Open Access

Erratum to: Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance

  • Ana Maldonado-Contreras1, 2,
  • Shrinivasrao P Mane3,
  • Xue-Song Zhang4,
  • Luis Pericchi5,
  • Teresa Alarcón6,
  • Monica Contreras7,
  • Bodo Linz8,
  • Martin J Blaser4, 9 and
  • María Gloria Domínguez-Bello1, 4Email author
Contributed equally
BMC Microbiology201414:122

DOI: 10.1186/1471-2180-14-122

Received: 12 March 2014

Accepted: 13 March 2014

Published: 12 May 2014

The original article was published in BMC Microbiology 2013 13:211

Correction

In this published article [1], a couple of typos in Table 2 were found:

  • The restriction enzymes Hy17VII and the Hpy44II should be Hpy178II and HpyF44II instead.

  • The cognate restriction site for Hpy188I, Hpy188III and HpyF2I should be TCNGA, TCNNGA, and CTRYAG, respectively.

  • The subtitle ‘Mean ± SD the frequency’ should by followed by ‘/1,000 bp’ instead of ‘/1.00 bp’

  • The footnotes were misleading and are now corrected.

In addition, we apologize for the omission of following source that it should be included on the methods section as a reference:

Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucl. Acids Res. 38: D234D236.
Table 2

Mean of the observed and expected combined values of the cognate recognition sites in H. pylori whole genome sequences and MLS for hspAmerind and hpEurope strains

RMS

Mean ± SD frequency/1,000 bp

O/E ratiob

Endonuclease/ Methylase

Cognate recognition sitea

Observed

Expected

Observed

Expected

MLS (N = 73)

WGS (N = 6)

Hpy166III

CCTC

2.7 + 0.41

5.49 + 0.07

2.93 + 0.02

4.50 + 0.03

0.50 c

0.65

Hpy178VI

GGATG

1.48 + 0.23

1.59 + 0.03

0.81 + 0.00

1.37 + 0.01

0.93

0.59

Hpy178VII

GGCC

1.24 + 0.31

1.96 + 0.05

0.98 + 0.02

1.43 + 0.02

0.63

0.68

Hpy188I

TCNGA

1.02 + 0.21

3.70 + 0.03

0.81 + 0.02

3.53 + 0.01

0.28

0.23

Hpy188III

TCNNGA

1.11 + 0.22

3.70 + 0.04

1.19 + 0.02

3.53 + 0.01

0.30

0.34

Hpy8I

GTNNAC

0.40 + 0.35

3.70 + 0.03

0.22 + 0.01

3.53 + 0.01

0.11

0.06

Hpy8II

GTSAC

0.00 + 0.00

1.56 + 0.02

0.05 + 0.00

1.37 + 0.01

0.00

0.04

Hpy8III

GWGCWC

0.07+ 0.12

0.66 + 0.01

0.19 + 0.01

0.54 + 0.00

0.10

0.36

Hpy99I

CGWCG

0.28 + 0.06

1.13 + 0.02

0.15 + 0.01

0.88 + 0.01

0.25

0.17

Hpy99III

GCGC

4.62 + 0.64

1.96 + 0.05

3.73 + 0.11

1.43 + 0.02

2.36

2.60

Hpy99IV

CCNNGG

1.62 + 0.26

1.96 + 0.05

0.70 + 0.01

1.43 + 0.03

0.83

0.49

Hpy99VIP

GATC

5.48 + 0.44

3.70 + 0.03

3.19 + 0.04

3.53 + 0.01

1.48

0.90

Hpy99XIIP

GTAC

0.37 + 0.20

3.70 + 0.04

0.07 + 0.00

3.53 + 0.01

0.10

0.02

HpyAV

CCTTC (6/5)

0.58 + 0.12

1.58 + 0.02

0.80 + 0.02

1.37 + 0.01

0.37

0.58

HpyC1I

CCATC(4/5)

1.94 + 0.26

1.60 + 0.02

1.39 + 0.01

1.37 + 0.01

1.22

1.01

HpyCH4II

CTNAG

0.60 + 0.28

3.70 + 0.03

1.84 + 0.04

3.53 + 0.01

0.16

0.52

HpyCH4III

ACNGT

0.89 + 0.22

3.70 + 0.04

0.34 + 0.00

3.53 + 0.01

0.24

0.10

HpyCH4IV

ACGT

0.39 + 0.22

3.70 + 0.04

0.18 + 0.01

3.53 + 0.01

0.11

0.05

HpyCH4V

TGCA

3.85 + 0.75

3.70 + 0.03

3.45 + 0.03

3.53 + 0.03

1.04

0.98

HpyCI

GATATC

0.00 + 0.03

0.31 + 0.01

0.02 + 0.00

0.33 + 0.00

0.01

0.07

HpyF10VI

GCNNNNNNNGC

2.70 + 0.35

1.96 + 0.04

2.97 + 0.09

1.43 + 0.02

1.38

2.07

HpyF14I

CGCG

2.26 + 0.46

1.96 + 0.05

1.55 + 0.05

1.43 + 0.02

1.15

1.08

HpyF2I

CTRYAG

1.16 + 0.17

0.92 + 0.01

0.37 + 0.01

0.88 + 0.00

1.26

0.42

HpyF36IV

GDGCHC

0.20 + 0.21

1.22 + 0.03

0.31 + 0.01

0.93 + 0.01

0.16

0.33

HpyF44II

GGNNCC

1.21 + 0.38

1.96 + 0.05

0.44 + 0.00

1.43 + 0.02

0.62

0.31

HpyII

GAAGA

2.29 + 0.23

2.14 + 0.03

2.87 + 0.02

2.16 + 0.00

1.07

1.33

HpyIP

CATG

4.63 + 0.25

3.70 + 0.03

4.43 + 0.04

3.53 + 0.01

1.25

1.25

HpyIV

GANTC

1.70 + 0.25

3.70 + 0.04

1.66 + 0.02

3.53 + 0.01

0.46

0.47

HpyNI

CCNGG

2.04 + 0.30

1.96 + 0.05

0.87 + 0.02

1.43 + 0.02

1.04

0.61

HpyPORF1389P

GAATTC

0.01 + 0.05

0.31 + 0.01

0.11 + 0.00

0.33 + 0.00

0.03

0.32

HpyV

TCGA

0.95 + 0.25

3.70 + 0.03

0.18 + 0.00

3.53 + 0.01

0.26

0.05

HpyVIII

CCGG

1.92 + 0.30

1.96 + 0.04

1.06 + 0.02

1.43 + 0.02

0.98

0.74

a Code of degenerate nucleotide letters: R = G or A; Y = C or T; S = G or C; W = A or T; D = not C (A or G or T); H = not G (A or C or T); N = any nucleotide.

b O/E ratio indicates the observed/expected (O/E) ratio values. O/E ratios that are significantly (pvalue <0.05) different from unity are highlighted in bold.

c Exclusively underrepresented in hp Europe MLS.

Notes

Authors’ Affiliations

(1)
Department of Biology, University of Puerto Rico
(2)
Microbiology and Physiological Systems Department, University of Massachusetts Medical School
(3)
Virginia Bioinformatics Institute, Virginia Tech
(4)
Department of Medicine, New York University Langone Medical Center
(5)
Department of Mathemati, University of Puerto Rico
(6)
Servicio de Microbiología, Hospital Universitario de la Princesa
(7)
Venezuelan Institute of Scientific Research (IVIC)
(8)
Department of Biochemistry and Molecular Biology, Pennsylvania State University
(9)
New York Harbor Veterans Affairs Medical Center

References

  1. Maldonado-Contreras A, Mane SP, Zhang XS, Pericchi L, Alarcón T, Contreras M, Linz B, Blaser MJ, Domínguez-Bello MG: Phylogeographic evidence of cognate recognition site patterns and transformation efficiency differences in H. pylori: theory of strain dominance. BMC Microbiol. 2013, 13: 211-10.1186/1471-2180-13-211.PubMed CentralView ArticlePubMedGoogle Scholar

Copyright

© Maldonado-Contreras et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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