Acinetobacter soli sp. nov., isolated from forest soil

Kim, Duwoon; Baik, Keun Sik; Kim, Mi Sun; Park, Seong Chan; Kim, Seon Suk; Rhee, Moon Soo; Kwak, Young Se; Seong, Chi Nam

doi:10.1007/s12275-008-0118-y

Cited by 69 publications

(36 citation statements)

References 27 publications

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“…S1 in the supplemental material.) Because A. soli is genetically distant from the ACB complex (72,73), it was used to root the tree. Similar to prior studies, our results showed that A. nosocomialis diverges first from the A. baumannii clade, followed by A. pittii (20).…”

Section: Resultsmentioning

confidence: 99%

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

2016

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bAcinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The bandbased techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.A n important role of clinical microbiology is to identify relationships between bacterial isolates. At a broad level, phenotypic and genotypic tests are used to categorize bacterial isolates into the same or different species. Within a bacterial species, techniques are used to group isolates into clonal lineages, which are groups of closely related bacteria that share a recent common ancestor but have spread regionally or globally. At a more local level, infection control practitioners must determine whether a group of isolates constitutes a hospital outbreak by ascertaining whether the isolates have a degree of similarity consistent with a common source within the hospital. Once isolates belonging to a hospital outbreak have been identified, similarities and differences between these isolates can be exploited to generate a transmission map to aid in finding the source of the outbreak and in disrupting ongoing pathways of transmission. For some groups of bacteria, such as Acinetobacter, discernment at each level has medically important consequences and therefore must be accomplished by hospital-associated clinical microbiology laboratories.Within the Acinetobacter genus, the Acinetobacter calcoaceticusAcinetobac...

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Section: Resultsmentioning

confidence: 99%

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

2016

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“…Species identifications of the isolates were initiated by partial sequencing of the rpoB gene (zone 1) according to the method of Karah et al (3,4). PCR products were purified with a QIAquick PCR purification kit (Qiagen, Hilden, Germany), followed by DNA sequencing using an ABI BigDye Terminator v3.1 cycle sequencing kit (Applied Biosystems, Foster City, CA, USA) and an ABI3730xl analyzer (Applied Biosystems).…”

Section: Methodsmentioning

confidence: 99%

“…are almost identical to those of each other, accurate identification at the species level is difficult with routine laboratory methods. Recently, some molecular techniques have been reported for identifying isolates at the species level, such as sequencing the 16S rRNA gene, the gyrB gene, the recA gene, or the RNA polymerase ␤-subunit (rpoB) gene (4)(5)(6)(7). These molecular methods recently led to progress in the accurate identification of Acinetobacter species.…”

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confidence: 99%

High Frequency of Acinetobacter soli among Acinetobacter Isolates Causing Bacteremia at a Tertiary Hospital in Japan

et al. 2014

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bAcinetobacter baumannii is generally the most frequently isolated Acinetobacter species. Sequence analysis techniques allow reliable identification of Acinetobacter isolates at the species level. Forty-eight clinical isolates of Acinetobacter spp. were obtained from blood cultures at Tohoku University Hospital. These isolates were identified at the species level by partial sequencing of the RNA polymerase ␤-subunit (rpoB), 16S rRNA, and gyrB genes. Then further characterization was done by using the PCR for detection of OXA-type ␤-lactamase gene clusters, metallo-␤-lactamases, and carO genes. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were also performed. The most frequent isolate was Acinetobacter soli (27.1%). Six of the 13 A. soli isolates were carbapenem nonsusceptible, and all of these isolates produced IMP-1. PFGE revealed that the 13 A. soli isolates were divided into 8 clusters. This study demonstrated that A. soli accounted for a high proportion of Acinetobacter isolates causing bacteremia at a Japanese tertiary hospital. Non-A. baumannii species were identified more frequently than A. baumannii and carbapenem-nonsusceptible isolates were found among the non-A. baumannii strains. These results emphasize the importance of performing epidemiological investigations of Acinetobacter species.

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“…Acinetobacter soli was first isolated from the forest soil in Korea, 2007. Since then, the bloodstream infection outbreak caused by this species in neonatal intensive care unit (ICU) has also been reported in Korea, 2011 and the first carbapenem-resistant isolates were detected in Japan, 2012 [5][6][7]. However, carbapenemresistant and bla NDM-1 producing A. soli has not yet been reported in China.…”

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confidence: 99%

Draft Genome Sequence of a Multidrug-Resistant bla NDM-1-Producing Acinetobacter soli Isolate in China

et al. 2014

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Acinetobacter soli sp. nov., isolated from forest soil

Cited by 69 publications

References 27 publications

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

High Frequency of Acinetobacter soli among Acinetobacter Isolates Causing Bacteremia at a Tertiary Hospital in Japan

Draft Genome Sequence of a Multidrug-Resistant bla NDM-1-Producing Acinetobacter soli Isolate in China

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