Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1

Álvarez, Verónica Elizabeth; Quiroga, María Paula; Galán, Angélica Viviana; Vilacoba, Elizabeth; Quiroga, Cecilia Medina; Ramírez, María Soledad; Centrón, Daniela

doi:10.3389/fmicb.2020.00342

Cited by 18 publications

(20 citation statements)

References 110 publications

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“…GC2 followed by GC1 contribute to the highest proportion of strains that cause multi-drug-resistant infections globally [4]. Over the last decade, studies have unravelled many complexities of: (i) how antibiotic resistance has developed in GC1 by providing the details of genetic mechanisms leading to antibiotic resistance [4,6,11,53,54], and (ii) characterizing variations in the K and OC surface polysaccharides [23,24,55]. Besides AB307-0294, all isolates studied previously are resistant to multiple antibiotics.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

et al. 2021

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Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.

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Section: Discussionmentioning

confidence: 99%

Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

et al. 2021

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“…A significant factor in the accessory genome variance is the acquisition of a wide variety of mobile genetic elements as well as hotspots of recombination, which has contributed to the evolution of extensive and pan-drug resistant phenotypes [9]. Notably, comparative analysis of isolates from international clonal lineage I has shown hotspots of recombination associated with capsular polysaccharide, lipooligosaccharide, and outer membrane proteins-surface structures which are commonly targeted by phages for adsorption [10,11].…”

Section: Introductionmentioning

confidence: 99%

Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter

Oliveira

Domingues

Evans

et al. 2022

Viruses

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The number of sequenced Acinetobacter phage genomes in the International Nucleotide Sequence Database Collaboration has increased significantly in recent years, from 37 in 2017 to a total of 139 as of January 2021 with genome sizes ranging from 31 to 378 kb. Here, we explored the genetic diversity of the Acinetobacter phages using comparative genomics approaches that included assessment of nucleotide similarity, shared gene content, single gene phylogeny, and the network-based classification tool vConTACT2. Phages infecting Acinetobacter sp. are genetically diverse and can be grouped into 8 clusters (subfamilies) and 46 sub-clusters (genera), of which 8 represent genomic singletons (additional genera). We propose the creation of five new subfamilies and suggest a reorganisation of the genus Obolenskvirus. These results provide an updated view of the viruses infecting Acinetobacter species, providing insights into their diversity.

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“…Considering that fitness studies have previously helped to understand the emergence of relevant antimicrobial-resistant lineages ( Luo et al., 2005 ; Otto, 2013 ; Ávarez et al., 2020 ; Hertz et al., 2022 ), it would be interesting to deeply investigate the interplay of most common KPC-producing clones from other institutions. Studying the ecological behavior of high-risk clones coexisting within the same hospital and their changing epidemiological patterns over time could contribute to identifying possible competitive emerging clones as well as prevent the further spread of KPC-producing strains.…”

Section: Discussionmentioning

confidence: 99%

“…Even though there are several methods to quantify microbial fitness, the approach that most closely corresponds to the meaning of fitness in evolutionary theory uses a competition assay ( Wiser and Lenski, 2015 ). Competition assays between isogenic strains are common ( Sander et al., 2002 ; Guo et al., 2012 ), but much less is explored about lineages or interspecies competitions that share the same ecological niche ( Hafza et al., 2018 ; Ávarez et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche

Knecht

Allende

Álvarez

et al. 2022

Front. Cell. Infect. Microbiol.

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According to the World Health Organization, carbapenem-resistant Enterobacteriaceae (CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria: Klebsiella pneumoniae and Enterobacter cloacae Complex (ECC). This scenario is mirrored in our hospital. It is known that K. pneumoniae and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one Enterobacter hormaechei and one K. pneumoniae) and in vitro competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing K. pneumoniae (KPC-Kp) high-risk clones from our institution. A KPC-producing E. hormaechei and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring blaKPC-2. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of blaKPC-2 within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.

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Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1

Cited by 18 publications

References 110 publications

Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1

Genomic Diversity of Bacteriophages Infecting the Genus Acinetobacter

Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche

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