What are the reference strains of <i>Acinetobacter baumannii</i> referring to?

Philippe, Chantal; Valček, Adam; Whiteway, Clémence; Robino, Etienne; Nešporová, Kristina; Bové, Mona; Coenye, Tom; Pooter, Tim De; Coster, Wouter De; Stražišar, Mojca; Kenyon, Johanna J.; Henst, Charles Van der

doi:10.1101/2022.02.27.482139

Cited by 3 publications

(3 citation statements)

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“…A. baumannii bacteria have a dynamic genome, with an estimated conserved core genome of only 16.5%, while 25% of the genome is unique to each strain, meaning that there is no counterpart in any other A. baumannii genome (Imperi et al ., 2011). Our recent study (Philippe et al ., 2022) on 47 strains of A. baumannii shows even lower core genome of 2009 genes from the pangenome of 13611 genes, accounting for 14.76%. A. baumannii isolates are impressively variable, at both genetic and phenotypic levels.…”

Section: Introductionmentioning

confidence: 95%

“…The observations gained about these reference strains shed a strong base of the knowledge about A. baumannii . However, in the other hand, type strains also showed the limitations of only using these strains when current clinical isolates of A. baumannii show extreme genetic and phenotypic variabilities (Philippe et al ., 2022). In order to fill this modern gap of knowledge, grasp the complexity of A. baumannii and widen the possibilities of the community to use and efficiently share genotypically and phenotypically characterized strains, we propose the database and strain repository Acinetobase as a new community tool (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Acinetobase: the comprehensive database and repository of Acinetobacter strains

Valček

Collier²,

Botzki³

et al. 2022

Preprint

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Background: Acinetobacter baumannii is one of the most problematic nosocomial pathogens that can efficiently thrive within hospital settings, mainly due to resistances towards antibiotics, desiccation, disinfectants, human serum and oxidative stress. Recently, increased resistance against last resort antibiotics earns this bacterium a highest priority concern classified by the CDC and the WHO. An obvious hallmark of this bacterium is the high heterogeneity observed amongst A. baumannii isolates, with a limited core genome. This feature complexifies the study of A. baumannii bacteria as an entity, subsequently reflected in a diversity of phenotypes of not only antimicrobial and environmental resistance but also virulence. Main body: High degree of genome plasticity, along with the use of a limited subset of established reference strains, can lead to strain-specific observations, decreasing the global understanding of this pathogenic agent. Phenotypic variability of A. baumannii strains is easily observable such as with the microcolony morphologies, in vitro and in vivo virulence, production of different capsular polysaccharide structures and cellular densities. Some strains encode an extensive amount of virulence factors while other, including the reference strains, lack several key ones. The lack/excess of genes or specific physiological processes might interfere with in vivo and in vitro experiments, thus providing limited impact on the global understanding of Acinetobacter bacteria. Conclusion: As an answer to the high heterogeneity amongst A. baumannii strains, we propose a first comprehensive database that includes the bacterial strains and the associated phenotypic and genetic data. This new repository, freely accessible to the entire community, allow selecting the best bacterial isolate(s) related to any biological question, using an efficient and fast exchange platform.

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Section: Introductionmentioning

confidence: 95%

Section: Introductionmentioning

confidence: 99%

Acinetobase: the comprehensive database and repository of Acinetobacter strains

Valček

Collier²,

Botzki³

et al. 2022

Preprint

Self Cite

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“…Similar genomic variations between different laboratories’ cultures have been seen in A. baumannii 19606 ( Artuso et al., 2022 ). These examples show how variable and constantly changing the A. baumannii genome is: only 14.8% to 16.5% of the genome is shared among 12 ( Imperi et al., 2011 ) or 47 ( Philippe et al., 2022 ) isolates, respectively.…”

Section: Introductionmentioning

confidence: 99%

DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

Cook,

Flannigan,

Chariker

et al. 2024

Front. Cell. Infect. Microbiol.

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IntroductionAcinetobacter baumannii strain 17978 is an opportunistic pathogen possessing a DNA damage response (DDR) in which multiple error-prone polymerase genes are co-repressed by a UmuD homolog, UmuDAb, and the small Acinetobacter-specific protein DdrR. Additionally, these regulators coactivate nine other genes. We identified the DNA damage-inducible transcriptome for wildtype, umuDAb, and recA strains, and later established the ddrR DDR transcriptome. However, the ATCC 17978 reference genome had several assembly errors and lacked the 44 kb virulence locus, AbaAL44, that is present in the strain 17978 UN.MethodsFor this project, we combined our earlier single-end read RNAseq data with the ddrR paired-end reads and aligned these data to the improved 17978 UN genome assembly that resembled our laboratory strain, 17978 JH.ResultsNew DESeq2 analyses verified previous differentially expressed genes (DEGs) but also found 339 genes in 17978 JH that were not annotated or physically present in the older genome assembly. Sixty-three were differentially expressed after DNA damage, and 182 had differential basal expression when comparing umuDAb, ddrR, or recA strains to wildtype, with 94 genes’ expression unchanged. This work identified and characterized the 55 gene DNA damage-repressible transcriptome, 98% of which required either umuDAb or ddrR for repression. Two-thirds of these DEGs required both regulators. We also identified 110 genes repressed only in the ddrR strain, ~50% of which were due to increased basal expression levels. Basal gene expression in the ddrR mutant was further dysregulated independent of the DDR. Over 800 genes were upregulated, and over 1200 genes were downregulated compared to wildtype expression. Half of A. baumannii’s essential genes were upregulated in the ddrR strain, including cell division genes, and two-thirds of these were downregulated in the umuDAb strain.DiscussionThe ddrR mutant upregulated genes enriched in translation, RNA metabolism, protein metabolism, AA/FA/cell-structure synthesis, and transport, while downregulating genes enriched in quorum sensing, biofilm production, secretion systems, pilus production, cell adhesion, and aromatics and chlorine degradation. Our data underscore the need for accurate and appropriately matched genome assemblies and indicate that ddrR affects approximately 60% of the genome, rendering it a potential target for Acinetobacter baumannii infection treatment.

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Acinetobase: the comprehensive database and repository of Acinetobacter strains

Valček

Collier²,

Botzki³

et al. 2022

Database

View full text Add to dashboard Cite

Acinetobacter baumannii is one of the most problematic nosocomial pathogens that can efficiently thrive within hospital settings, mainly due to resistances toward antibiotics, desiccation, disinfectants, human serum and oxidative stress. Recently, increased resistance against last-resort antibiotics earns this bacterium the highest priority concern classified by the Centers for Disease Control and Prevention and the World Health Organization. An obvious hallmark of this bacterium is the high heterogeneity observed among A. baumannii isolates, with a limited core genome. This feature complexifies the study of A. baumannii bacteria as an entity, subsequently reflected in a diversity of phenotypes of not only antimicrobial and environmental resistance but also virulence. A high degree of genome plasticity, along with the use of a limited subset of established strains, can lead to strain-specific observations, decreasing the global understanding of this pathogenic agent. Phenotypic variability of A. baumannii strains is easily observable such as with the macrocolony morphologies, in vitro and in vivo virulence, natural competence level, production of different capsular polysaccharide structures and cellular densities. Some strains encode an extensive amount of virulence factors, while others, including the established strains, lack several key ones. The lack/excess of genes or specific physiological processes might interfere with in vivo and in vitro experiments, thus providing a limited impact on the global understanding of Acinetobacter bacteria. As an answer to the high heterogeneity among A. baumannii strains, we propose a first comprehensive database that includes the bacterial strains and the associated phenotypic and genetic data. This new repository, freely accessible to the entire scientific community, allows selecting the best bacterial isolate(s) related to any biological question, using an efficient and fast exchange platform. Database URL: https://acinetobase.vib.be/

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What are the reference strains of Acinetobacter baumannii referring to?

Cited by 3 publications

References 77 publications

Acinetobase: the comprehensive database and repository of Acinetobacter strains

Acinetobase: the comprehensive database and repository of Acinetobacter strains

DNA damage response coregulator ddrR affects many cellular pathways and processes in Acinetobacter baumannii 17978

Acinetobase: the comprehensive database and repository of Acinetobacter strains

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