Accessory Genomic Epidemiology of Cocirculating Acinetobacter baumannii Clones

Mateo-Estrada, Valeria; Fernández-Vázquez, José Luís; Moreno-Manjón, Julia; Hernández-González, Ismael; Rodríguez-Noriega, Eduardo; Morfín‐Otero, Rayo; Alcántar‐Curiel, María Dolores; Castillo-Ramírez, Santiago

doi:10.1128/msystems.00626-21

Cited by 17 publications

(22 citation statements)

References 48 publications

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“…This strategy has been very useful to appraise the dissemination of bacterial pathogens over different scales, from global to national and even in local settings. [4][5][6] However, core genomic epidemiology neglects an important amount of the phylogenetic information contained in the accessory genome, which are regions of the genome present in some but not all of the isolates considered. In bacterial genomic epidemiology the accessory genome is commonly discarded as it does not follow vertical transmission; however, we now have a much better understanding of this part of the genome and a better framework to integrate it with the phylogenetic signals residing the in the core genome.…”

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confidence: 99%

“…In a 2021 study, which analysed the dissemination of A baumannii within a hospital, the potential for using the accessory genome to conduct genomic epidemiology was shown. 6 To fully understand the transmission of several co-circulating lineages of A baumannii, Mateo-Estrada and colleagues 6 made use of gene content variation within the accessory genome in addition to using classical core genomic epidemiology. Notably, the variation in the accessory genome was of paramount importance to establish the high rate of transmission across the different wards in the hospital.…”

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confidence: 99%

“…By integrating and contrasting core and accessory genomic epidemiology (termed pan genomic epidemiology) we can gain unprecedented insights into the transmission dynamics of bacterial populations. [6][7][8] However, whether to use core or accessory genomic epidemiology or even pan genomic epidemiology will depend on the genetics of the bacterial species in question; accessory genomic epidemiology is more suitable for species with dynamic genomes. 9 Another important factor to consider is the spatiotemporal scale: core genomic epidemiology should be sufficient for global, intercontinental, and even national investigations but might not be suitable for analysing transmission dynamics over very short periods of time.…”

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Beyond microbial core genomic epidemiology: towards pan genomic epidemiology

Castillo-Ramírez¹

2022

The Lancet Microbe

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Beyond microbial core genomic epidemiology: towards pan genomic epidemiology

Castillo-Ramírez¹

2022

The Lancet Microbe

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“…We have recently shown that different lineages of A. baumannii can co-exist in individual hospital settings [22, 31].…”

Section: Discussionmentioning

confidence: 99%

“…We also run a maximum-likelihood (ML) non-recombinant core phylogeny as we have done previously in a genomic epidemiology study of A. baumannii [22]. First, we defined the core genes and excluded all the core genes that had recombination signals (recombination was detected as stated below).…”

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confidence: 99%

The promiscuous and highly mobile resistome of Acinetobacter baumannii

2022

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Antimicrobial resistance (AR) is a major global threat to public health. Understanding the population dynamics of AR is critical to restrain and control this issue. However, no study has provided a global picture of the whole resistome of Acinetobacter baumannii , a very important nosocomial pathogen. Here we analyse 1450+ genomes (covering >40 countries and >4 decades) to infer the global population dynamics of the resistome of this species. We show that gene flow and horizontal transfer have driven the dissemination of AR genes in A. baumannii . We found considerable variation in AR gene content across lineages. Although the individual AR gene histories have been affected by recombination, the AR gene content has been shaped by the phylogeny. Furthermore, many AR genes have been transferred to other well-known pathogens, such as Pseudomonas aeruginosa or Klebsiella pneumoniae . Despite using this massive data set, we were not able to sample the whole diversity of AR genes, which suggests that this species has an open resistome. Our results highlight the high mobilization risk of AR genes between important pathogens. On a broader perspective, this study gives a framework for an emerging perspective (resistome-centric) on the genomic epidemiology (and surveillance) of bacterial pathogens.

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Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance

Picazo

Werner

Kupczok

2022

Genome Biology and Evolution

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Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.

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Accessory Genomic Epidemiology of Cocirculating Acinetobacter baumannii Clones

Cited by 17 publications

References 48 publications

Beyond microbial core genomic epidemiology: towards pan genomic epidemiology

Beyond microbial core genomic epidemiology: towards pan genomic epidemiology

The promiscuous and highly mobile resistome of Acinetobacter baumannii

Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance

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