Validation of partial rpoB gene sequence analysis for the identification of clinically important and emerging Acinetobacter species

Gundi, Vijay A.K.B.; Dijkshoorn, Lenie; Burignat, Sophie; Raoult, Didier; Scola, Bernard La

doi:10.1099/mic.0.026054-0

Cited by 170 publications

(128 citation statements)

References 38 publications

(53 reference statements)

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“…Although all 11 bloodstream isolates were misidentified by the phenotypic identification methods using the Vitek 2, MicroScan, and API 20 NE systems, all were correctly identified as Acinetobacter GS 13BJ/14TU by rpoB gene (zone 2) sequencing, confirming the suitability of this region for species identification, as reported previously (13,27,28). Misidentification by commercial systems may have arisen due to limitations in existing databases and the lack of nonspecialized substrates for Acinetobacter GS 13BJ/14TU species identification, as reported previously (2,(29)(30)(31).…”

Section: Discussionsupporting

confidence: 52%

Identification, Genotypic Relation, and Clinical Features of Colistin-Resistant Isolates of Acinetobacter Genomic Species 13BJ/14TU from Bloodstreams of Patients in a University Hospital

Lee¹,

Shin²,

Park³

et al. 2014

J Clin Microbiol

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Colistin resistance remains rare among clinical isolates of Acinetobacter species. We noted the emergence of colistin-resistant bloodstream isolates of the Acinetobacter genomic species (GS) 13BJ/14TU from patients at a university hospital between 2003 and 2011. We report here, for the first time, the microbiological and molecular characteristics of these isolates, with clinical features of Acinetobacter GS 13BJ/14TU bacteremia. All 11 available patient isolates were correctly identified as Acinetobacter GS 13BJ/14TU using partial rpoB gene sequencing but were misidentified using the phenotypic methods Vitek 2 (mostly as Acinetobacter baumannii), MicroScan (mostly as A. baumannii/Acinetobacter haemolyticus), and the API 20 NE system (all as A. haemolyticus). Most isolates were susceptible to commonly used antibiotics, including carbapenems, but all were resistant to colistin, for which it is unknown whether the resistance is acquired or intrinsic. However, the fact that none of the patients had a history of colistin therapy strongly suggests that Acinetobacter GS 13BJ/14TU is innately resistant to colistin. The phylogenetic tree of multilocus sequence typing (MLST) showed that all 11 isolates formed a separate cluster from other Acinetobacter species and yielded five sequence types. However, pulsed-field gel electrophoresis (PFGE) revealed 11 distinct patterns, suggesting that the bacteremia had occurred sporadically. Four patients showed persistent bacteremia (6 to 17 days), and all 11 patients had excellent outcomes with cleared bacteremia, suggesting that patients with Acinetobacter GS 13BJ/14TU-associated bacteremia show a favorable outcome. These results emphasize the importance of precise species identification, especially regarding colistin resistance in Acinetobacter species. In addition, MLST offers another approach to the identification of Acinetobacter GS 13BJ/ 14TU, whereas PFGE is useful for genotyping for this species.

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Section: Discussionsupporting

confidence: 52%

Identification, Genotypic Relation, and Clinical Features of Colistin-Resistant Isolates of Acinetobacter Genomic Species 13BJ/14TU from Bloodstreams of Patients in a University Hospital

Lee¹,

Shin²,

Park³

et al. 2014

J Clin Microbiol

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“…Rodents are considered to be important reservoirs of bartonellae, as they host a great variety of Bartonella species and strains (Birtles et al, 2001;Kosoy et al, 2012). To date, 417 Bartonella species have been isolated from wild rodents (Gundi et al, 2004(Gundi et al, , 2009Kosoy, 2010;Sato et al, 2012). Moreover, several studies have reported a wider diversity of Bartonella genotypes that surpass the current classification of Bartonella species (Pretorius et al, 2004;Inoue et al, 2009;Gundi et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

The effect of ecological and temporal factors on the composition of Bartonella infection in rodents and their fleas

et al. 2014

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The composition of Bartonella infection was explored in wild Gerbillus andersoni rodents and their Synosternus cleopatrae fleas. Rodent blood samples and fleas were collected in two periods (two different seasons; 4 months apart) from juveniles and adult hosts, and their bartonellae lineages were identified by a 454-pyrosequencing analysis targeting a specific Bartonella citrate synthase gene (gltA) fragment. The rate of Bartonella spp. co-infection was estimated and the assemblage and distribution of bartonellae lineages across the samples with respect to ecological and phylogenetic distance similarities were analyzed. Moreover, environmental factors that could explain potential differences between samples were investigated. Out of the 91 bartonellae-positive samples, 89% were found to be co-infected with more than two phylogenetically distant Bartonella genotypes and additional closely related (but distinguishable) variants. These bartonellae lineages were distributed in a non-random manner, and a negative interaction between lineages was discovered. Interestingly, the overall composition of those infections greatly varied among samples. This variability was partially explained by factors, such as type of sample (blood versus fleas), flea sex and period of collection. This investigation sheds light on the patterns of Bartonella infection and the organization of Bartonella lineages in fleas and rodents in nature.

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“…Unfortunately, commercially available platforms and phenotypic identification methods used in clinical microbiology laboratories are unable to differentiate related species within the ACB complex, and, as such, infections are often reported clinically as "A. baumannii complex" or simply grouped together as "A. baumannii" (14). Molecular techniques, such as rpoB gene sequence analysis, are necessary to accurately identify ACB complex isolates to the species level (15,16).…”

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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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Validation of partial rpoB gene sequence analysis for the identification of clinically important and emerging Acinetobacter species

Cited by 170 publications

References 38 publications

Identification, Genotypic Relation, and Clinical Features of Colistin-Resistant Isolates of Acinetobacter Genomic Species 13BJ/14TU from Bloodstreams of Patients in a University Hospital

Identification, Genotypic Relation, and Clinical Features of Colistin-Resistant Isolates of Acinetobacter Genomic Species 13BJ/14TU from Bloodstreams of Patients in a University Hospital

The effect of ecological and temporal factors on the composition of Bartonella infection in rodents and their fleas

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

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