Molecular characterization of the whole genome in clinical multidrug-resistant strains of Klebsiella pneumoniae

Rahmani, Amina; Meradi, Laarem; Piris, Rudolph

doi:10.3855/jidc.17168

Cited by 2 publications

(1 citation statement)

References 42 publications

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“…S16 Quality of raw reads was assessed using FastQC v0.11.9 (124) by examining average quality scores across read sequences to remove samples with average phred scores <20. Assemblies were generated with Shovill v1.1.0 (125) (https://github.com/tseemann/shovill) at default settings, which uses the assembler Spades v3.14 (126) at its core with pre and post-processing steps to refine the final assemblies. The resulting contiguous sequences were assessed for quality using both QUAST v5.2.0 (127) and CheckM v1.2.2 (128).…”

Section: Methodsmentioning

confidence: 99%

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Foo,

Brettell,

Nichols

et al. 2023

Preprint

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Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such asPlasmodiumspp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterialMosquito-Associated IsolateCollection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of theEnterobacteriaceaecomprising 40% of the collection. Phylogenomic analysis of three genera,Enterobacter, Serratia, andElizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species’ pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to identify functions underlying mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource to investigate factors for bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.

show abstract

Section: Methodsmentioning

confidence: 99%

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Foo,

Brettell,

Nichols

et al. 2023

Preprint

View full text Add to dashboard Cite

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MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies

Foo,

Brettell,

Nichols

et al. 2024

PLoS Biol

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Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such as Plasmodium spp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterial Mosquito-Associated Isolate Collection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available, both isolates and sequence data, for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of the Enterobacteriaceae comprising 40% of the collection. Phylogenomic analysis of 3 genera, Enterobacter, Serratia, and Elizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species’ pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to test for functions connected to mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource for research on bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.

show abstract

Molecular characterization of the whole genome in clinical multidrug-resistant strains of Klebsiella pneumoniae

Cited by 2 publications

References 42 publications

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

Establishment and comparative genomics of a high-quality collection of mosquito-associated bacterial isolates - MosAIC (Mosquito-Associated Isolate Collection)

MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies

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