Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures

Raghuram, Vishnu; Gunoskey, Jessica J.; Hofstetter, Katrina S.; Jacko, Natasia F.; Shumaker, Margot J.; Hu, Yi-Juan; Read, Timothy D.; David, Michael Z.

doi:10.1099/mgen.0.001111

Cited by 2 publications

(1 citation statement)

References 54 publications

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“…Plate sweeps were taken daily to avoid excessive growth on the plate, and other groups have shown high agreement in inferred population structures when comparing deep sequencing of plate sweeps with sequencing of multiple colony picks. 81 , 82 …”

Section: Resultsmentioning

confidence: 99%

Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium

McHugh,

Pettigrew,

Taori

et al. 2024

Journal of Antimicrobial Chemotherapy

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Background WGS is increasingly being applied to healthcare-associated vancomycin-resistant Enterococcus faecium (VREfm) outbreaks. Within-patient diversity could complicate transmission resolution if single colonies are sequenced from identified cases. Objectives Determine the impact of within-patient diversity on transmission resolution of VREfm. Materials and methods Fourteen colonies were collected from VREfm positive rectal screens, single colonies were collected from clinical samples and Illumina WGS was performed. Two isolates were selected for Oxford Nanopore sequencing and hybrid genome assembly to generate lineage-specific reference genomes. Mapping to closely related references was used to identify genetic variations and closely related genomes. A transmission network was inferred for the entire genome set using Phyloscanner. Results and discussion In total, 229 isolates from 11 patients were sequenced. Carriage of two or three sequence types was detected in 27% of patients. Presence of antimicrobial resistance genes and plasmids was variable within genomes from the same patient and sequence type. We identified two dominant sequence types (ST80 and ST1424), with two putative transmission clusters of two patients within ST80, and a single cluster of six patients within ST1424. We found transmission resolution was impaired using fewer than 14 colonies. Conclusions Patients can carry multiple sequence types of VREfm, and even within related lineages the presence of mobile genetic elements and antimicrobial resistance genes can vary. VREfm within-patient diversity could be considered in future to aid accurate resolution of transmission networks.

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Section: Resultsmentioning

confidence: 99%

Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium

McHugh,

Pettigrew,

Taori

et al. 2024

Journal of Antimicrobial Chemotherapy

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A community-curated, global atlas ofBacillus cereus sensu latogenomes for epidemiological surveillance

Ramnath,

Larralde,

Menchik

et al. 2023

Preprint

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The ability to cause foodborne illness, anthrax, and other infections has been attributed to numerous lineages withinBacillus cereus sensu lato(s.l.). However, existing pathogen surveillance databases facilitate dangerous pathogen misidentifications when applied toB. cereus s.l., potentially hindering outbreak or bioterrorism attack response efforts. To address this, we developed BTyperDB (www.btyper.app), an atlas ofB. cereus s.l.genomes with standardized, community-curated metadata. BTyperDB aggregates all publicly availableB. cereus s.l.genomes (including >2,600 previously unassembled genomes) with novel genomes donated by laboratories around the world, nearly doubling the number of publicly availableB. cereus s.l.genomes. To showcase its utility for pathogen surveillance, we use BTyperDB to identify emerging anthrax toxin- and capsule-harboring lineages. Overall, our study provides insight into the epidemiology of an under-studied group of emerging pathogens and highlights the benefits of inclusive, community-driven metadata FAIRification efforts.

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Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures

Abstract: Graphical abstract

Cited by 2 publications

References 54 publications

Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium

Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin-resistant Enterococcus faecium

A community-curated, global atlas ofBacillus cereus sensu latogenomes for epidemiological surveillance

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