D a Genome Sequences o 29 Helicobac e pylo i S ains
Isola ed om Colombia
Angela B. Muñoz,
a
Johanna S epanian,
a
Ca men Acos a,
a
Juan S. Solano-Gu ie ez,
b
Filipa F. Vale,
c
Alba A. T espalacios-Rangel
a
a
In ec ious Diseases Resea ch G oup, Mic obiology Depa men , Sciences Facul y, Pon ificia Uni e sidad Ja e iana, Bogo á, Colombia
b
AXOMICS-Sequencing Cen e , Biological Science Depa men , Science School, Uni e sidad EAFIT, Medellín, Colombia
c
Hos -Pa hogen In e ac ions Uni , Resea ch Ins i u e o Medicines (iMed-ULisboa), Faculdade de Fa mácia, Uni e sidade de Lisboa, Lisbon, Po ugal
ABSTRACT He e, we p esen he d a genome sequences o 29 Colombian Helicobac e
pylo i s ains. These s ains we e isola ed in Bogo á, Colombia, om pa ien s diagnosed
wi h ch onic gas i is. The genomic cha ac e iza ion o hese s ains will p o ide mo e in-
o ma ion on he gene ic composi ion o H. pylo i s ains om Colombia.
Helicobac e pylo i is a G am-nega i e, pa hogenic bac e ium capable o colonizing
and pe sis ing in he human s omach. The in ec ion is conside ed he mos e-
quen ch onic bac e ial in ec ion wo ldwide (1–3), eaching p e alence a es o up o
80% in Colombia (4).
This epo announces he genome sequences o 29 H. pylo i s ains isola ed
be ween 2009 and 2010 om pa ien s esiding in Bogo á, Colombia. The pa ien s who
signed in o med consen we e 48 yea s old on a e age ( ange, 18 o 79 yea s); om
he his ology esul s, 65.5% we e diagnosed wi h ch onic nona ophic gas i is and
34.5% wi h ch onic a ophic gas i is. The s ains we e eco e ed om gas ic biopsy
samples, and hose we e cul i a ed on BBL B ucella aga (Bec on, Dickinson) supple-
men ed wi h 7% ho se blood, 0.4% IsoVi alex (BD, USA), and 0.2% Den selec i e sup-
plemen (Oxoid, UK) unde mic oae ophilic condi ions (11% CO
2
) a 37°C o 4 o
7 days. The s ains we e p ese ed in 20% glyce ol and s o ed un il equi ed o DNA
ex ac ion. They we e eco e ed by cul u e e e y ime. A e ha , o al DNA was
ex ac ed using a DNeasy blood and issue ki (Qiagen, Hilden, Ge many) ollowing he
manu ac u e ’s ins uc ions. Fluo ome ic assay DNA quan ifica ion was pe o med
using a Qubi 2.0 fluo ome e and he Qubi double-s anded DNA (dsDNA) high-sensi-
i i y (HS) assay ki (Li e Technologies, Ca lsbad, CA, USA). To e i y ha he DNA
ob ained was om H. pylo i, a con en ional PCR echnique o he acA gene was ca -
ied ou . The p ime s and p o ocols p e iously desc ibed by A he on e al. (5) we e
used.
Genomic DNA was sequenced using he MiSeq pla o m (Illumina, San Diego, CA);
DNA lib a ies we e p epa ed using a Nex e a XT DNA lib a y p epa a ion ki (Illumina),
ollowed by 2 300-bp pai ed-end sequencing esul ing in 80co e age. The low-
quali y sequences we e emo ed wi h he so wa e package T immoma ic 0.39 (6).
The eads we e used o de no o genome assembly wi h SPAdes 13.3 (7). Assembly
s a is ics o analyzed s ains a e p o ided in Table 1. The sequences we e anno a ed
using he NCBI P oka yo ic Genome Au oma ic Anno a ion Pipeline (PGAAP) (8).
De aul pa ame e s we e used o all so wa e ools unless o he wise specified.
A mul ilocus sequence yping (MLST) analysis was pe o med based on se en H.
pylo i housekeeping genes (a pA,e p, pC,ppa,mu Y,yphC, and u el). The sequences
o hese genes om 741 s ains a ailable a PubMLST (h p://pubmls .o g/helicobac e /)
(9) and p e iously desc ibed by Falush e al. (10) and Linz e al. (11), plus he 29 s ains
included in his s udy, we e aligned using MAFFT 7 (12). Then, he aligned sequences
Ci a ion Muñoz AB, S epanian J, Acos a C,
Solano-Gu ie ez JS, Vale FF, T espalacios-
Rangel AA. 2021. D a genome sequences o 29
Helicobac e pylo i s ains isola ed om Colombia.
Mic obiol Resou Announc 10:e00218-21. h ps://
doi.o g/10.1128/MRA.00218-21.
Edi o Ca he ine Pu on i, Loyola Uni e si y
Chicago
Copy igh © 2021 Muñoz e al. This is an
open-access a icle dis ibu ed unde he e ms
o he C ea i e Commons A ibu ion 4.0
In e na ional license.
Add ess co espondence o Angela B. Muñoz,
[email p o ec ed], o Alba A.
T espalacios-Rangel,
[email p o ec ed].
Recei ed 28 Feb ua y 2021
Accep ed 16 Ap il 2021
Published 13 May 2021
Volume 10 Issue 19 e00218-21 m a.asm.o g 1
GENOME SEQUENCES
TABLE 1 Genome s a is ics o sequences epo ed
S ain name
GenBank accession
no.
SRA accession
no.
No. o
CDS
a
Genome
size (bp)
GC
con en (%) MLST
No. o
con igs
N
50
alue (bp)
Genome
co e age (×)
No. o
aw eads
COL 1-PUJ JAFCHS000000000 SRR13796410 1,582 1,679,429 38.8 HpEu ope 72 58,624 135 1,163,956
COL 2-PUJ JACSDV000000000 SRR13796434 1,632 1,607,581 39 HpEu ope 46 82,542 392 2,633,600
COL 5-PUJ JACSDU000000000 SRR13796433 1,667 1,624,361 39.1 HpEu ope 133 21,560 105 850,310
COL 6-PUJ JACSDT000000000 SRR13796422 1,673 1,625,175 39.1 HpEu ope 133 20,478 95 745,268
COL 8-PUJ JAFCHT000000000 SRR13796409 1,664 1,661,424 38.9 HpEu ope 43 93,756 286 2,823,146
COL 9-PUJ JAFCHU000000000 SRR13796408 1,653 1,613,788 39 HpEu ope 47 84,065 311 2,073,864
COL 10-PUJ JAFCHV000000000 SRR13796407 1,680 1,642,843 39.4 HpEu ope 58 107,835 375 2,741,078
COL 11-PUJ JAFCHW000000000 SRR13796406 1,663 1,626,191 39.4 HpEu ope 58 86,547 221 1,639,572
COL 12-PUJ JAFCHX000000000 SRR13796432 1,633 1,637,127 38.9 HpEu ope 43 96,559 368 2,773,188
COL 13-PUJ JAFCHY000000000 SRR13796431 1,714 1,658,899 39.3 HpEu ope 58 59,276 554 4,615,312
COL 14-PUJ JAFCHZ000000000 SRR13796430 1,701 1,673,807 38.9 HpEu ope 54 80,670 256 1,758,244
COL 15-PUJ JAFCIA000000000 SRR13796429 1,563 1,546,556 39.2 HpEu ope 46 60,019 133 987,226
COL 16-PUJ JACSDS000000000 SRR13796412 1,665 1,634,541 39.3 HpEu ope 64 54,632 482 2,363,616
COL 18-PUJ JAFCIB000000000 SRR13796428 1,662 1,658,604 38.9 HpEu ope 37 93,756 580 436,440
COL 19-PUJ JAFCIC000000000 SRR13796427 1,654 1,656,342 38.9 HpEu ope 42 81,649 371 2,363,966
COL 20-PUJ JAFCID000000000 SRR13796426 1,674 1,619,537 39 HpEu ope 56 59,593 340 2,201,658
COL 21-PUJ JAFCIE000000000 SRR13796425 1,670 1,618,229 39 HpEu ope 55 58,359 435 3,168,290
COL 23-PUJ JACSDR000000000 SRR13796411 1,661 1,614,131 39.1 HpEu ope 91 32,948 99 762,738
COL 24-PUJ JAFCIF000000000 SRR13796424 1,674 1,622,244 39 HpEu ope 119 25,019 119 922,348
COL 25-PUJ JAFCIG000000000 SRR13796423 1,681 1,662,282 38.9 HpEu ope 88 37,899 113 909,004
COL 26-PUJ JAFCIH000000000 SRR13796421 1,631 1,619,895 39 HpEu ope 52 97,025 208 1,447,706
COL 27-PUJ JAFCII000000000 SRR13796420 1,656 1,653,551 38.9 HpEu ope 36 80,500 359 2,247,256
COL 28-PUJ JAFCIJ000000000 SRR13796419 1,671 1,653,809 38.9 HpEu ope 23 132,947 479 3,095,502
COL 29-PUJ JAFCIK000000000 SRR13796418 1,585 1,586,826 39.2 HpEu ope 31 144,624 340 2,443,034
COL 30-PUJ JAFCIL000000000 SRR13796417 1,596 1,587,263 39.1 HpEu ope 35 92,323 339 2,478,576
COL 31-PUJ JAFCIM000000000 SRR13796416 1,795 1,711,739 39 HpEu ope 14 41,620 363 2,430,084
COL 49-PUJ JAFCIN000000000 SRR13796415 1,786 1,735,252 39 HpEu ope 96 59,657 255 2,107,660
COL 50-PUJ JAFCIO000000000 SRR13796414 1,726 1,711,312 38.9 HpEu ope 57 118,609 522 4,410,236
COL 51-PUJ JAFCIP000000000 SRR13796413 1,656 1,666,802 38.9 HpEu ope 39 82,225 404 2,801,844
a
CDS, coding DNA sequences.
Muñoz e al.
Volume 10 Issue 19 e00218-21 m a.asm.o g 2
we e analyzed in he S uc u e 2.3.4 so wa e (13–15) and he MEGA 7.0 so wa e (16).
Fo hese analyses, p e iously epo ed ecommenda ions (17, 18) we e ollowed, and
he esul s e ealed ha all Colombian isola es included in his s udy we e classified as
HpEu ope.
The da a epo ed he e p o ide in o ma ion on he gene ic popula ion s uc u e o
Colombian H. pylo i. This in o ma ion will help u u e unc ional compa a i e genomic
s udies ha will g ea ly enhance he unde s anding o H. pylo i in ec ion dynamics in
he La in Ame ican egion.
Da a a ailabili y. This whole-genome sho gun p ojec has been deposi ed in
GenBank unde accession numbe PRJNA656306. The accession numbe s o he genomes
a ep o idedinTable1
.
ACKNOWLEDGMENTS
We hank he en i ies ha financially suppo ed he de elopmen o his wo k.
A.B.M. is a ecipien o a schola ship om he Cen o de Es udios In e disciplina ios
Básicos y Aplicados (CEIBA) Founda ion, Colombia; and A.B.M., C.A., J.S., and A.A.T.-R.
a e ecipien s o a p ojec g an (120380763025/2018) om MinCiencias, Colombia. The
wo k is pa ially suppo ed by Resea ch Vice-Rec o y, Pon ificia Uni e sidad Ja e iana
(PPTA_7676) and F.P.I.T. BanRepCul u al (p ojec 3956). F.F.V. is financed by na ional
unds om he Fundação pa a a Ciência e a Tecnologia (FCT) h ough an assis an
esea che g an (CEECIND/03023/2017), a p ojec g an (PTDC/BTM-SAL/28978/2017),
and p ojec s UIDB/04138/2020 and UIDP/04138/2020; hese unds pa ially suppo ed
his wo k. The unde s had no ole in s udy design, da a collec ion and in e p e a ion, o
he decision o submi he wo k o publica ion.
REFERENCES
1. Dang BN, G aham DY. 2017. Helicobac e pylo i in ec ion and an ibio ic e-
sis ance: a WHO high p io i y? Na Re Gas oen e ol Hepa ol 14:383–384.
h ps://doi.o g/10.1038/n gas o.2017.57.
2. Peek RM, Blase MJ. 2002. Helicobac e pylo i and gas oin es inal ac
adenoca cinomas. Na Re Cance 2:28–37. h ps://doi.o g/10.1038/n c703.
3. Camilo V, Sugiyama T, Toua i E. 2017. Pa hogenesis o Helicobac e pylo i
in ec ion. Helicobac e 22:e12405. h ps://doi.o g/10.1111/hel.12405.
4. B a o LE, Co és A, Ca ascal E, Ja amillo R, Ga cía LS, B a o PE, Badel A,
B a o PA. 2003. Helicobac e pylo i: pa ología y p e alencia en biopsias
gás icas en Colombia. Colomb Med 34:124–131.
5. A he on JC, Cao P, Peek RM, Tummu u MK, Blase MJ, Co e TL. 1995. Mo-
saicism in acuola ing cy o oxin alleles o Helicobac e pylo i. Associa ion
o specific acA ypes wi h cy o oxin p oduc ion and pep ic ulce a ion. J
Biol Chem 270:17771–17777. h ps://doi.o g/10.1074/jbc.270.30.17771.
6. Bolge AM, Lohse M, Usadel B. 2014. T immoma ic: a flexible imme o
Illumina sequence da a. Bioin o ma ics 30:2114–2120. h ps://doi.o g/10
.1093/bioin o ma ics/b u170.
7. Banke ich A, Nu k S, An ipo D, Gu e ich AA, D o kin M, Kuliko AS, Lesin
VM, Nikolenko SI, Pham S, P jibelski AD, Pyshkin AV, Si o kin AV, Vyahhi N,
Tesle G, Alekseye MA, Pe zne PA. 2012. SPAdes: a new genome assem-
bly algo i hm and i s applica ions o single-cell sequencing. J Compu
Biol 19:455–477. h ps://doi.o g/10.1089/cmb.2012.0021.
8. Ta uso a T, DiCuccio M, Bad e din A, Che e nin V, Naw ocki EP, Zasla sky
L, Lomsadze A, P ui KD, Bo odo sky M, Os ell J. 2016. NCBI P oka yo ic Ge-
nome Anno a ion Pipeline. Nucleic Acids Res 44:6614–6624. h ps://doi
.o g/10.1093/na /gkw569.
9. Jolley KA, B ay JE, Maiden MCJ. 2018. Open-access bac e ial popula ion
genomics: BIGSdb so wa e, he PubMLST.o g websi e and hei applica ions.
Wellcome Open Res 3:124. h ps://doi.o g/10.12688/wellcomeopen es.14826.1.
10. Falush D, Wi h T, Linz B, P i cha d JK, S ephens M, Kidd M, Blase MJ,
G aham DY, Vache S, Pe ez-Pe ez GI, Yamaoka Y, Még aud F, O o K,
Reicha d U, Ka zowi sch E, Wang X, Ach man M, Sue baum S. 2003. T aces
o human mig a ions in Helicobac e pylo i popula ions. Science
299:1582–1585. h ps://doi.o g/10.1126/science.1080857.
11. Linz B, Balloux F, Moodley Y, Manica A, Liu H, Roumagnac P, Falush D,
S ame C, P ugnolle F, an de Me we SW, Yamaoka Y, G aham DY, Pe ez-
T alle o E, Wads om T, Sue baum S, Ach man M. 2007. An A ican o igin
o he in ima e associa ion be ween humans and Helicobac e pylo i. Na-
u e 445:915–918. h ps://doi.o g/10.1038/na u e05562.
12. Ka oh K, S andley DM. 2013. MAFFT mul iple sequence alignmen so -
wa e e sion 7: imp o emen s in pe o mance and usabili y. Mol Biol E ol
30:772–780. h ps://doi.o g/10.1093/molbe /ms 010.
13. P i cha d JK, S ephens M, Donnelly P. 2000. In e ence o popula ion s uc-
u e using mul ilocus geno ype da a. Gene ics 155:945–959.
14. Falush D, S ephens M, P i cha d JK. 2007. In e ence o popula ion s uc-
u e using mul ilocus geno ype da a: dominan ma ke s and null alleles.
Mol Ecol No es 7:574–578. h ps://doi.o g/10.1111/j.1471-8286.2007
.01758.x.
15. Falush D, S ephens M, P i cha d JK. 2003. In e ence o popula ion s uc-
u e using mul ilocus geno ype da a: linked loci and co ela ed allele e-
quencies. Gene ics 164:1567–1587.
16. Kuma S, S eche G, Tamu a K. 2016. MEGA7: Molecula E olu iona y
Gene ics Analysis e sion 7.0 o bigge da ase s. Mol Biol E ol
33:1870–1874. h ps://doi.o g/10.1093/molbe /msw054.
17. Vale FF, Vadi elu J, Oleas o M, B eu ec S, Engs and L, Pe e s TT,
Még aud F, Lehou s P. 2015. Do man phages o Helicobac e pylo i
e eal dis inc popula ions in Eu ope. Sci Rep 5:14333. h ps://doi.o g/10
.1038/s ep14333.
18. Muñoz AB, T espalacios-Rangel AA, Vale FF. 2021. An Ame ican lineage o
Helicobac e pylo i p ophages ound in Colombia. Helicobac e 26:e12779.
h ps://doi.o g/10.1111/hel.12779.
Mic obiology Resou ce Announcemen
Volume 10 Issue 19 e00218-21 m a.asm.o g 3
