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