Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai

Blaser MJ, Perez-Perez GI, Kleanthous H, Cover TL, Peek RM, Chyou PH, Stemmermann GN, Nomura A. Infection with Helicobacter pylori strains possessing cagA is associated with an increased risk of developing adenocarcinoma of the stomach. Cancer Res. 1995;55(10):2111–5.

CAS  PubMed  Google Scholar 

Hatakeyama M. Helicobacter pylori CagA and gastric cancer: a paradigm for hit-and-run carcinogenesis. Cell Host Microbe. 2014;15(3):306–16.

CAS  PubMed  Google Scholar 

Kuipers EJ, Perez-Perez GI, Meuwissen SG, Blaser MJ. Helicobacter pylori and atrophic gastritis: importance of the cagA status. J Natl Cancer Inst. 1995;87(23):1777–80.

CAS  PubMed  Google Scholar 

Chey WD, Leontiadis GI, Howden CW, Moss SF. ACG Clinical guideline: treatment of Helicobacter pylori infection. Am J Gastroenterol. 2017;112(2):212–39.

PubMed  Google Scholar 

Nezami BG, Jani M, Alouani D, Rhoads DD, Sadri N. Helicobacter pylori mutations detected by next-generation sequencing in formalin-fixed, paraffin-embedded gastric biopsy specimens are associated with treatment failure. J Clin Microbiol. 2019. https://doi.org/10.1128/JCM.01834-18.

Article  PubMed  PubMed Central  Google Scholar 

Savoldi A, Carrara E, Graham DY, Conti M, Tacconelli E. Prevalence of antibiotic resistance in Helicobacter pylori: a systematic review and meta-analysis in world health organization regions. Gastroenterology. 2018;155(5):1372-1382 e1317.

PubMed  Google Scholar 

Liu WZ, Xie Y, Lu H, Cheng H, Zeng ZR, Zhou LY, Chen Y, Wang JB, Du YQ, Lu NH, et al. Fifth Chinese national consensus report on the management of Helicobacter pylori infection. Helicobacter. 2018;23(2):e12475.

PubMed  Google Scholar 

Chen D, Cunningham SA, Cole NC, Kohner PC, Mandrekar JN, Patel R. Phenotypic and molecular antimicrobial susceptibility of Helicobacter pylori. Antimicrob Agents Chemother. 2017. https://doi.org/10.1128/AAC.02530-16.

Article  PubMed  PubMed Central  Google Scholar 

Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M, Monnet DL, Pulcini C, Kahlmeter G, Kluytmans J, Carmeli Y, et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis. 2018;18(3):318–27.

PubMed  Google Scholar 

Alba C, Blanco A, Alarcon T. Antibiotic resistance in Helicobacter pylori. Curr Opin Infect Dis. 2017;30(5):489–97.

CAS  PubMed  Google Scholar 

Gong Y, Yuan Y. Resistance mechanisms of Helicobacter pylori and its dual target precise therapy. Crit Rev Microbiol. 2018;44(3):371–92.

CAS  PubMed  Google Scholar 

Smiley R, Bailey J, Sethuraman M, Posecion N, Showkat Ali M. Comparative proteomics analysis of sarcosine insoluble outer membrane proteins from clarithromycin resistant and sensitive strains of Helicobacter pylori. J Microbiol. 2013;51(5):612–8.

CAS  PubMed  Google Scholar 

Co EM, Schiller NL. Resistance mechanisms in an in vitro-selected amoxicillin-resistant strain of Helicobacter pylori. Antimicrob Agents Chemother. 2006;50(12):4174–6.

CAS  PubMed  PubMed Central  Google Scholar 

Cai Y, Wang C, Chen Z, Xu Z, Li H, Li W, Sun Y. Transporters HP0939, HP0497, and HP0471 participate in intrinsic multidrug resistance and biofilm formation in Helicobacter pylori by enhancing drug efflux. Helicobacter. 2020;25(4):e12715.

CAS  PubMed  Google Scholar 

Iwamoto A, Tanahashi T, Okada R, Yoshida Y, Kikuchi K, Keida Y, Murakami Y, Yang L, Yamamoto K, Nishiumi S, et al. Whole-genome sequencing of clarithromycin resistant Helicobacter pylori characterizes unidentified variants of multidrug resistant efflux pump genes. Gut Pathog. 2014;6:27.

PubMed  PubMed Central  Google Scholar 

Krzyżek P, Grande R, Migdał P, Paluch E, Gościniak G. Biofilm formation as a complex result of virulence and adaptive responses of Helicobacter pylori. Pathogens. 2020. https://doi.org/10.3390/pathogens9121062.

Article  PubMed  PubMed Central  Google Scholar 

Miftahussurur M, Syam AF, Nusi IA, Makmun D, Waskito LA, Zein LH, Akil F, Uwan WB, Simanjuntak D, Wibawa ID, et al. Surveillance of Helicobacter pylori antibiotic susceptibility in indonesia: different resistance types among regions and with novel genetic mutations. PLoS ONE. 2016;11(12):e0166199.

PubMed  PubMed Central  Google Scholar 

Miftahussurur M, Shrestha PK, Subsomwong P, Sharma RP, Yamaoka Y. Emerging Helicobacter pylori levofloxacin resistance and novel genetic mutation in Nepal. BMC Microbiol. 2016;16(1):256.

PubMed  PubMed Central  Google Scholar 

Hussein NR, Tunjel I, Majed HS, Yousif ST, Aswad SI, Assafi MS. Duodenal ulcer promoting gene 1 (dupA1) is associated with A2147G clarithromycin-resistance mutation but not interleukin-8 secretion from gastric mucosa in Iraqi patients. New Microbes New Infect. 2015;6:5–10.

CAS  PubMed  PubMed Central  Google Scholar 

Fasciana T, Cala C, Bonura C, Di Carlo E, Matranga D, Scarpulla G, Manganaro M, Camilleri S, Giammanco A. Resistance to clarithromycin and genotypes in Helicobacter pylori strains isolated in Sicily. J Med Microbiol. 2015;64(11):1408–14.

CAS  PubMed  Google Scholar 

Li HY, Kao CY, Lin WH, Zheng PX, Yan JJ, Wang MC, Teng CH, Tseng CC, Wu JJ. Characterization of CRISPR-Cas systems in clinical Klebsiella pneumoniae isolates uncovers its potential association with antibiotic susceptibility. Front Microbiol. 2018;9:1595.

PubMed  PubMed Central  Google Scholar 

Mangas EL, Rubio A, Alvarez-Marin R, Labrador-Herrera G, Pachon J, Pachon-Ibanez ME, Divina F, Perez-Pulido AJ. Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation. Microb Genom. 2019. https://doi.org/10.1099/mgen.0.000309.

Article  PubMed  PubMed Central  Google Scholar 

Touchon M, Charpentier S, Pognard D, Picard B, Arlet G, Rocha EP, Denamur E, Branger C. Antibiotic resistance plasmids spread among natural isolates of Escherichia coli in spite of CRISPR elements. Microbiology. 2012;158(12):2997–3004.

CAS  PubMed  Google Scholar 

Touchon M, Cury J, Yoon EJ, Krizova L, Cerqueira GC, Murphy C, Feldgarden M, Wortman J, Clermont D, Lambert T, et al. The genomic diversification of the whole Acinetobacter genus: origins, mechanisms, and consequences. Genome Biol Evol. 2014;6(10):2866–82.

CAS  PubMed  PubMed Central  Google Scholar 

Shehreen S, Chyou TY, Fineran PC, Brown CM. Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. Philos Trans R Soc Lond B Biol Sci. 2019;374(1772):20180384.

CAS  PubMed  PubMed Central  Google Scholar 

Corbinais C, Mathieu A, Kortulewski T, Radicella JP, Marsin S. Following transforming DNA in Helicobacter pylori from uptake to expression. Mol Microbiol. 2016;101(6):1039–53.

CAS  PubMed  Google Scholar 

Jaillard M, van Belkum A, Cady KC, Creely D, Shortridge D, Blanc B, Barbu EM, Dunne WM Jr, Zambardi G, Enright M, et al. Correlation between phenotypic antibiotic susceptibility and the resistome in Pseudomonas aeruginosa. Int J Antimicrob Agents. 2017;50(2):210–8.

CAS  PubMed  Google Scholar 

Clinical and Laboratory Standards Institute. Methods for antimicrobial dilution and disk susceptibility testing of infrequently isolated or fastidious bacteria (M45). 3rd ed. 2016.

Jin Y, Deng J, Liang J, Shan C, Tong M. Efficient bacteria capture and inactivation by cetyltrimethylammonium bromide modified magnetic nanoparticles. Colloids Surf B Biointerfaces. 2015;136:659–65.

CAS  PubMed  Google Scholar 

Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016;9:88.

PubMed  PubMed Central  Google Scholar 

Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012;1(1):18.

PubMed  PubMed Central  Google Scholar 

Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics. 2015;31(4):587–9.

CAS  PubMed  Google Scholar 

Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999;27(23):4636–41.

CAS  PubMed  PubMed Central  Google Scholar 

Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):955–64.

CAS  PubMed  PubMed Central  Google Scholar 

Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35(9):3100–8.

CAS  PubMed  PubMed Central  Google Scholar 

Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007;8:209.

PubMed  PubMed Central  Google Scholar 

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–10.

CAS  PubMed  PubMed Central  Google Scholar 

Blake JD, Cohen FE. Pairwise sequence alignment below the twilight zone. J Mol Biol. 2001;307(2):721–35.

CAS  PubMed  Google Scholar 

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldon T, Rattei T, Creevey C, Kuhn M, et al. eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 2014;42(Database issue):D231-239.

CAS  PubMed  Google Scholar 

Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, Shanmugam D, Roos DS, Stoeckert CJ. Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Vol 12. In: Goodsell DS, editor. Current protocols in bioinformatics. Hoboken: Wiley; 2011. p. 11–9.

Google Scholar 

Chen L, Xiong Z, Sun L, Yang J, Jin Q. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 2012;40(Database issue):D641-645.

CAS  PubMed  Google Scholar 

Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S, Cattoir V, Philippon A, Allesoe RL, Rebelo AR, Florensa AF, et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother. 2020;75(12):3491–500.

CAS  PubMed  PubMed Central 

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