Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity.

Abstract:

BACKGROUND:Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study examines the genomic content of three A. baumannii strains isolated from distinct body sites. Isolates from blood, peri-anal, and wound sources were examined in an attempt to identify genetic features that could be correlated to each isolation source. RESULTS:Pulsed-field gel electrophoresis, multi-locus sequence typing and antibiotic resistance profiles demonstrated genotypic and phenotypic variation. Each isolate was sequenced to high-quality draft status, which allowed for comparative genomic analyses with existing A. baumannii genomes. A high resolution, whole genome alignment method detailed the phylogenetic relationships of sequenced A. baumannii and found no correlation between phylogeny and body site of isolation. This method identified genomic regions unique to both those isolates found on the surface of the skin or in wounds, termed colonization isolates, and those identified from body fluids, termed invasive isolates; these regions may play a role in the pathogenesis and spread of this important pathogen. A PCR-based screen of 74 A. baumanii isolates demonstrated that these unique genes are not exclusive to either phenotype or isolation source; however, a conserved genomic region exclusive to all sequenced A. baumannii was identified and verified. CONCLUSIONS:The results of the comparative genome analysis and PCR assay show that A. baumannii is a diverse and genomically variable pathogen that appears to have the potential to cause a range of human disease regardless of the isolation source.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Sahl JW,Johnson JK,Harris AD,Phillippy AM,Hsiao WW,Thom KA,Rasko DA

doi

10.1186/1471-2164-12-291

subject

Has Abstract

pub_date

2011-06-04 00:00:00

pages

291

issn

1471-2164

pii

1471-2164-12-291

journal_volume

12

pub_type

杂志文章
  • Functional genomic analysis of constitutive and inducible defense responses to Fusarium verticillioides infection in maize genotypes with contrasting ear rot resistance.

    abstract:BACKGROUND:Fusarium verticillioides causes ear rot in maize (Zea mays L.) and accumulation of mycotoxins, that affect human and animal health. Currently, chemical and agronomic measures to control Fusarium ear rot are not very effective and selection of more resistant genotypes is a desirable strategy to reduce contami...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-710

    authors: Lanubile A,Ferrarini A,Maschietto V,Delledonne M,Marocco A,Bellin D

    更新日期:2014-08-25 00:00:00

  • Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

    abstract:BACKGROUND:Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs) of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen f...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-214

    authors: Docherty SJ,Butcher LM,Schalkwyk LC,Plomin R

    更新日期:2007-07-04 00:00:00

  • Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2.

    abstract:BACKGROUND:Circular chromosome conformation capture (4C) has provided important insights into three dimensional (3D) genome organization and its critical impact on the regulation of gene expression. We developed a new quantitative framework based on polymer physics for the analysis of paired-end sequencing 4C (PE-4Cseq...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2137-5

    authors: Zepeda-Mendoza CJ,Mukhopadhyay S,Wong ES,Harder N,Splinter E,de Wit E,Eckersley-Maslin MA,Ried T,Eils R,Rohr K,Mills A,de Laat W,Flicek P,Sengupta AM,Spector DL

    更新日期:2015-11-21 00:00:00

  • Major aging-associated RNA expressions change at two distinct age-positions.

    abstract:BACKGROUND:Genome-wide expression profiles are altered during biological aging and can describe molecular regulation of tissue degeneration. Age-regulated mRNA expression trends from cross-sectional studies could describe how aging progresses. We developed a novel statistical methodology to identify age-regulated expre...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-132

    authors: Gheorghe M,Snoeck M,Emmerich M,Bäck T,Goeman JJ,Raz V

    更新日期:2014-02-14 00:00:00

  • Mining microsatellite markers from public expressed sequence tags databases for the study of threatened plants.

    abstract:BACKGROUND:Simple Sequence Repeats (SSRs) are widely used in population genetic studies but their classical development is costly and time-consuming. The ever-increasing available DNA datasets generated by high-throughput techniques offer an inexpensive alternative for SSRs discovery. Expressed Sequence Tags (ESTs) hav...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2031-1

    authors: Lopez L,Barreiro R,Fischer M,Koch MA

    更新日期:2015-10-13 00:00:00

  • Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea.

    abstract:BACKGROUND:While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes. Here, we performed a comparative analysis of the predicted (proved in part) orc/cdc6-associated replication origins in 15 completely sequenced haloarchaeal genomes to investigate t...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-478

    authors: Wu Z,Liu H,Liu J,Liu X,Xiang H

    更新日期:2012-09-14 00:00:00

  • Functional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.

    abstract:BACKGROUND:Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of i...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2474-z

    authors: Cho YB,Lee EJ,Cho S,Kim TY,Park JH,Cho BK

    更新日期:2016-02-29 00:00:00

  • Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells.

    abstract:BACKGROUND:Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-757

    authors: Rengaraj D,Lee SI,Park TS,Lee HJ,Kim YM,Sohn YA,Jung M,Noh SJ,Jung H,Han JY

    更新日期:2014-09-04 00:00:00

  • Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.

    abstract:BACKGROUND:The freshwater planarian Schmidtea mediterranea is recognised as a valuable model for research into adult stem cells and regeneration. With the advent of the high-throughput sequencing technologies, it has become feasible to undertake detailed transcriptional analysis of its unique stem cell population, the ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1533-1

    authors: Rodríguez-Esteban G,González-Sastre A,Rojo-Laguna JI,Saló E,Abril JF

    更新日期:2015-05-08 00:00:00

  • The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.

    abstract:BACKGROUND:Large difference in cerebrum size exist between avian species and populations of the same species and is believed to reflect differences in processing power, i.e. in the speed and efficiency of processing information in this brain region. During domestication chickens developed a larger cerebrum compared to ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06908-0

    authors: Höglund A,Strempfl K,Fogelholm J,Wright D,Henriksen R

    更新日期:2020-07-29 00:00:00

  • Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality.

    abstract:BACKGROUND:Infectious salmon anemia virus (ISAV) causes a multisystemic disease responsible for severe losses in salmon aquaculture. Better understanding of factors that explain variations in resistance between individuals and families is essential for development of strategies for disease control. To approach this, we...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-179

    authors: Jørgensen SM,Afanasyev S,Krasnov A

    更新日期:2008-04-18 00:00:00

  • LinkImputeR: user-guided genotype calling and imputation for non-model organisms.

    abstract:BACKGROUND:Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3873-5

    authors: Money D,Migicovsky Z,Gardner K,Myles S

    更新日期:2017-07-10 00:00:00

  • Whole exome sequencing (WES) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue in gastrointestinal stromal tumors (GIST).

    abstract:BACKGROUND:Next generation sequencing (NGS) technology has been rapidly introduced into basic and translational research in oncology, but the reduced availability of fresh frozen (FF) tumor tissues and the poor quality of DNA extracted from formalin-fixed, paraffin-embedded (FFPE) has significantly impaired this proces...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1982-6

    authors: Astolfi A,Urbini M,Indio V,Nannini M,Genovese CG,Santini D,Saponara M,Mandrioli A,Ercolani G,Brandi G,Biasco G,Pantaleo MA

    更新日期:2015-11-03 00:00:00

  • Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

    abstract:BACKGROUND:New and improved antimicrobial countermeasures are urgently needed to counteract increased resistance to existing antimicrobial treatments and to combat currently untreatable or new emerging infectious diseases. We demonstrate that computational comparative genomics, together with experimental screening, can...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-501

    authors: Stubben CJ,Duffield ML,Cooper IA,Ford DC,Gans JD,Karlyshev AV,Lingard B,Oyston PC,de Rochefort A,Song J,Wren BW,Titball RW,Wolinsky M

    更新日期:2009-10-29 00:00:00

  • Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa.

    abstract:BACKGROUND:The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will fac...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-594

    authors: Xu J,Qian X,Wang X,Li R,Cheng X,Yang Y,Fu J,Zhang S,King GJ,Wu J,Liu K

    更新日期:2010-10-22 00:00:00

  • Semantic integration of gene expression analysis tools and data sources using software connectors.

    abstract:BACKGROUND:The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists exe...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-S6-S2

    authors: Miyazaki FA,Guardia GD,Vêncio RZ,de Farias CR

    更新日期:2013-10-25 00:00:00

  • A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection.

    abstract:BACKGROUND:Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS:To overcome these limitations, we developed a novel RoV capture and genome sequencing method combin...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3714-6

    authors: Dung TTN,Duy PT,Sessions OM,Sangumathi UK,Phat VV,Tam PTT,To NTN,Phuc TM,Hong Chau TT,Chau NNM,Minh NN,Thwaites GE,Rabaa MA,Baker S

    更新日期:2017-04-24 00:00:00

  • The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.

    abstract:BACKGROUND:There are no commercially available vaccines against human protozoan parasitic diseases, despite the success of vaccination-induced long-term protection against infectious diseases. East Coast fever, caused by the protist Theileria parva, kills one million cattle each year in sub-Saharan Africa, and contribu...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-1910-9

    authors: Norling M,Bishop RP,Pelle R,Qi W,Henson S,Drábek EF,Tretina K,Odongo D,Mwaura S,Njoroge T,Bongcam-Rudloff E,Daubenberger CA,Silva JC

    更新日期:2015-09-24 00:00:00

  • Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity.

    abstract:BACKGROUND:The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most importa...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-415

    authors: Ashraf N,Ghai D,Barman P,Basu S,Gangisetty N,Mandal MK,Chakraborty N,Datta A,Chakraborty S

    更新日期:2009-09-05 00:00:00

  • Flashy flagella: flagellin modification is relatively common and highly versatile among the Enterobacteriaceae.

    abstract:BACKGROUND:Post-translational glycosylation of the flagellin protein is relatively common among Gram-negative bacteria, and has been linked to several phenotypes, including flagellar biosynthesis and motility, biofilm formation, host immune evasion and manipulation and virulence. However to date, despite extensive phys...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-016-2735-x

    authors: De Maayer P,Cowan DA

    更新日期:2016-05-20 00:00:00

  • Evolutionary origin of regulatory regions of retrogenes in Drosophila.

    abstract:BACKGROUND:Retrogenes are processed copies of other genes. This duplication mechanism produces a copy of the parental gene that should not contain introns, and usually does not contain cis-regulatory regions. Here, we computationally address the evolutionary origin of promoter and other cis-regulatory regions in retrog...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-241

    authors: Bai Y,Casola C,Betrán E

    更新日期:2008-05-22 00:00:00

  • Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences.

    abstract:BACKGROUND:Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. Often, crop improvement and management activities are segregated by crop type, thus preserving unique genome diversity and organization. Full interfertility is typically retained in crosses betwe...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6451-1

    authors: Galewski P,McGrath JM

    更新日期:2020-03-02 00:00:00

  • Bidirectional promoters exhibit characteristic chromatin modification signature associated with transcription elongation in both sense and antisense directions.

    abstract:BACKGROUND:In contrast to unidirectional promoters wherein antisense transcription results in short transcripts which are rapidly degraded, bidirectional promoters produce mature transcripts in both sense and antisense orientation. To understand the molecular mechanism of how productive bidirectional transcription is r...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4697-7

    authors: Jangid RK,Kelkar A,Muley VY,Galande S

    更新日期:2018-05-02 00:00:00

  • Identification of functional regulatory elements in the human genome using pooled CRISPR screens.

    abstract:BACKGROUND:Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function. However, protein-coding genes comprise < 2% of the se...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-6497-0

    authors: Borys SM,Younger ST

    更新日期:2020-01-31 00:00:00

  • Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing.

    abstract:BACKGROUND:Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.)...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-211

    authors: Straub SC,Fishbein M,Livshultz T,Foster Z,Parks M,Weitemier K,Cronn RC,Liston A

    更新日期:2011-05-04 00:00:00

  • Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands.

    abstract:BACKGROUND:Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1(CA) oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecula...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-182

    authors: Ma L,Ma Q,Li X,Cheng L,Li K,Li S

    更新日期:2014-03-09 00:00:00

  • Transcriptome analysis of the central nervous system of the mollusc Lymnaea stagnalis.

    abstract:BACKGROUND:The freshwater snail Lymnaea stagnalis (L. stagnalis) has served as a successful model for studies in the field of Neuroscience. However, a serious drawback in the molecular analysis of the nervous system of L. stagnalis has been the lack of large-scale genomic or neuronal transcriptome information, thereby ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-10-451

    authors: Feng ZP,Zhang Z,van Kesteren RE,Straub VA,van Nierop P,Jin K,Nejatbakhsh N,Goldberg JI,Spencer GE,Yeoman MS,Wildering W,Coorssen JR,Croll RP,Buck LT,Syed NI,Smit AB

    更新日期:2009-09-23 00:00:00

  • QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies.

    abstract:BACKGROUND:The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyse...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1004

    authors: Saatchi M,Beever JE,Decker JE,Faulkner DB,Freetly HC,Hansen SL,Yampara-Iquise H,Johnson KA,Kachman SD,Kerley MS,Kim J,Loy DD,Marques E,Neibergs HL,Pollak EJ,Schnabel RD,Seabury CM,Shike DW,Snelling WM,Spangler ML,

    更新日期:2014-11-20 00:00:00

  • Thrifty metabolic programming in rats is induced by both maternal undernutrition and postnatal leptin treatment, but masked in the presence of both: implications for models of developmental programming.

    abstract:BACKGROUND:Maternal undernutrition leads to an increased risk of metabolic disorders in offspring including obesity and insulin resistance, thought to be due to a programmed thrifty phenotype which is inappropriate for a subsequent richer nutritional environment. In a rat model, both male and female offspring of undern...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-49

    authors: Ellis PJ,Morris TJ,Skinner BM,Sargent CA,Vickers MH,Gluckman PD,Gilmour S,Affara NA

    更新日期:2014-01-21 00:00:00

  • Antennal transcriptome analysis of the chemosensory gene families in the tree killing bark beetles, Ips typographus and Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae).

    abstract:BACKGROUND:The European spruce bark beetle, Ips typographus, and the North American mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae), are severe pests of coniferous forests. Both bark beetle species utilize aggregation pheromones to coordinate mass-attacks on host trees, while odora...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-198

    authors: Andersson MN,Grosse-Wilde E,Keeling CI,Bengtsson JM,Yuen MM,Li M,Hillbur Y,Bohlmann J,Hansson BS,Schlyter F

    更新日期:2013-03-21 00:00:00