Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core

Mann, Rachel; Smits, Theo H. M.; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E.; Plummer, Kim M.; Beer, Steven V.; Luck, Jo; Duffy, Brion; Rodoni, Brendan

doi:10.1371/journal.pone.0055644

Cited by 80 publications

(105 citation statements)

References 67 publications

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“…On diagnosis, this result shows that only the primers as pEA71, EaIsc are reliable. In addition, other strain of fire blight reported absence of plasmid pEA29 [24], [25].…”

Section: Discussionmentioning

confidence: 99%

Characterizationof Moroccan Population of ErwiniaAmylovora, the Causal Agent of Fire Blighton Rosacea

Ameur¹,

Ennaji²,

Cesbron³

et al. 2014

IJBBB

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“…On diagnosis, this result shows that only the primers as pEA71, EaIsc are reliable. In addition, other strain of fire blight reported absence of plasmid pEA29 [24], [25].…”

Section: Discussionmentioning

confidence: 99%

Characterizationof Moroccan Population of ErwiniaAmylovora, the Causal Agent of Fire Blighton Rosacea

Ameur¹,

Ennaji²,

Cesbron³

et al. 2014

IJBBB

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“…It displayed 98.2% nucleotide sequence identity to the corresponding region in plasmid pEA3. Plasmid pEA3 has a size of 29,585 bp and was originally identified in the plant pathogen Erwinia amylovora CFBP 2585 (GenBank accession number HF560646.1), which causes fire blight, a devastating disease that threatens a wide range of plants, including apple, pear, cotoneaster, and hawthorn shrubs and trees (17,18). Region B also harbored the genes of a type IV secretion system (T4SS) gene cluster (Fig.…”

mentioning

confidence: 99%

Characterization of a cfr -Carrying Plasmid from Porcine Escherichia coli That Closely Resembles Plasmid pEA3 from the Plant Pathogen Erwinia amylovora

Rong-ming

Sun

Wang

et al. 2016

Antimicrob Agents Chemother

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The multiresistance gene cfr was found in two porcine Escherichia coli isolates, one harboring it on the conjugative 33,885-bp plasmid pFSEC-01, the other harboring it in the chromosomal DNA. Sequence analysis of pFSEC-01 revealed that a 6,769-bp fragment containing the cfr gene bracketed by two IS26 elements was inserted into a plasmid closely related to pEA3 from the plant pathogen Erwinia amylovora, suggesting that pFSEC-01 may be transferred between different bacterial genera of both animal and plant origin. The multiresistance gene cfr confers resistance to phenicols, lincosamides, pleuromutilins, streptogramin, and oxazolidinones and decreased susceptibility to the 16-membered macrolides spiramycin and josamycin (1-3). While the cfr gene is found mainly in Gram-positive bacteria (4), it has also been detected in two species of Gram-negative bacteria, Proteus vulgaris and Escherichia coli, during recent years (5-10). Here, we report IS26-flanked cfr genes from porcine E. coli are located either on a plasmid that most likely originated from the plant pathogen Erwinia amylovora or in the chromosomal DNA.During July and August 2013, a total of 396 samples were collected from the lungs of diseased animals (pigs, n ϭ 334; chickens, n ϭ 40; ducks, n ϭ 22) at an animal diagnostic laboratory at Foshan University, Foshan City, Guangdong, China. A total of 64 E. coli isolates grew on MacConkey agar plates supplemented with 10 mg/liter florfenicol. Of these, only two isolates, FSEC-01 and FSEC-02, which were obtained from swine suffering from pneumonia and sepsis, respectively, that originated from two different pig farms were positive for the cfr gene by PCR as described previously (11, 12).In vitro susceptibility testing (13,14) showed that isolates FSEC-01 and FSEC-02 were resistant to chloramphenicol, ampicillin, tetracycline, gentamicin, and streptomycin and also had high MIC values of florfenicol (128 g/ml). Isolate FSEC-02 also exhibited resistance to amoxicillin-clavulanic acid and sulfamethoxazole. In addition to harboring the cfr gene, both isolates harbored the phenicol exporter gene floR, the ␤-lactam resistance gene bla TEM-1 , and the tetracycline resistance gene tet(A). Isolate FSEC-01 also carried the aminoglycoside resistance gene aacC2 and the ␤-lactam resistance gene bla CTX-M-65 , whereas isolate FSEC-02 also harbored the aminoglycoside resistance genes aac(3)-VI, aadA2, aacC3, strA, and strB, the sulfonamide resistance gene sul2, and the ␤-lactam resistance gene bla (Table 1). S1 nuclease pulsed-field gel electrophoresis (PFGE) and Southern blot analysis (15) showed that the cfr gene was located on an ϳ34-kb plasmid, designated pFSEC-01, in isolate FSEC-01 and in the chromosomal DNA of isolate FSEC-02 (see Fig. S1 in the supplemental material). Conjugation experiments by filter mating (15) using isolate FSEC-01 as the donor and E. coli C600 as the recipient proved to be successful. The transconjugant, designated EC-600-FS-01, which harbored only the cfr-carrying plasmid pFSEC-01, was negative fo...

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“…From the two different primer pairs tested, the primers Peant1/Peant2 and AJ75/AJ76 were much more sensitive and allowed us to detect even small amounts of DNA in the samples where it was not detected using the primers Ea71/72. This is related to the fact that these first two primer pairs are complementary to plasmid pEA29, which occurs in one to five copies per bacterial cell (Mann et al 2013;Smits et al 2010), while primers Ea71/72 are complementary to chromosomal DNA.…”

Section: Resultsmentioning

confidence: 99%

“…E. amylovora is generally considered to be a homogeneous species in terms of phenotypic and genetic features (reviewed by Puławska and Sobiczewski 2012). Recent genomic analysis confirmed that the chromosome of E. amylovora is highly conserved and displays over 99 % amino acid sequence identity among all strains tested (Mann et al 2013). On the other hand, recent application of multi-locus variable number of tandem repeats (MLVA) and clustered regularly interspaced short palindromic repeats (CRISPR) revealed some diversity within E. amylovora (Bühlmann et al 2014;Rezzonico et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Evaluation of different RNA extraction methods for high-quality total RNA and mRNA from Erwinia amylovora in planta

et al. 2016

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Obtaining a sufficient quantity of high-quality, intact RNA is the first crucial step in its study by RNA sequencing on next-generation sequencing platforms or quantitative PCR. Different RNA extraction methods or commercial kits vary in yield and in the quality and integrity of the RNA obtained, which may affect the results of downstream applications. Often, these factors depend on the organism under study and nature of the sample. Therefore, the selection of an appropriate RNA isolation method is critical. In this study, we present the results of an evaluation of three different commercial kits for the isolation of total RNA from Erwinia amylovora in apple tissue as well as the usefulness of different kinds of Deoxyribonuclease I for DNA removal and kits for rRNA depletion. To our knowledge, this is the first report on the method of isolation of high-quality E.amylovora mRNA for RNA-seq.

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Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core

Cited by 80 publications

References 67 publications

Characterizationof Moroccan Population of ErwiniaAmylovora, the Causal Agent of Fire Blighton Rosacea

Characterizationof Moroccan Population of ErwiniaAmylovora, the Causal Agent of Fire Blighton Rosacea

Characterization of a cfr -Carrying Plasmid from Porcine Escherichia coli That Closely Resembles Plasmid pEA3 from the Plant Pathogen Erwinia amylovora

Evaluation of different RNA extraction methods for high-quality total RNA and mRNA from Erwinia amylovora in planta

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