Acinetobacter dijkshoorniae sp. nov., a member of the Acinetobacter calcoaceticus–Acinetobacter baumannii complex mainly recovered from clinical samples in different countries

Cosgaya, Clara; Marí-Almirall, Marta; Assche, Ado Van; Fernández‐Orth, Dietmar; Mosqueda, Noraida; Telli, Murat; Huys, Geert; Higgins, Paul G.; Seifert, Harald; Lievens, Bart; Roca, Ignasi; Vila, Jordi

doi:10.1099/ijsem.0.001318

Cited by 76 publications

(66 citation statements)

References 35 publications

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“…Alternative markers are increasingly used when 16S rRNA gene is not enough informative for robust phylogeny. This is particularly the case for bacteria organized in species complex such as Ralstonia (Li et al, 2016), Burkholderia cepacia (Vandamme and Dawyndt, 2011), Acinetobacter baumanii (Cosgaya et al, 2016). Alternative markers are genes encoding housekeeping proteins frequently associated in MLP studies (Roger et al, 2012b) that also allow population structure studies.…”

Section: Discussionmentioning

confidence: 99%

Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

et al. 2017

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Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and isDDH (in silico DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species Aeromonas media and Aeromonas rivipollensis. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside A. media species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the A. media complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.

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Section: Discussionmentioning

confidence: 99%

Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

et al. 2017

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“…Recently, two new species, Acinetobacter seifertii and Acinetobacter dijkshoorniae, were also included within the ACB complex. Hence, the ACB complex collectively includes five Acinetobacter species associated with human diseases (A. baumannii, A. pittii, A. nosocomialis, A. seifertti, and A. dijkshoorniae) and one environmental species (A. calcoaceticus), which is commonly isolated from soil and has not been described as a human pathogen [12,13].…”

Section: Taxonomy and Microbiological Properties Of Acinetobacter Baumentioning

confidence: 99%

Insights into Acinetobacter baumannii: A Review of Microbiological, Virulence, and Resistance Traits in a Threatening Nosocomial Pathogen

2020

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Being a multidrug-resistant and an invasive pathogen, Acinetobacter baumannii is one of the major causes of nosocomial infections in the current healthcare system. It has been recognized as an agent of pneumonia, septicemia, meningitis, urinary tract and wound infections, and is associated with high mortality. Pathogenesis in A. baumannii infections is an outcome of multiple virulence factors, including porins, capsules, and cell wall lipopolysaccharide, enzymes, biofilm production, motility, and iron-acquisition systems, among others. Such virulence factors help the organism to resist stressful environmental conditions and enable development of severe infections. Parallel to increased prevalence of infections caused by A. baumannii, challenging and diverse resistance mechanisms in this pathogen are well recognized, with major classes of antibiotics becoming minimally effective. Through a wide array of antibiotic-hydrolyzing enzymes, efflux pump changes, impermeability, and antibiotic target mutations, A. baumannii models a unique ability to maintain a multidrug-resistant phenotype, further complicating treatment. Understanding mechanisms behind diseases, virulence, and resistance acquisition are central to infectious disease knowledge about A. baumannii. The aims of this review are to highlight infections and disease-producing factors in A. baumannii and to touch base on mechanisms of resistance to various antibiotic classes.

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“…The genus Acinetobacter is taxonomically complex with unambiguous identification at the species level particularly problematic ( Gundi et al, 2009 ). A. baumannii, A. nosocomialis, A. pittii and A. calcoaceticus , which is usually an environmental species, along with two novel pathogenic species, A. seifertii and A. djikshoorniae cannot be reliably differentiated by phenotypic tests, and are thus usually grouped together as the Abc complex ( Gerner-Smidt et al, 1991 ; Nemec et al, 2015 ; Cosgaya et al, 2016 ; Marí-Almirall et al, 2017 ). Accurate identification at the species level requires sequencing of the RNA polymerase β-subunit gene, rpoB , and/or the DNA gyrase B gene, gyrB ( Gundi et al, 2009 ), with full-length 16S rRNA gene sequencing proven unreliable ( Wang et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Acinetobacter spp. Infections in Malaysia: A Review of Antimicrobial Resistance Trends, Mechanisms and Epidemiology

et al. 2017

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Acinetobacter spp. are important nosocomial pathogens, in particular the Acinetobacter baumannii-calcoaceticus complex, which have become a global public health threat due to increasing resistance to carbapenems and almost all other antimicrobial compounds. High rates of resistance have been reported among countries in Southeast Asia, including Malaysia. In this review, we examine the antimicrobial resistance profiles of Acinetobacter spp. hospital isolates from Malaysia over a period of nearly three decades (1987–2016) with data obtained from various peer-reviewed publications as well as the Malaysian National Surveillance on Antibiotic Resistance (NSAR). NSAR data indicated that for most antimicrobial compounds, including carbapenems, the peak resistance rates were reached around 2008–2009 and thereafter, rates have remained fairly constant (e.g., 50–60% for carbapenems). Individual reports from various hospitals in Peninsular Malaysia do not always reflect the nationwide resistance rates and often showed higher rates of resistance. We also reviewed the epidemiology and mechanisms of resistance that have been investigated in Malaysian Acinetobacter spp. isolates, particularly carbapenem resistance and found that blaOXA-23 is the most prevalent acquired carbapenemase-encoding gene. From the very few published reports and whole genome sequences that are available, most of the Acinetobacter spp. isolates from Malaysia belonged to the Global Clone 2 (GC2) CC92 group with ST195 being the predominant sequence type. The quality of data and analysis in the national surveillance reports could be improved and more molecular epidemiology and genomics studies need to be carried out for further in-depth understanding of Malaysian Acinetobacter spp. isolates.

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Acinetobacter dijkshoorniae sp. nov., a member of the Acinetobacter calcoaceticus–Acinetobacter baumannii complex mainly recovered from clinical samples in different countries

Cited by 76 publications

References 35 publications

Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

Insights into Acinetobacter baumannii: A Review of Microbiological, Virulence, and Resistance Traits in a Threatening Nosocomial Pathogen

Acinetobacter spp. Infections in Malaysia: A Review of Antimicrobial Resistance Trends, Mechanisms and Epidemiology

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