Population Dynamics of an Acinetobacter baumannii Clonal Complex during Colonization of Patients

Wen, Huang; Wang, Ke; Liu, Yang; Tay, Martin; Lauro, Federico M.; Huang, Hong; Wu, Huayu; Liang, Hongjie; Ding, Yichen; Givskov, Michael; Chen, Yiqiang; Yang, Liang

doi:10.1128/jcm.00921-14

Cited by 30 publications

(25 citation statements)

References 37 publications

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“…Our threshold value was also in agreement with sequencing of distinct isolates from the same patient in our ICU outbreak; such isolates had a maximum difference of 1 SNP, demonstrating that A. baumannii accumulated SNPs slowly over the time frame of an intrahospital outbreak. In contrast to our results, some studies have identified greater SNP differences between A. baumannii isolates recovered at different times from the same patient (106,107). In one study (107), the authors detected SNPs via alignment to a reference genome, followed by SNP filtering based on a "probability score."…”

Section: Figcontrasting

confidence: 99%

“…In contrast to our results, some studies have identified greater SNP differences between A. baumannii isolates recovered at different times from the same patient (106,107). In one study (107), the authors detected SNPs via alignment to a reference genome, followed by SNP filtering based on a "probability score." Alignment-based methods can result in false-positive SNP calls.…”

Section: Figcontrasting

confidence: 99%

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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: Figcontrasting

confidence: 99%

Section: Figcontrasting

confidence: 99%

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

2016

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“…This is the first time that sequential outbreaks within a single hospital have been reported in which the second outbreak represents a recombinant with the original outbreak strain as a parent. Previously, several studies described that A. baumannii hospital outbreaks can be polyclonal, and a variety of recombination and horizontal gene transfer events occurred in A. baumannii strains and contributed to the genetic diversity in the microorganism, even among colonized patients (49)(50)(51)(52). Horizontal gene transfer that occurs between sampled and unsampled A. baumannii isolates may explain discrepancies between NGSbased SNV typing and PFGE typing results, as was seen here (13).…”

Section: Discussionmentioning

confidence: 78%

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

Kanamori

Parobek

Weber

et al. 2016

Antimicrob Agents Chemother

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f Next-generation sequencing (NGS) analysis has emerged as a promising molecular epidemiological method for investigating health care-associated outbreaks. Here, we used NGS to investigate a 3-year outbreak of multidrug-resistant Acinetobacter baumannii (MDRAB) at a large academic burn center. A reference genome from the index case was generated using de novo assembly of PacBio reads. Forty-six MDRAB isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and sequenced using an Illumina platform. After mapping to the index case reference genome, four samples were excluded due to low coverage, leaving 42 samples for further analysis. Multilocus sequence types (MLST) and the presence of acquired resistance genes were also determined from the sequencing data. A transmission network was inferred from genomic and epidemiological data using a Bayesian framework. Based on single-nucleotide variant (SNV) differences, this MDRAB outbreak represented three sequential outbreaks caused by distinct clones. The first and second outbreaks were caused by sequence type 2 (ST2), while the third outbreak was caused by ST79. For the second outbreak, the MLST and PFGE results were discordant. However, NGS-based SNV typing detected a recombination event and consequently enabled a more accurate phylogenetic analysis. The distribution of resistance genes varied among the three outbreaks. The first-and second-outbreak strains possessed a bla OXA-23-like group, while the thirdoutbreak strains harbored a bla OXA-40-like group. NGS-based analysis demonstrated the superior resolution of outbreak transmission networks for MDRAB and provided insight into the mechanisms of strain diversification between sequential outbreaks through recombination.H ealth care-associated infections (HAI) are a substantial cause of morbidity and mortality in acute-care hospitals (1). Acinetobacter baumannii is an important opportunistic pathogen causing HAI (2) and has become one of the most common colonizing pathogens in burn patients (3, 4). A. baumannii may cause serious outbreaks despite the implementation of rigorous infection prevention interventions and control measures, which occur most commonly in intensive care units (5-8). Furthermore, the emergence of multidrug-resistant A. baumannii (MDRAB), especially carbapenem-resistant A. baumannii (CRAB), has become a global concern (5, 9). Patients infected by multidrug-resistant Acinetobacter strains are likely to have higher mortality rates and longer lengths of hospitalization than those infected by susceptible strains (10).Pulsed-field gel electrophoresis (PFGE) has been the gold standard approach for bacterial strain typing in hospital outbreak investigations, but several disadvantages have been described, including that it is a time-consuming, labor-intensive, and technically demanding assay and that is has limited reproducibility among laboratories; also, the interpretation of the relative relatedness of strains using this method may be discordant and subjective (11-13). For these reasons, next...

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“…Microscale genome modification has been revealed through the analysis of single nucleotide polymorphisms (SNPs) between A. baumannii strains isolated from the same patient. This modification can lead the emergence of resistance and to different sequence typing by modifying a single allele [10]. However, this explanation cannot be applied to our case, because ST2 and ST25 have only two common alleles.…”

Section: Discussionmentioning

confidence: 91%

Co-occurrence of carbapenemase encoding genes in Acinetobacter baumannii, a dream or reality?

2018

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BackgroundAcinetobacter baumannii is an important opportunistic pathogen that is rapidly evolving towards multidrug resistance and is responsible for life-threatening infections. Carbapenems are commonly used to treat A. baumannii infections but the emergence of carbapenemase encoding genes, such as blaOXA-23-like, blaOXA-24-like, blaOXA-58-like, and blaNDM has been reported. Moreover, several studies have reported the co-occurrence of two distinct carbapenemases in some isolates. The aim of the present study is to demonstrate whether the phenomenon of co-occurrence of two distinct carbapenemase encoding genes in a single isolate still exists.ResultsWe studied six strains of A. baumannii including one harboring blaOXA-23-like and blaOXA-24-like genes and five with blaOXA-23-like and blaNDM genes. One colony of each strain was inoculated in sterile water and diluted ten-fold. Each dilution was cultivated on trypticase soy agar plates for 24 h at 37 °C and the isolated bacteria were analyzed. For two of the six tested strains, we identified two different populations of A. baumannii, each with a different carbapenemase, genes encoding aminoglycoside modifying enzymes, resistance phenotype, and clonal type. In addition, the two different populations had the same aspect on the agar plate.ConclusionsHere, we demonstrate that A. baumannii infections could be linked to multiple clones harboring different carbapenemase encoding genes in the same sample. In addition, we describe an easy method of verifying the presence of co-occurrence of carbapenemase in one isolate.

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Population Dynamics of an Acinetobacter baumannii Clonal Complex during Colonization of Patients

Cited by 30 publications

References 37 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

Next-Generation Sequencing and Comparative Analysis of Sequential Outbreaks Caused by Multidrug-Resistant Acinetobacter baumannii at a Large Academic Burn Center

Co-occurrence of carbapenemase encoding genes in Acinetobacter baumannii, a dream or reality?

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