Od června 2015 do května 2016 byly v sedmi nemocnicích České republiky zachyceny extenzivně rezistentní kmeny Acinetobacter baumannii náležející k celosvětově rozšířenému epidemickému klonu II. Tyto kmeny nesly geny pro karbapenemázu OXA-23 a metylázu ArmA a byly rezistentní ke všem ß-laktamům a aminoglykosidům.Tento rezistotyp je v České republice nový a jeho šíření může dále omezit léčebné možnosti u acinetobakterových infekcí.
Extensively drug-resistant strains of Acinetobacter baumannii belonging to worldwide epidemic clone II were isolated in seven Czech hospitals between June 2015 and April 2016. These strains carried the genes encoding the OXA-23 carbapenemase and ArmA methylase and were resistant to all ß-lactams and aminoglycosides. Thisresistotype is new in the Czech Republic and its dissemination may further complicate the therapy of Acinetobacter infections.
- MeSH
- Acinetobacter baumannii * enzymologie genetika účinky léků MeSH
- aminoglykosidy farmakologie terapeutické užití MeSH
- beta-laktamasy škodlivé účinky MeSH
- beta-laktamová rezistence genetika MeSH
- infekce spojené se zdravotní péčí enzymologie mikrobiologie prevence a kontrola MeSH
- karbapenemy farmakologie terapeutické užití MeSH
- lidé MeSH
- mnohočetná bakteriální léková rezistence * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
A taxonomically unique bacterial strain, Acinetobacter sp. A47, has been recovered from several soft tissue samples from a patient undergoing reconstructive surgery owing to a traumatic amputation. The results of 16S rRNA, rpoB, and gyrB gene comparative sequence analyses showed that A47 does not belong to any of the hitherto-known taxa and may represent an as-yet-unknown Acinetobacter species. The recognition of this novel organism contributes to our knowledge of the taxonomic complexity underlying infections caused by Acinetobacter.
- MeSH
- Acinetobacter klasifikace genetika fyziologie MeSH
- bakteriální geny genetika MeSH
- DNA bakterií analýza genetika MeSH
- fenotyp MeSH
- infekce bakteriemi rodu Acinetobacter * diagnóza mikrobiologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- molekulární sekvence - údaje MeSH
- poranění měkkých tkání * diagnóza mikrobiologie MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
- práce podpořená grantem MeSH
This study aimed to define the taxonomic status of a phenetically distinct group of 16 strains that corresponds to Acinetobacter genomic species 'close to 13TU', a provisional genomic species of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex recognized by Gerner-Smidt and Tjernberg in 1993. These strains have been isolated in different countries since the early 1990s and were mostly recovered from human clinical specimens. They were compared with 45 reference strains representing the known taxa of the ACB complex using taxonomic methods relevant to the genus Acinetobacter. Based on sequence analysis of the concatenated partial sequences (2976 bp) of seven housekeeping genes, the 16 strains formed a tight and well-supported cluster (intracluster sequence identity of ≥98.4 %) that was clearly separated from the other members of the ACB complex (≤94.7 %). The species status of the group was supported by average nucleotide identity values of ≤91.7 % between the whole genome sequence of representative strain NIPH 973(T) (NCBI accession no. APOO00000000) and those of the other species. In addition, whole-cell matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) MS analyses indicated the distinctness of the group at the protein level. Metabolic and physiological tests revealed several typical features of the group, although they did not allow its reliable differentiation from the other members of the ACB complex. We conclude that the 16 strains represent a distinct novel species, for which we propose the name Acinetobacter seifertii sp. nov. The type strain is NIPH 973(T) ( = CIP 110471(T) = CCUG 34785(T) = CCM 8535(T)).
- MeSH
- Acinetobacter klasifikace genetika izolace a purifikace MeSH
- bakteriální geny MeSH
- DNA bakterií genetika MeSH
- fylogeneze * MeSH
- genotyp MeSH
- infekce bakteriemi rodu Acinetobacter mikrobiologie MeSH
- lidé MeSH
- molekulární sekvence - údaje MeSH
- multilokusová sekvenční typizace MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice MeSH
- techniky typizace bakterií MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
We aimed to define the taxonomic status of 16 strains which were phenetically congruent with Acinetobacter DNA group 15 described by Tjernberg & Ursing in 1989. The strains were isolated from a variety of human and animal specimens in geographically distant places over the last three decades. Taxonomic analysis was based on an Acinetobacter-targeted, genus-wide approach that included the comparative sequence analysis of housekeeping, protein-coding genes, whole-cell profiling based on matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), an array of in-house physiological and metabolic tests, and whole-genome comparative analysis. Based on analyses of the rpoB and gyrB genes, the 16 strains formed respective, strongly supported clusters clearly separated from the other species of the genus Acinetobacter. The distinctness of the group at the species level was indicated by average nucleotide identity values of ≤82 % between the whole genome sequences of two of the 16 strains (NIPH 2171(T) and NIPH 899) and those of the known species. In addition, the coherence of the group was also supported by MALDI-TOF MS. All 16 strains were non-haemolytic and non-gelatinase-producing, grown at 41 °C and utilized a rather limited number of carbon sources. Virtually every strain displayed a unique combination of metabolic and physiological features. We conclude that the 16 strains represent a distinct species of the genus Acinetobacter, for which the name Acinetobacter variabilis sp. nov. is proposed to reflect its marked phenotypic heterogeneity. The type strain is NIPH 2171(T) ( = CIP 110486(T) = CCUG 26390(T) = CCM 8555(T)).
- MeSH
- Acinetobacter klasifikace genetika izolace a purifikace MeSH
- bakteriální geny MeSH
- DNA bakterií genetika MeSH
- fylogeneze * MeSH
- hybridizace nukleových kyselin MeSH
- lidé MeSH
- molekulární sekvence - údaje MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice MeSH
- techniky typizace bakterií MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Research Support, N.I.H., Extramural MeSH
Bacterial genomics has greatly expanded our understanding of microdiversification patterns within a species, but analyses at higher taxonomical levels are necessary to understand and predict the independent rise of pathogens in a genus. We have sampled, sequenced, and assessed the diversity of genomes of validly named and tentative species of the Acinetobacter genus, a clade including major nosocomial pathogens and biotechnologically important species. We inferred a robust global phylogeny and delimited several new putative species. The genus is very ancient and extremely diverse: Genomes of highly divergent species share more orthologs than certain strains within a species. We systematically characterized elements and mechanisms driving genome diversification, such as conjugative elements, insertion sequences, and natural transformation. We found many error-prone polymerases that may play a role in resistance to toxins, antibiotics, and in the generation of genetic variation. Surprisingly, temperate phages, poorly studied in Acinetobacter, were found to account for a significant fraction of most genomes. Accordingly, many genomes encode clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems with some of the largest CRISPR-arrays found so far in bacteria. Integrons are strongly overrepresented in Acinetobacter baumannii, which correlates with its frequent resistance to antibiotics. Our data suggest that A. baumannii arose from an ancient population bottleneck followed by population expansion under strong purifying selection. The outstanding diversification of the species occurred largely by horizontal transfer, including some allelic recombination, at specific hotspots preferentially located close to the replication terminus. Our work sets a quantitative basis to understand the diversification of Acinetobacter into emerging resistant and versatile pathogens.
- MeSH
- Acinetobacter baumannii * fyziologie izolace a purifikace účinky léků MeSH
- beta-laktamasy genetika sekrece MeSH
- beta-laktamová rezistence genetika účinky léků MeSH
- infekce spojené se zdravotní péčí * farmakoterapie genetika mikrobiologie MeSH
- mnohočetná bakteriální léková rezistence * genetika MeSH
- sulbaktam * farmakologie terapeutické užití MeSH
We investigated the taxonomic status of a phenetically unique group of 25 Acinetobacter strains which were isolated from multiple soil and water samples collected in natural ecosystems in the Czech Republic. Based on the comparative sequence analyses of the rpoB, gyrB, and 16S rRNA genes, the strains formed a coherent and well separated branch within the genus Acinetobacter. The genomic uniqueness of the group at the species level was supported by the low average nucleotide identity values (≤77.37%) between the whole genome sequences of strain ANC 3994(T) (NCBI accession no. APOH00000000) and the representatives of the known Acinetobacter species. Moreover, all 25 strains created a tight cluster clearly separated from all hitherto described species based on whole-cell protein profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and shared a unique combination of metabolic and physiological properties. The capacity to assimilate l-histidine and the inability to grow at 35°C differentiated them from their phenotypically closest neighbor, Acinetobacter johnsonii. We conclude that the 25 strains represent a novel Acinetobacter species, for which the name Acinetobacter bohemicus sp. nov. is proposed. The type strain of A. bohemicus is ANC 3994(T) (=CIP 110496(T)=CCUG 63842(T)=CCM 8462(T)).
- MeSH
- Acinetobacter chemie klasifikace genetika izolace a purifikace MeSH
- DNA bakterií chemie genetika MeSH
- DNA gyráza genetika MeSH
- DNA řízené RNA-polymerasy genetika MeSH
- ekosystém MeSH
- fylogeneze MeSH
- histidin metabolismus MeSH
- mikrobiologie vody * MeSH
- molekulární sekvence - údaje MeSH
- půdní mikrobiologie * MeSH
- ribozomální DNA chemie genetika MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- shluková analýza MeSH
- spektrometrie hmotnostní - ionizace laserem za účasti matrice MeSH
- techniky typizace bakterií MeSH
- teplota MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
The amikacin resistance gene aphA6 was first detected in the nosocomial pathogen Acinetobacter baumannii and subsequently in other genera. Analysis of 133 whole-genome sequences covering the taxonomic diversity of Acinetobacter spp. detected aphA6 in the chromosome of 2 isolates of A. guillouiae, which is an environmental species, 1 of 8 A. parvus isolates, and 5 of 34 A. baumannii isolates. The gene was also present in 29 out of 36 A. guillouiae isolates screened by PCR, indicating that it is ancestral to this species. The Pnative promoter for aphA6 in A. guillouiae and A. parvus was replaced in A. baumannii by PaphA6, which was generated by use of the insertion sequence ISAba125, which brought a -35 sequence. Study of promoter strength in Escherichia coli and A. baumannii indicated that PaphA6 was four times more potent than Pnative. There was a good correlation between aminoglycoside MICs and aphA6 transcription in A. guillouiae isolates that remained susceptible to amikacin. The marked topology differences of the phylogenetic trees of aphA6 and of the hosts strongly support its recent direct transfer within Acinetobacter spp. and also to evolutionarily remote bacterial genera. Concomitant expression of aphA6 must have occurred because, contrary to the donors, it can confer resistance to the new hosts. Mobilization and expression of aphA6 via composite transposons and the upstream IS-generating hybrid PaphA6, followed by conjugation, seems the most plausible mechanism. This is in agreement with the observation that, in the recipients, aphA6 is carried by conjugative plasmids and flanked by IS that are common in Acinetobacter spp. Our data indicate that resistance genes can also be found in susceptible environmental bacteria. Importance: We speculated that the aphA6 gene for an enzyme that confers resistance to amikacin, the most active aminoglycoside for the treatment of nosocomial infections due to Acinetobacter spp., originated in this genus before disseminating to phylogenetically distant genera pathogenic for humans. Using a combination of whole-genome sequencing of a collection of Acinetobacter spp. covering the breadth of the known taxonomic diversity of the genus, gene cloning, detailed promoter analysis, study of heterologous gene expression, and comparative analysis of the phylogenetic trees of aphA6 and of the bacterial hosts, we found that aphA6 originated in Acinetobacter guillouiae, an amikacin-susceptible environmental species. The gene conferred, upon mobilization, high-level resistance to the new hosts. This work stresses that nonpathogenic bacteria can act as reservoirs of resistance determinants, and it provides an example of the use of a genomic library to study the origin and dissemination of an antibiotic resistance gene to human pathogens.
- MeSH
- Acinetobacter účinky léků enzymologie genetika izolace a purifikace MeSH
- aminoglykosidy farmakologie MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence MeSH
- Escherichia coli enzymologie genetika MeSH
- fylogeneze MeSH
- kanamycinkinasa genetika MeSH
- konjugace genetická MeSH
- mikrobiální testy citlivosti MeSH
- mikrobiologie životního prostředí MeSH
- molekulární evoluce MeSH
- molekulární sekvence - údaje MeSH
- přenos genů horizontální MeSH
- promotorové oblasti (genetika) MeSH
- rozptýlené repetitivní sekvence MeSH
- sekvence aminokyselin MeSH
- sekvence nukleotidů MeSH
- sekvenční homologie MeSH
- shluková analýza MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
We previously reported the presence of an OXA-23 carbapenemase in an undescribed species of the genus Acinetobacter isolated from horse dung at the Faculty of Veterinary Medicine, Ghent University, Belgium. Here we include six strains to corroborate the delineation of this taxon by phenotypic characterization, DNA-DNA hybridization, 16S rRNA gene and rpoB sequence analysis, % G+C determination, MALDI-TOF MS and fatty acid analysis. The nearly complete 16S rRNA gene sequence of strain UG 60467(T) showed the highest similarities with those of the type strains of Acinetobacter bouvetii (98.4 %), Acinetobacter haemolyticus (97.7 %), and Acinetobacter schindleri (97.2 %). The partial rpoB sequence of strain UG 60467(T) showed the highest similarities with 'Acinetobacter bohemicus' ANC 3994 (88.6 %), A. bouvetii NIPH 2281 (88.6 %) and A. schindleri CIP 107287T (87.3 %). Whole-cell MALDI-TOF MS analyses supported the distinctness of the group at the protein level. The predominant fatty acids of strain UG 60467(T) were C12 : 0 3-OH, C12 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). Strains UG 60467(T) and UG 60716 showed a DNA-DNA relatedness of 84 % with each other and a DNA-DNA relatedness with A. schindleri LMG 19576(T) of 17 % and 20 %, respectively. The DNA G+C content of strain UG 60467(T) was 39.6 mol%. The name Acinetobacter gandensis sp. nov. is proposed for the novel taxon. The type strain is UG 60467(T) ( = ANC 4275(T) = LMG 27960(T) = DSM 28097(T)).
- MeSH
- Acinetobacter klasifikace genetika izolace a purifikace MeSH
- bakteriální geny MeSH
- DNA bakterií genetika MeSH
- feces mikrobiologie MeSH
- fylogeneze * MeSH
- hybridizace nukleových kyselin MeSH
- koně mikrobiologie MeSH
- mastné kyseliny chemie MeSH
- molekulární sekvence - údaje MeSH
- RNA ribozomální 16S genetika MeSH
- sekvenční analýza DNA MeSH
- skot mikrobiologie MeSH
- techniky typizace bakterií MeSH
- zastoupení bazí MeSH
- zvířata MeSH
- Check Tag
- skot mikrobiologie MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Belgie MeSH
