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Sociology
General Social Sciences

Comparison in Qualitative Research

Profile image of Lesley BartlettLesley Bartlett

2020, Oxford Research Encyclopedia of Education

https://doi.org/10.3389/FMICB.2020.01592
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Abstract

Comparison is a valuable and widely touted analytical technique in social research, but different disciplines and fields have markedly different notions of comparison. There are at least two important logics for comparison. The first, the logic of juxtaposition, is guided by a neopositivist orientation. It uses a regularity theory of causation; it structures the study by defining cases, variables, and units of analysis a priori; and it decontextualizes knowledge. The second, the logic of tracing, engages a realist theory of causation and examines how processes unfold, influenced by actors and the meanings they make, over time, in different locations, and at different scales. These two logics of comparison lead to distinct methodological techniques. However, with either logic of comparison, three dangers merit attention: decontextualization, commensurability, and ethnocentrism. One promising research heuristic that attends to different logics of comparison while avoiding these danger...

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References (120)

  1. Alandiyjany, M. N., Croxall, N. J., Grove, J. I., and Delahay, R. M. (2017). A role for the tfs3 ICE-encoded type IV secretion system in pro-inflammatory signalling by the Helicobacter pylori Ser/Thr kinase, CtkA. PLoS One 12:e0182144. doi: 10.1371/journal.pone.0182144
  2. Alvi, A., Devi, S. M., Ahmed, I., Hussain, M. A., Rizwan, M., Lamouliatte, H., et al. (2007). Microevolution of Helicobacter pylori type IV secretion systems in an ulcer disease patient over a ten-year period. J. Clin. Microbiol. 45, 4039-4043. doi: 10.1128/jcm.01631-07
  3. Backert, S., Haas, R., Gerhard, M., and Naumann, M. (2017). The Helicobacter pylori type IV secretion system encoded by the cag pathogenicity Island: architecture, function, and signaling. Curr. Top. Microbiol. Immunol. 413, 187-220. doi: 10.1007/978-3-319-75241-9\_8
  4. Backert, S., Kwok, T., and König, W. (2005). Conjugative plasmid DNA transfer in Helicobacter pylori mediated by chromosomally encoded relaxase and TraG- like proteins. Microbiology 151, 3493-3503. doi: 10.1099/mic.0.28250-0
  5. Backert, S., and Naumann, M. (2010). What a disorder: proinflammatory signaling pathways induced by Helicobacter pylori. Trends Microbiol. 18, 479-486. doi: 10.1016/j.tim.2010.08.003
  6. Backert, S., Tegtmeyer, N., and Fischer, W. (2015). Composition, structure and function of the Helicobacter pylori cag pathogenicity island encoded type IV secretion system. Future Microbiol. 10, 955-965. doi: 10.2217/fmb.15.32
  7. Barrozo, R. M., Cooke, C. L., Hansen, L. M., Lam, A. M., Gaddy, J. A., Johnson, E. M., et al. (2013). Functional plasticity in the type IV secretion system of Helicobacter pylori. PLoS Pathog. 9:e1003189. doi: 10.1371/journal.ppat. 1003189
  8. Behrens, I. K., Busch, B., Ishikawa-Ankerhold, H., Palamides, P., Shively, J. E., Stanners, C., et al. (2020). The HopQ-CEACAM interaction controls CagA translocation, phosphorylation, and phagocytosis of Helicobacter pylori in neutrophils. mBio 11:e03256-19.
  9. Blaser, N., Backert, S., and Pachathundikandi, S. K. (2019). Immune cell signaling by Helicobacter pylori: impact on gastric pathology. Adv. Exp. Med. Biol. 1149, 77-106. doi: 10.1007/5584_2019_360
  10. Boccellato, F., Woelffling, S., Imai-Matsushima, A., Sanchez, G., Goosmann, C., Schmid, M., et al. (2019). Polarised epithelial monolayers of the gastric mucosa reveal insights into mucosal homeostasis and defence against infection. Gut 68, 400-413. doi: 10.1136/gutjnl-2017-3 14540
  11. Bönig, T., Olbermann, P., Bats, S. H., Fischer, W., and Josenhans, C. (2016). Systematic site-directed mutagenesis of the Helicobacter pylori CagL protein of the Cag type IV secretion system identifies novel functional domains. Sci. Rep. 6:38101. doi: 10.1038/srep38101
  12. Busch, B., Weimer, R., Woischke, C., Fischer, W., and Haas, R. (2015). Helicobacter pylori interferes with leukocyte migration via the outer membrane protein HopQ and via CagA translocation. Int. J. Med. Microbiol. 305, 355-364. doi: 10.1016/j.ijmm.2015.02.003
  13. Cascales, E., and Christie, P. J. (2004). Definition of a bacterial type IV secretion pathway for a DNA substrate. Science 304, 1170-1173. doi: 10.1126/science. 1095211
  14. Censini, S., Lange, C., Xiang, Z., Crabtree, J. E., Ghiara, P., Borodovsky, M., et al. (1996). cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc. Natl. Acad. Sci. U.S.A. 93, 14648-14653. doi: 10.1073/pnas.93.25.14648
  15. Chandran, V., Fronzes, R., Duquerroy, S., Cronin, N., Navaza, J., and Waksman, G. (2009). Structure of the outer membrane complex of a type IV secretion system. Nature 462, 1011-1015. doi: 10.1038/nature08588
  16. Chang, Y. W., Shaffer, C. L., Rettberg, L. A., Ghosal, D., and Jensen, G. J. (2018). In vivo structures of the Helicobacter pylori cag type IV secretion system. Cell Rep. 23, 673-681. doi: 10.1016/j.celrep.2018.03.085
  17. Chung, J. M., Sheedlo, M. J., Campbell, A. M., Sawhney, N., Frick-Cheng, A. E., Lacy, D. B., et al. (2019). Structure of the Helicobacter pylori cag type IV secretion system. eLife 8:e47644. doi: 10.7554/eLife.47644
  18. Corbinais, C., Mathieu, A., Damke, P. P., Kortulewski, T., Busso, D., Prado-Acosta, M., et al. (2017). ComB proteins expression levels determine Helicobacter pylori competence capacity. Sci. Rep. 7:41495. doi: 10.1038/srep41495
  19. Corbinais, C., Mathieu, A., Kortulewski, T., Radicella, J. P., and Marsin, S. (2016). Following transforming DNA in Helicobacter pylori from uptake to expression. Mol. Microbiol. 101, 1039-1053. doi: 10.1111/mmi.13440
  20. Covacci, A., and Rappuoli, R. (2000). Tyrosine-phosphorylated bacterial proteins: trojan horses for the host cell. J. Exp. Med. 191, 587-592. doi: 10.1084/jem.191. 4.587
  21. Damke, P. P., Di Guilmi, A. M., Varela, P. F., Velours, C., Marsin, S., Veaute, X., et al. (2019). Identification of the periplasmic DNA receptor for natural transformation of Helicobacter pylori. Nat. Commun. 10:5357.
  22. de Martel, C., Georges, D., Bray, F., Ferlay, J., and Clifford, G. M. (2020). Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis. Lancet Glob. Health 8, e180-e190. doi: 10.1016/s2214-109x(19)30 488-7
  23. Delahay, R. M., Balkwill, G. D., Bunting, K. A., Edwards, W., Atherton, J. C., and Searle, M. S. (2008). The highly repetitive region of the Helicobacter pylori CagY protein comprises tandem arrays of an α-helical repeat module. J. Mol. Biol. 377, 956-971. doi: 10.1016/j.jmb.2008.01.053
  24. Delahay, R. M., Croxall, N. J., and Stephens, A. D. (2018). Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements. Mob. DNA 9:5.
  25. Dorer, M. S., Cohen, I. E., Sessler, T. H., Fero, J., and Salama, N. R. (2013). Natural competence promotes Helicobacter pylori chronic infection. Infect. Immun. 81, 209-215. doi: 10.1128/iai.01042-12
  26. Fischer, W. (2011). Assembly and molecular mode of action of the Helicobacter pylori Cag type IV secretion apparatus. FEBS J. 278, 1203-1212. doi: 10.1111/j. 1742-4658.2011.08036.x
  27. Fischer, W., Breithaupt, U., Kern, B., Smith, S. I., Spicher, C., and Haas, R. (2014). A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity. BMC Genomics 15:310. doi: 10.1186/1471-2164-15-310
  28. Fischer, W., Püls, J., Buhrdorf, R., Gebert, B., Odenbreit, S., and Haas, R. (2001). Systematic mutagenesis of the Helicobacter pylori cag pathogenicity island: essential genes for CagA translocation in host cells and induction of interleukin- 8. Mol. Microbiol. 42, 1337-1348. doi: 10.1046/j.1365-2958.2001.02714.x
  29. Fischer, W., Windhager, L., Rohrer, S., Zeiller, M., Karnholz, A., Hoffmann, R., et al. (2010). Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer. Nucleic Acids Res. 38, 6089-6101. doi: 10.1093/nar/gkq378
  30. Franco, A. T., Johnston, E., Krishna, U., Yamaoka, Y., Israel, D. A., Nagy, T. A., et al. (2008). Regulation of gastric carcinogenesis by Helicobacter pylori virulence factors. Cancer Res. 68, 379-387.
  31. Frick-Cheng, A. E., Pyburn, T. M., Voss, B. J., McDonald, W. H., Ohi, M. D., and Cover, T. L. (2016). Molecular and structural analysis of the Helicobacter pylori cag type IV secretion system core complex. mBio 7:e02001-15.
  32. Gall, A., Gaudet, R. G., Gray-Owen, S. D., and Salama, N. R. (2017). TIFA signaling in gastric epithelial cells initiates the cag type 4 secretion system-dependent innate immune response to Helicobacter pylori infection. mBio 8:e01168-17.
  33. Gangel, H., Hepp, C., Müller, S., Oldewurtel, E. R., Aas, F. E., Koomey, M., et al. (2014). Concerted spatio-temporal dynamics of imported DNA and ComE DNA uptake protein during gonococcal transformation. PLoS Pathog. 10:e1004043. doi: 10.1371/journal.ppat.1004043
  34. Gobert, A. P., Verriere, T., Asim, M., Barry, D. P., Piazuelo, M. B., de Sablet, T., et al. (2014). Heme oxygenase-1 dysregulates macrophage polarization and the immune response to Helicobacter pylori. J. Immunol. 193, 3013-3022. doi: 10.4049/jimmunol.1401075
  35. Gong, Y., Peng, X., He, L., Liang, H., You, Y., and Zhang, J. (2015). The distribution of jhp0940, jhp0945, jhp0947, jhp0949 and jhp0951 genes of Helicobacter pylori in China. BMC Gastroenterol. 15:115. doi: 10.1186/s12876-015-0341-z
  36. Gressmann, H., Linz, B., Ghai, R., Pleissner, K. P., Schlapbach, R., Yamaoka, Y., et al. (2005). Gain and loss of multiple genes during the evolution of Helicobacter pylori. PLoS Genet. 1:e43. doi: 10.1371/journal.pgen.0010043
  37. Grohmann, E., Christie, P. J., Waksman, G., and Backert, S. (2018). Type IV secretion in gram-negative and gram-positive bacteria. Mol. Microbiol. 107, 455-471. doi: 10.1111/mmi.13896
  38. Grove, J. I., Alandiyjany, M. N., and Delahay, R. M. (2013). Site-specific relaxase activity of a VirD2-like protein encoded within the tfs4 genomic Island of Helicobacter pylori. J. Biol. Chem. 288, 26385-26396. doi: 10.1074/jbc.M113. 496430
  39. Hayashi, T., Senda, M., Morohashi, H., Higashi, H., Horio, M., Kashiba, Y., et al. (2012). Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA. Cell Host Microbe 12, 20-33. doi: 10.1016/j.chom.2012.05.010
  40. He, S., Corneloup, A., Guynet, C., Lavatine, L., Caumont-Sarcos, A., Siguier, P., et al. (2015). The IS200/IS605 family and "peel and paste" single-strand transposition mechanism. Microbiol. Spectr. 3:MDNA3-0039-2014. doi: 10. 1128/microbiolspec.MDNA3-0039-2014
  41. Heintschel von Heinegg, E., Nalik, H. P., and Schmid, E. N. (1993). Characterisation of a Helicobacter pylori phage (HP1). J. Med. Microbiol. 38, 245-249. doi: 10.1099/00222615-38-4-245
  42. Hepp, C., and Maier, B. (2016). Kinetics of DNA uptake during transformation provide evidence for a translocation ratchet mechanism. Proc. Natl. Acad. Sci. U.S.A. 113, 12467-12472. doi: 10.1073/pnas.1608110113
  43. Higashi, H., Tsutsumi, R., Muto, S., Sugiyama, T., Azuma, T., Asaka, M., et al. (2002). SHP-2 tyrosine phosphatase as an intracellular target of Helicobacter pylori CagA protein. Science 295, 683-686. doi: 10.1126/science.1067147
  44. Höfler, C., Fischer, W., Hofreuter, D., and Haas, R. (2004). Cryptic plasmids in Helicobacter pylori: putative functions in conjugative transfer and microcin production. Int. J. Med. Microbiol. 294, 141-148. doi: 10.1016/j.ijmm.2004. 06.021
  45. Hofreuter, D., and Haas, R. (2002). Characterization of two cryptic Helicobacter pylori plasmids: a putative source for horizontal gene transfer and gene shuffling. J. Bacteriol. 184, 2755-2766. doi: 10.1128/jb.184.10.2755-2766.2002
  46. Hofreuter, D., Karnholz, A., and Haas, R. (2003). Topology and membrane interaction of Helicobacter pylori ComB proteins involved in natural transformation competence. Int. J. Med. Microbiol. 293, 153-165. doi: 10.1078/ 1438-4221-00258
  47. Hofreuter, D., Odenbreit, S., and Haas, R. (2001). Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system. Mol. Microbiol. 41, 379-391. doi: 10.1046/j.1365- 2958.2001.02502.x
  48. Hooi, J. K. Y., Lai, W. Y., Ng, W. K., Suen, M. M. Y., Underwood, F. E., Tanyingoh, D., et al. (2017). Global prevalence of Helicobacter pylori infection: systematic review and meta-analysis. Gastroenterology 153, 420-429. doi: 10.1053/j.gastro. 2017.04.022
  49. Hu, B., Khara, P., Song, L., Lin, A. S., Frick-Cheng, A. E., Harvey, M. L., et al. (2019). In situ molecular architecture of the Helicobacter pylori cag type IV secretion system. mBio 10:e00849-19. doi: 10.1128/mBio.00849-19
  50. Javaheri, A., Kruse, T., Moonens, K., Mejías-Luque, R., Debraekeleer, A., Asche, C. I., et al. (2016). Helicobacter pylori adhesin HopQ engages in a virulence- enhancing interaction with human CEACAMs. Nat. Microbiol. 2:16243. doi: 10.1038/nmicrobiol.2016.243
  51. Jiménez-Soto, L. F., Kutter, S., Sewald, X., Ertl, C., Weiss, E., Kapp, U., et al. (2009). Helicobacter pylori type IV secretion apparatus exploits β1 integrin in a novel RGD-independent manner. PLoS Pathog. 5:e1000684. doi: 10.1371/ journal.ppat.1000684
  52. Joo, J. S., Song, J. Y., Baik, S. C., Lee, W. K., Cho, M. J., Lee, K. H., et al. (2012). Genetic organization and conjugal plasmid DNA transfer of pHP69, a plasmid from a Korean isolate of Helicobacter pylori. J. Microbiol. 50, 955-961. doi: 10.1007/s12275-012-2580-9
  53. Jung, S. W., Sugimoto, M., Shiota, S., Graham, D. Y., and Yamaoka, Y. (2012). The intact dupA cluster is a more reliable Helicobacter pylori virulence marker than dupA alone. Infect. Immun. 80, 381-387.
  54. Kaplan-Türköz, B., Jiménez-Soto, L. F., Dian, C., Ertl, C., Remaut, H., Louche, A., et al. (2012). Structural insights into Helicobacter pylori oncoprotein CagA interaction with β1 integrin. Proc. Natl. Acad. Sci. U.S.A. 109, 14640-14645. doi: 10.1073/pnas.1206098109
  55. Karnholz, A., Höfler, C., Odenbreit, S., Fischer, W., Hofreuter, D., and Haas, R. (2006). Functional and topological characterization of novel components of the comB DNA transformation competence system in Helicobacter pylori. J. Bacteriol. 188, 882-893. doi: 10.1128/jb.188.3.882-89 3.2006
  56. Kavermann, H., Burns, B. P., Angermüller, K., Odenbreit, S., Fischer, W., Melchers, K., et al. (2003). Identification and characterization of Helicobacter pylori genes essential for gastric colonization. J. Exp. Med. 197, 813-822. doi: 10.1084/jem. 20021531
  57. Kersulyte, D., Akopyants, N. S., Clifton, S. W., Roe, B. A., and Berg, D. E. (1998). Novel sequence organization and insertion specificity of IS605 and IS606: chimaeric transposable elements of Helicobacter pylori. Gene 223, 175-186. doi: 10.1016/s0378-1119(98)00164-4
  58. Kersulyte, D., Lee, W., Subramaniam, D., Anant, S., Herrera, P., Cabrera, L., et al. (2009). Helicobacter pylori's plasticity zones are novel transposable elements. PLoS One 4:e6859. doi: 10.1371/journal.pone.0006859
  59. Kersulyte, D., Velapatino, B., Mukhopadhyay, A. K., Cahuayme, L., Bussalleu, A., Combe, J., et al. (2003). Cluster of type IV secretion genes in Helicobacter pylori's plasticity zone. J. Bacteriol. 185, 3764-3772. doi: 10.1128/jb.185.13.3764-3772. 2003
  60. Kim, D. J., Park, K. S., Kim, J. H., Yang, S. H., Yoon, J. Y., Han, B. G., et al. (2010). Helicobacter pylori proinflammatory protein up-regulates NF-κB as a cell- translocating Ser/Thr kinase. Proc. Natl. Acad. Sci. U.S.A. 107, 21418-21423. doi: 10.1073/pnas.1010153107
  61. Kleanthous, H., Clayton, C. L., and Tabaqchali, S. (1991). Characterization of a plasmid from Helicobacter pylori encoding a replication protein common to plasmids in Gram-positive bacteria. Mol. Microbiol. 5, 2377-2389. doi: 10.1111/ j.1365-2958.1991.tb02084.x
  62. Koch, M., Mollenkopf, H. J., Klemm, U., and Meyer, T. F. (2012). Induction of microRNA-155 is TLR-and type IV secretion system-dependent in macrophages and inhibits DNA-damage induced apoptosis. Proc. Natl. Acad. Sci. U.S.A. 109, E1153-E1162. doi: 10.1073/pnas.1116125109
  63. Koch, M., Mollenkopf, H. J., and Meyer, T. F. (2016). Macrophages recognize the Helicobacter pylori type IV secretion system in the absence of toll-like receptor signalling. Cell. Microbiol. 18, 137-147. doi: 10.1111/cmi.12492
  64. Koelblen, T., Bergé, C., Cherrier, M. V., Brillet, K., Jiménez-Soto, L., Ballut, L., et al. (2017). Molecular dissection of protein-protein interactions between integrin α5β1 and the Helicobacter pylori Cag type IV secretion system. FEBS J. 284, 4143-4157. doi: 10.1111/febs.14299
  65. Königer, V., Holsten, L., Harrison, U., Busch, B., Loell, E., Zhao, Q., et al. (2016). Helicobacter pylori exploits human CEACAMs via HopQ for adherence and translocation of CagA. Nat. Microbiol. 2:16233. doi: 10.1038/nmicrobiol. 2016.233
  66. Krüger, N. J., Knüver, M. T., Zawilak-Pawlik, A., Appel, B., and Stingl, K. (2016). Genetic diversity as consequence of a microaerobic and neutrophilic lifestyle. PLoS Pathog. 12:e1005626. doi: 10.1371/journal.ppat.1005626
  67. Kwok, T., Zabler, D., Urman, S., Rohde, M., Hartig, R., Wessler, S., et al. (2007). Helicobacter exploits integrin for type IV secretion and kinase activation. Nature 449, 862-866. doi: 10.1038/nature06187
  68. Lehours, P., Vale, F. F., Bjursell, M. K., Melefors, O., Advani, R., Glavas, S., et al. (2011). Genome sequencing reveals a phage in Helicobacter pylori. mBio 2:e00239-11.
  69. Low, H. H., Gubellini, F., Rivera-Calzada, A., Braun, N., Connery, S., Dujeancourt, A., et al. (2014). Structure of a type IV secretion system. Nature 508, 550-553. doi: 10.1038/nature13081
  70. Lu, H., Hsu, P. I., Graham, D. Y., and Yamaoka, Y. (2005). Duodenal ulcer promoting gene of Helicobacter pylori. Gastroenterology 128, 833-848. doi: 10.1053/j.gastro.2005.01.009
  71. Luo, C. H., Chiou, P. Y., Yang, C. Y., and Lin, N. T. (2012). Genome, integration, and transduction of a novel temperate phage of Helicobacter pylori. J. Virol. 86, 8781-8792. doi: 10.1128/jvi.00446-12
  72. Moese, S., Selbach, M., Meyer, T. F., and Backert, S. (2002). cag+ Helicobacter pylori induces homotypic aggregation of macrophage-like cells by up-regulation and recruitment of intracellular adhesion molecule 1 to the cell surface. Infect. Immun. 70, 4687-4691. doi: 10.1128/iai.70.8.4687-4691.2002
  73. Moese, S., Selbach, M., Zimny-Arndt, U., Jungblut, P. R., Meyer, T. F., and Backert, S. (2001). Identification of a tyrosine-phosphorylated 35 kDa carboxy-terminal fragment (p35CagA) of the Helicobacter pylori CagA protein in phagocytic cells: processing or breakage? Proteomics 1, 618-629. doi: 10.1002/1615- 9861(200104)1:4<618::aid-prot618>3.0.co;2-c
  74. Moodley, Y., Linz, B., Bond, R. P., Nieuwoudt, M., Soodyall, H., Schlebusch, C. M., et al. (2012). Age of the association between Helicobacter pylori and man. PLoS Pathog. 8:e1002693. doi: 10.1371/journal.ppat.1002693
  75. Mueller, D., Tegtmeyer, N., Brandt, S., Yamaoka, Y., De Poire, E., Sgouras, D., et al. (2012). c-Src and c-Abl kinases control hierarchic phosphorylation and function of the CagA effector protein in Western and East Asian Helicobacter pylori strains. J. Clin. Invest. 122, 1553-1566. doi: 10.1172/jci 61143
  76. Naumann, M., Sokolova, O., Tegtmeyer, N., and Backert, S. (2017). Helicobacter pylori: a paradigm pathogen for subverting host cell signal transmission. Trends Microbiol. 25, 316-328. doi: 10.1016/j.tim.2016.12.004
  77. Neal, J. T., Peterson, T. S., Kent, M. L., and Guillemin, K. (2013). H. pylori virulence factor CagA increases intestinal cell proliferation by Wnt pathway activation in a transgenic zebrafish model. Dis. Model. Mech. 6, 802-810. doi: 10.1242/dmm. 011163
  78. Odenbreit, S., Gebert, B., Püls, J., Fischer, W., and Haas, R. (2001). Interaction of Helicobacter pylori with professional phagocytes: role of the cag pathogenicity island and translocation, phosphorylation and processing of CagA. Cell. Microbiol. 3, 21-31. doi: 10.1046/j.1462-5822.2001.00088.x
  79. Ohnishi, N., Yuasa, H., Tanaka, S., Sawa, H., Miura, M., Matsui, A., et al. (2008). Transgenic expression of Helicobacter pylori CagA induces gastrointestinal and hematopoietic neoplasms in mouse. Proc. Natl. Acad. Sci. U.S.A. 105, 1003-1008. doi: 10.1073/pnas.0711183105
  80. Olbermann, P., Josenhans, C., Moodley, Y., Uhr, M., Stamer, C., Vauterin, M., et al. (2010). A global overview of the genetic and functional diversity in the Helicobacter pylori cag pathogenicity island. PLoS Genet. 6:e1001069. doi: 10. 1371/journal.pgen.1001069
  81. Oyarzabal, O. A., Rad, R., and Backert, S. (2007). Conjugative transfer of chromosomally encoded antibiotic resistance from Helicobacter pylori to Campylobacter jejuni. J. Clin. Microbiol. 45, 402-408. doi: 10.1128/jcm.014 56-06
  82. Pachathundikandi, S. K., Tegtmeyer, N., Arnold, I. C., Lind, J., Neddermann, M., Falkeis-Veits, C., et al. (2019). T4SS-dependent TLR5 activation by Helicobacter pylori infection. Nat. Commun. 10:5717.
  83. Pfannkuch, L., Hurwitz, R., Traulsen, J., Sigulla, J., Poeschke, M., Matzner, L., et al. (2019). ADP heptose, a novel pathogen-associated molecular pattern identified in Helicobacter pylori. FASEB J. 33, 9087-9099. doi: 10.1096/fj.201802555R
  84. Reid, D. W., Muyskens, J. B., Neal, J. T., Gaddini, G. W., Cho, L. Y., Wandler, A. M., et al. (2012). Identification of genetic modifiers of CagA-induced epithelial disruption in Drosophila. Front. Cell. Infect. Microbiol. 2:24. doi: 10.3389/fcimb. 2012.00024
  85. Rohrer, S., Holsten, L., Weiss, E., Benghezal, M., Fischer, W., and Haas, R. (2012). Multiple pathways of plasmid DNA transfer in Helicobacter pylori. PLoS One 7:e45623. doi: 10.1371/journal.pone.0045623
  86. Romo-González, C., Consuelo-Sánchez, A., Camorlinga-Ponce, M., Velázquez- Guadarrama, N., García-Zúniga, M., Burgueno-Ferreira, J., et al. (2015). Plasticity region genes jhp0940, jhp0945, jhp0947, and jhp0949 of Helicobacter pylori in isolates from Mexican children. Helicobacter 20, 231-237. doi: 10.1111/ hel.12194
  87. Saadat, I., Higashi, H., Obuse, C., Umeda, M., Murata-Kamiya, N., Saito, Y., et al. (2007). Helicobacter pylori CagA targets PAR1/MARK kinase to disrupt epithelial cell polarity. Nature 447, 330-333. doi: 10.1038/nature05765
  88. Salama, N. R., Hartung, M. L., and Müller, A. (2013). Life in the human stomach: persistence strategies of the bacterial pathogen Helicobacter pylori. Nat. Rev. Microbiol. 11, 385-399. doi: 10.1038/nrmicro3016
  89. Schmid, E. N., von Recklinghausen, G., and Ansorg, R. (1990). Bacteriophages in Helicobacter (Campylobacter) pylori. J. Med. Microbiol. 32, 101-104.
  90. Schmidt, T. P., Perna, A. M., Fugmann, T., Böhm, M., Hiss, J., Haller, S., et al. (2016). Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA. Sci. Rep. 6:23264. doi: 10.1038/srep23264
  91. Sebrell, T. A., Hashimi, M., Sidar, B., Wilkinson, R. A., Kirpotina, L., Quinn, M. T., et al. (2019). A Novel gastric spheroid co-culture model reveals chemokine- dependent recruitment of human dendritic cells to the gastric epithelium. Cell. Mol. Gastroenterol. Hepatol. 8, 157-171.e3. doi: 10.1016/j.jcmgh.2019.02.010
  92. Seitz, P., Pezeshgi Modarres, H., Borgeaud, S., Bulushev, R. D., Steinbock, L. J., Radenovic, A., et al. (2014). ComEA is essential for the transfer of external DNA into the periplasm in naturally transformable Vibrio cholerae cells. PLoS Genet. 10:e1004066. doi: 10.1371/journal.pgen.1004066
  93. Selbach, M., Paul, F. E., Brandt, S., Guye, P., Daumke, O., Backert, S., et al. (2009). Host cell interactome of tyrosine-phosphorylated bacterial proteins. Cell Host Microbe 5, 397-403. doi: 10.1016/j.chom.2009.03.004
  94. Shiota, S., Matsunari, O., Watada, M., Hanada, K., and Yamaoka, Y. (2010). Systematic review and meta-analysis: the relationship between the Helicobacter pylori dupA gene and clinical outcomes. Gut Pathog. 2:13. doi: 10.1186/1757- 4749-2-13
  95. Sierra, J. C., Suarez, G., Piazuelo, M. B., Luis, P. B., Baker, D. R., Romero-Gallo, J., et al. (2019). α-Difluoromethylornithine reduces gastric carcinogenesis by causing mutations in Helicobacter pylori cagY. Proc. Natl. Acad. Sci. U.S.A. 116, 5077-5085. doi: 10.1073/pnas.1814497116
  96. Sigal, M., Rothenberg, M. E., Logan, C. Y., Lee, J. Y., Honaker, R. W., Cooper, R. L., et al. (2015). Helicobacter pylori activates and expands Lgr5(+) stem cells through direct colonization of the gastric glands. Gastroenterology 148, 1392-1404.e21. doi: 10.1053/j.gastro.2015.02.049
  97. Stein, S. C., Faber, E., Bats, S. H., Murillo, T., Speidel, Y., Coombs, N., et al. (2017). Helicobacter pylori modulates host cell responses by CagT4SS- dependent translocation of an intermediate metabolite of LPS inner core heptose biosynthesis. PLoS Pathog. 13:e1006514. doi: 10.1371/journal.ppat. 1006514
  98. Stingl, K., Müller, S., Scheidgen-Kleyboldt, G., Clausen, M., and Maier, B. (2010). Composite system mediates two-step DNA uptake into Helicobacter pylori. Proc. Natl. Acad. Sci. U.S.A. 107, 1184-1189. doi: 10.1073/pnas.0909955107
  99. Su, H., Tissera, K., Jang, S., Choi, Y. H., Kim, A., Cho, Y. J., et al. (2019). Evolutionary mechanism leading to the multi-cagA genotype in Helicobacter pylori. Sci. Rep. 9:11203.
  100. Suerbaum, S., and Josenhans, C. (2007). Helicobacter pylori evolution and phenotypic diversification in a changing host. Nat. Rev. Microbiol. 5, 441-452. doi: 10.1038/nrmicro1658
  101. Suzuki, M., Mimuro, H., Suzuki, T., Park, M., Yamamoto, T., and Sasakawa, C. (2005). Interaction of CagA with Crk plays an important role in Helicobacter pylori-induced loss of gastric epithelial cell adhesion. J. Exp. Med. 202, 1235- 1247. doi: 10.1084/jem.20051027
  102. Tacconelli, E., Carrara, E., Savoldi, A., Harbarth, S., Mendelson, M., Monnet, D. L., et al. (2018). Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect. Dis. 18, 318-327.
  103. Tegtmeyer, N., Neddermann, M., Asche, C. I., and Backert, S. (2017a). Subversion of host kinases: a key network in cellular signaling hijacked by Helicobacter pylori CagA. Mol. Microbiol. 105, 358-372. doi: 10.1111/mmi.13707
  104. Tegtmeyer, N., Wessler, S., Necchi, V., Rohde, M., Harrer, A., Rau, T. T., et al. (2017b). Helicobacter pylori employs a unique basolateral type IV secretion mechanism for CagA delivery. Cell Host Microbe 22, 552-560.e5. doi: 10.1016/ j.chom.2017.09.005
  105. Tegtmeyer, N., Rivas Traverso, F., Rohde, M., Oyarzabal, O. A., Lehn, N., Schneider-Brachert, W., et al. (2013). Electron microscopic, genetic and protein expression analyses of Helicobacter acinonychis strains from a Bengal tiger. PLoS One 8:e71220. doi: 10.1371/journal.pone.0071220
  106. Tegtmeyer, N., Wittelsberger, R., Hartig, R., Wessler, S., Martinez-Quiles, N., and Backert, S. (2011). Serine phosphorylation of cortactin controls focal adhesion kinase activity and cell scattering induced by Helicobacter pylori. Cell Host Microbe 9, 520-531. doi: 10.1016/j.chom.2011.05.007
  107. Tenguria, S., Ansari, S. A., Khan, N., Ranjan, A., Devi, S., Tegtmeyer, N., et al. (2014). Helicobacter pylori cell translocating kinase (CtkA/JHP0940) is pro- apoptotic in mouse macrophages and acts as auto-phosphorylating tyrosine kinase. Int. J. Med. Microbiol. 304, 1066-1076. doi: 10.1016/j.ijmm.2014.07.017
  108. Tomb, J. F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., et al. (1997). The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388, 539-547.
  109. Uchiyama, J., Takeuchi, H., Kato, S., Takemura-Uchiyama, I., Ujihara, T., Daibata, M., et al. (2012). Complete genome sequences of two Helicobacter pylori bacteriophages isolated from Japanese patients. J. Virol. 86, 11400-11401. doi: 10.1128/jvi.01767-12
  110. Vale, F. F., and Lehours, P. (2018). Relating phage genomes to Helicobacter pylori population structure: general steps using whole-genome sequencing data. Int. J. Mol. Sci. 19:1831. doi: 10.3390/ijms19071831
  111. Varga, M. G., Shaffer, C. L., Sierra, J. C., Suarez, G., Piazuelo, M. B., Whitaker, M. E., et al. (2016). Pathogenic Helicobacter pylori strains translocate DNA and activate TLR9 via the cancer-associated cag type IV secretion system. Oncogene 35, 6262-6269. doi: 10.1038/onc.2016.158
  112. Waskito, L. A., and Yamaoka, Y. (2019). The story of Helicobacter pylori: depicting human migrations from the phylogeography. Adv. Exp. Med. Biol. 1149, 1-16. doi: 10.1007/5584_2019_356
  113. Waskito, L. A., Yih-Wu, J., and Yamaoka, Y. (2018). The role of integrating conjugative elements in Helicobacter pylori: a review. J. Biomed. Sci. 25:86. doi: 10.1186/s12929-018-0489-2
  114. Weiss, E., Spicher, C., Haas, R., and Fischer, W. (2019). Excision and transfer of an integrating and conjugative element in a bacterial species with high recombination efficiency. Sci. Rep. 9:8915. doi: 10.1038/s41598-019-45429-z
  115. Wozniak, R. A., and Waldor, M. K. (2010). Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow. Nat. Rev. Microbiol. 8, 552-563. doi: 10.1038/nrmicro2382
  116. Yamaoka, Y. (2008). Roles of the plasticity regions of Helicobacter pylori in gastroduodenal pathogenesis. J. Med. Microbiol. 57, 545-553. doi: 10.1099/ jmm.0.2008/000570-0
  117. Yeh, Y. C., Lin, T. L., Chang, K. C., and Wang, J. T. (2003). Characterization of a ComE3 homologue essential for DNA transformation in Helicobacter pylori. Infect. Immun. 71, 5427-5431. doi: 10.1128/iai.71.9.5427-5431. 2003
  118. Zhang, X. S., Tegtmeyer, N., Traube, L., Jindal, S., Perez-Perez, G., Sticht, H., et al. (2015). A specific A/T polymorphism in Western tyrosine phosphorylation B-motifs regulates Helicobacter pylori CagA epithelial cell interactions. PLoS Pathog. 11:e1004621. doi: 10.1371/journal.ppat.1004621
  119. Zhao, Q., Busch, B., Jiménez-Soto, L. F., Ishikawa-Ankerhold, H., Massberg, S., Terradot, L., et al. (2018). Integrin but not CEACAM receptors are dispensable for Helicobacter pylori CagA translocation. PLoS Pathog. 14:e1007359. doi: 10. 1371/journal.ppat.1007359
  120. Zimmermann, S., Pfannkuch, L., Al-Zeer, M. A., Bartfeld, S., Koch, M., Liu, J., et al. (2017). ALPK1-and TIFA-dependent innate immune response triggered by the Helicobacter pylori type IV secretion system. Cell Rep. 20, 2384-2395. doi: 10.1016/j.celrep.2017.08.039

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