhoeae isolates collected from patients at Faculty of Medicine Siriraj Hospital, a university hospital in Bangkok, Thailand, in 2009 to 2011.

Read the publication here: https://mra.asm.org/content/9/19/e00198-20

Fighting the enemy: one health approach against microbial resistance

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Zulema Udaondo and María José Huertas

Microb Biotechnol. 2020;13(4):888-891. doi:10.1111/1751-7915.13587.

Abstract

This article highlights publications in Enviromental Microbiology and Microbial Biotechnology papers about antibiotic resistance. It concludes that the One health approach is basic to addressing this problem.

Read the publication here: https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/1751-7915.13587