Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
Objectives: To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR).
Methods: WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder.
Results: Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified.
Conclusions: WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/jac/dkad346 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Assessment of genomic prediction capabilities of transcriptome data in a barley multi-parent RIL population.
Theor Appl Genet
September 2025
Institute for Breeding Research on Agricultural Crops, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Sanitz, 18190, Germany.
Low-cost and high-throughput RNA sequencing data for barley RILs achieved GP performance comparable to or better than traditional SNP array datasets when combined with parental whole-genome sequencing SNP data. The field of genomic selection (GS) is advancing rapidly on many fronts including the utilization of multi-omics datasets with the goal of increasing prediction ability and becoming an integral part of an increasing number of breeding programs ensuring future food security. In this study, we used RNA sequencing (RNA-Seq) data to perform genomic prediction (GP) on three related barley RIL populations.
View Article and Find Full Text PDFGenomic analysis of transmission within an urban region.
Microb Genom
September 2025
Regional Innovative Public Health Laboratory, Rush University Medical Center, Chicago, IL 60612, USA.
emerged in Chicago, IL, USA, in 2016 and has since become endemic. We used whole-genome sequencing (WGS) of 494 isolates, epidemiologic metadata and patient transfer data to describe the transmission of among Chicago healthcare facilities between 2016 and 2021. In total, 99% of isolates formed a single clade IV phylogenetic lineage, suggesting a single introduction.
View Article and Find Full Text PDFPathogenicity and whole-genome analysis of a -derived strain.
Front Microbiol
August 2025
Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Science, Nanning, Guangxi, China.
A bacterial strain (No. 20230510) was isolated from the kidneys of diseased in Guangxi, China, since 2023. Artificial infection experiments demonstrated that this strain caused the observed disease in .
View Article and Find Full Text PDFProfiling Listeria monocytogenes in Hummus, Fresh Produce, and Food Processing Environments in the Western Cape, South Africa.
Microbiologyopen
October 2025
Department of Food Science, Stellenbosch University, Stellenbosch, Western Cape, South Africa.
Listeria monocytogenes is pervasive in agricultural environments and difficult to eradicate from food-processing facilities. Consequently, various foods become contaminated, posing health risks to immunocompromised individuals. This surveillance study aimed to enhance the understanding of the genetic diversity, virulence, plasmid content, sanitizer tolerance, and antibiotic resistance of L.
View Article and Find Full Text PDFProspective Whole Genome Sequencing to Aid the Identification and Control of Methicillin-Susceptible Staphylococcus aureus Transmissions in a Neonatal ICU.
J Infect
September 2025
Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA; Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Boston, MA, USA. Electronic address:
Background: Conventional surveillance methods may miss healthcare-associated pathogen transmission, particularly for common, drug-susceptible organisms. It is unclear if prospective genomic analyses can help identify otherwise silent transmission events and inform prevention efforts.
Methods: We sequenced methicillin susceptible Staphylococcus aureus (MSSA) surveillance and clinical isolates in the neonatal intensive care unit (NICU) of an academic hospital between Feb 2022 and Mar 2024.