Draft Genome Sequences of 29 Helicobacter pylori Strains Isolated from Colombia

Draft Genome Sequences of 29 Helicobacter pylori Strains Isolated from Colombia Angela B. Muñoz, a Johanna Stepanian, a Carmen Acosta, a Juan S. Solano-Gutierrez, b Filipa F. Vale, c Alba A. Trespalacios-Rangel a a Infectious Diseases Research Group, Microbiology Department, Sciences Faculty, Pontificia Universidad Javeriana, Bogotá, Colombia b AXOMICS-Sequencing Center, Biological Science Department, Science School, Universidad EAFIT, Medellín, Colombia c Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal ABSTRACT Here, we present the draft genome sequences of 29 Colombian Helicobacter pylori strains. These strains were isolated in Bogotá, Colombia, from patients diagnosed with chronic gastritis. The genomic characterization of these strains will provide more information on the genetic composition of H. pylori strains from Colombia. Helicobacter pylori is a Gram-negative, pathogenic bacterium capable of colonizing and persisting in the human stomach. The infection is considered the most frequent chronic bacterial infection worldwide (1–3), reaching prevalence rates of up to 80% in Colombia (4). This report announces the genome sequences of 29 H. pylori strains isolated between 2009 and 2010 from patients residing in Bogotá, Colombia. The patients who signed informed consent were 48 years old on average (range, 18 to 79 years); from the histology results, 65.5% were diagnosed with chronic nonatrophic gastritis and 34.5% with chronic atrophic gastritis. The strains were recovered from gastric biopsy samples, and those were cultivated on BBL Brucella agar (Becton, Dickinson) supplemented with 7% horse blood, 0.4% IsoVitalex (BD, USA), and 0.2% Dent selective supplement (Oxoid, UK) under microaerophilic conditions (11% CO 2 ) at 37°C for 4 to 7 days. The strains were preserved in 20% glycerol and stored until required for DNA extraction. They were recovered by culture every time. After that, total DNA was extracted using a DNeasy blood and tissue kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. Fluorometric assay DNA quantification was performed using a Qubit 2.0 fluorometer and the Qubit double-stranded DNA (dsDNA) high-sensitivity (HS) assay kit (Life Technologies, Carlsbad, CA, USA). To verify that the DNA obtained was from H. pylori, a conventional PCR technique for the vacA gene was carried out. The primers and protocols previously described by Atherton et al. (5) were used. Genomic DNA was sequenced using the MiSeq platform (Illumina, San Diego, CA); DNA libraries were prepared using a Nextera XT DNA library preparation kit (Illumina), followed by 2 300-bp paired-end sequencing resulting in 80coverage. The lowquality sequences were removed with the software package Trimmomatic v0.39 (6). The reads were used for de novo genome assembly with SPAdes v13.3 (7). Assembly statistics for analyzed strains are provided in Table 1. The sequences were annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) (8). Default parameters were used for all software tools unless otherwise specified. A multilocus sequence typing (MLST) analysis was performed based on seven H. pylori housekeeping genes (atpA,efp,trpC,ppa,mutY,yphC, and urel). The sequences of these genes from 741 strains available at PubMLST (http://pubmlst.org/helicobacter/) (9) and previously described by Falush et al. (10) and Linz et al. (11), plus the 29 strains included in this study, were aligned using MAFFT v7 (12). Then, the aligned sequences Citation Muñoz AB, Stepanian J, Acosta C, Solano-Gutierrez JS, Vale FF, TrespalaciosRangel AA. 2021. Draft genome sequences of 29 Helicobacter pylori strains isolated from Colombia. Microbiol Resour Announc 10:e00218-21. https:// doi.org/10.1128/MRA.00218-21. Editor Catherine Putonti, Loyola University Chicago Copyright © 2021 Muñoz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Angela B. Muñoz, [email protected], or Alba A. Trespalacios-Rangel, [email protected]. Received 28 February 2021 Accepted 16 April 2021 Published 13 May 2021 Volume 10 Issue 19 e00218-21 mra.asm.org 1 GENOME SEQUENCES TABLE 1 Genome statistics of sequences reported Strain name GenBank accession no. SRA accession no. No. of CDS a Genome size (bp) GC content (%) MLST No. of contigs N 50 value (bp) Genome coverage (×) No. of raw reads COL 1-PUJ JAFCHS000000000 SRR13796410 1,582 1,679,429 38.8 HpEurope 72 58,624 135 1,163,956 COL 2-PUJ JACSDV000000000 SRR13796434 1,632 1,607,581 39 HpEurope 46 82,542 392 2,633,600 COL 5-PUJ JACSDU000000000 SRR13796433 1,667 1,624,361 39.1 HpEurope 133 21,560 105 850,310 COL 6-PUJ JACSDT000000000 SRR13796422 1,673 1,625,175 39.1 HpEurope 133 20,478 95 745,268 COL 8-PUJ JAFCHT000000000 SRR13796409 1,664 1,661,424 38.9 HpEurope 43 93,756 286 2,823,146 COL 9-PUJ JAFCHU000000000 SRR13796408 1,653 1,613,788 39 HpEurope 47 84,065 311 2,073,864 COL 10-PUJ JAFCHV000000000 SRR13796407 1,680 1,642,843 39.4 HpEurope 58 107,835 375 2,741,078 COL 11-PUJ JAFCHW000000000 SRR13796406 1,663 1,626,191 39.4 HpEurope 58 86,547 221 1,639,572 COL 12-PUJ JAFCHX000000000 SRR13796432 1,633 1,637,127 38.9 HpEurope 43 96,559 368 2,773,188 COL 13-PUJ JAFCHY000000000 SRR13796431 1,714 1,658,899 39.3 HpEurope 58 59,276 554 4,615,312 COL 14-PUJ JAFCHZ000000000 SRR13796430 1,701 1,673,807 38.9 HpEurope 54 80,670 256 1,758,244 COL 15-PUJ JAFCIA000000000 SRR13796429 1,563 1,546,556 39.2 HpEurope 46 60,019 133 987,226 COL 16-PUJ JACSDS000000000 SRR13796412 1,665 1,634,541 39.3 HpEurope 64 54,632 482 2,363,616 COL 18-PUJ JAFCIB000000000 SRR13796428 1,662 1,658,604 38.9 HpEurope 37 93,756 580 436,440 COL 19-PUJ JAFCIC000000000 SRR13796427 1,654 1,656,342 38.9 HpEurope 42 81,649 371 2,363,966 COL 20-PUJ JAFCID000000000 SRR13796426 1,674 1,619,537 39 HpEurope 56 59,593 340 2,201,658 COL 21-PUJ JAFCIE000000000 SRR13796425 1,670 1,618,229 39 HpEurope 55 58,359 435 3,168,290 COL 23-PUJ JACSDR000000000 SRR13796411 1,661 1,614,131 39.1 HpEurope 91 32,948 99 762,738 COL 24-PUJ JAFCIF000000000 SRR13796424 1,674 1,622,244 39 HpEurope 119 25,019 119 922,348 COL 25-PUJ JAFCIG000000000 SRR13796423 1,681 1,662,282 38.9 HpEurope 88 37,899 113 909,004 COL 26-PUJ JAFCIH000000000 SRR13796421 1,631 1,619,895 39 HpEurope 52 97,025 208 1,447,706 COL 27-PUJ JAFCII000000000 SRR13796420 1,656 1,653,551 38.9 HpEurope 36 80,500 359 2,247,256 COL 28-PUJ JAFCIJ000000000 SRR13796419 1,671 1,653,809 38.9 HpEurope 23 132,947 479 3,095,502 COL 29-PUJ JAFCIK000000000 SRR13796418 1,585 1,586,826 39.2 HpEurope 31 144,624 340 2,443,034 COL 30-PUJ JAFCIL000000000 SRR13796417 1,596 1,587,263 39.1 HpEurope 35 92,323 339 2,478,576 COL 31-PUJ JAFCIM000000000 SRR13796416 1,795 1,711,739 39 HpEurope 14 41,620 363 2,430,084 COL 49-PUJ JAFCIN000000000 SRR13796415 1,786 1,735,252 39 HpEurope 96 59,657 255 2,107,660 COL 50-PUJ JAFCIO000000000 SRR13796414 1,726 1,711,312 38.9 HpEurope 57 118,609 522 4,410,236 COL 51-PUJ JAFCIP000000000 SRR13796413 1,656 1,666,802 38.9 HpEurope 39 82,225 404 2,801,844 a CDS, coding DNA sequences. Muñoz et al. Volume 10 Issue 19 e00218-21 mra.asm.org 2 were analyzed in the Structure 2.3.4 software (13–15) and the MEGA 7.0 software (16). For these analyses, previously reported recommendations (17, 18) were followed, and the results revealed that all Colombian isolates included in this study were classified as HpEurope. The data reported here provide information on the genetic population structure of Colombian H. pylori. This information will help future functional comparative genomic studies that will greatly enhance the understanding of H. pylori infection dynamics in the Latin American region. Data availability. This whole-genome shotgun project has been deposited in GenBank under accession number PRJNA656306. The accession numbers for the genomes areprovidedinTable1 . ACKNOWLEDGMENTS We thank the entities that financially supported the development of this work. 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