1887

Microbiology Society logo

Volume 169, Issue 4

ST11 (O157:H7) does not encode a functional AcrF efflux pump Open Access

This article is part of the Antimicrobial Efflux collection

Abstract

is a facultative anaerobe found in a wide range of environments. Commonly described as the laboratory workhorse, is one of the best characterized bacterial species to date, however much of our understanding comes from studies involving the laboratory strain K-12. Resistance-nodulation-division efflux pumps are found in Gram-negative bacteria and can export a diverse range of substrates, including antibiotics. K-12 has six RND pumps; AcrB, AcrD, AcrF, CusA, MdtBC and MdtF, and it is frequently reported that all strains possess these six pumps. However, this is not true of ST11, a lineage of , which is primarily composed of the highly virulent important human pathogen, O157:H7. Here we show that is absent from the pangenome of ST11 and that this lineage of has a highly conserved insertion within the gene, which when translated encodes 13 amino acids and two stop codons. This insertion was found to be present in 97.59 % of 1787 ST11 genome assemblies. Non-function of AcrF in ST11 was confirmed in the laboratory as complementation with from ST11 was unable to restore AcrF function in K-12 substr. MG1655 Δ Δ. This shows that the complement of RND efflux pumps present in laboratory bacterial strains may not reflect the situation in virulent strains of bacterial pathogens.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): acrF , efflux , Escherichia coli , RND and ST11
Funding
This study was supported by the:
  • MRC (Award MR/N013913/1)
    • Principle Award Recipient: PaulineSiasat
  • BBSRC (Award BB/M01116X/1)
    • Principle Award Recipient: HannahL Pugh
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.001324
2023-04-19
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/169/4/mic001324.html?itemId=/content/journal/micro/10.1099/mic.0.001324&mimeType=html&fmt=ahah

References

  1. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V et al. The complete genome sequence of Escherichia coli K-12. Science 1997; 277:1453–1462 [View Article] [PubMed]
     [Google Scholar]
  2. Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001; 8:11–22 [View Article] [PubMed]
     [Google Scholar]
  3. Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 2013; 5:58–65 [View Article] [PubMed]
     [Google Scholar]
  4. Horesh G, Blackwell GA, Tonkin-Hill G, Corander J, Heinz E et al. A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Microb Genom 2021; 7:000499 [View Article] [PubMed]
     [Google Scholar]
  5. Dutta C, Paul S. Microbial lifestyle and genome signatures. CG 2012; 13:153–162 [View Article] [PubMed]
     [Google Scholar]
  6. Cummins EA, Hall RJ, Connor C, McInerney JO, McNally A. Pangenome evolution in Escherichia coli is sequence type, not phylogroup. bioRxiv 2022
     [Google Scholar]
  7. Nikaido H, Takatsuka Y. Mechanisms of RND multidrug efflux pumps. Biochim Biophys Acta 2009; 1794:769–781 [View Article] [PubMed]
     [Google Scholar]
  8. Koutsolioutsou A, Martins EA, White DG, Levy SB, Demple B. A soxRS-constitutive mutation contributing to antibiotic resistance in a clinical isolate of Salmonella enterica (Serovar typhimurium). Antimicrob Agents Chemother 2001; 45:38–43 [View Article] [PubMed]
     [Google Scholar]
  9. Koutsolioutsou A, Peña-Llopis S, Demple B. Constitutive soxR mutations contribute to multiple-antibiotic resistance in clinical Escherichia coli isolates. Antimicrob Agents Chemother 2005; 49:2746–2752 [View Article] [PubMed]
     [Google Scholar]
  10. Blair JMA, Bavro VN, Ricci V, Modi N, Cacciotto P et al. AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity. Proc Natl Acad Sci U S A 2015; 112:3511–3516 [View Article] [PubMed]
     [Google Scholar]
  11. Padilla E, Llobet E, Doménech-Sánchez A, Martínez-Martínez L, Bengoechea JA et al. Klebsiella pneumoniae AcrAB efflux pump contributes to antimicrobial resistance and virulence. Antimicrob Agents Chemother 2010; 54:177–183 [View Article] [PubMed]
     [Google Scholar]
  12. McNeil HE, Alav I, Torres RC, Rossiter AE, Laycock E et al. Identification of binding residues between periplasmic adapter protein (PAP) and RND efflux pumps explains PAP-pump promiscuity and roles in antimicrobial resistance. PLoS Pathog 2019; 15:e1008101 [View Article] [PubMed]
     [Google Scholar]
  13. Burse A, Weingart H, Ullrich MS. The phytoalexin-inducible multidrug efflux pump AcrAB contributes to virulence in the fire blight pathogen, Erwinia amylovora. Mol Plant Microbe Interact 2004; 17:43–54 [View Article] [PubMed]
     [Google Scholar]
  14. Pérez A, Poza M, Fernández A, Fernández M del C, Mallo S et al. Involvement of the AcrAB-TolC efflux pump in the resistance, fitness, and virulence of Enterobacter cloacae. Antimicrob Agents Chemother 2012; 56:2084–2090 [View Article] [PubMed]
     [Google Scholar]
  15. Nishino K, Yamaguchi A. Analysis of a complete library of putative drug transporter genes in Escherichia coli. J Bacteriol 2001; 183:5803–5812 [View Article] [PubMed]
     [Google Scholar]
  16. Rosenberg EY, Ma D, Nikaido H. AcrD of Escherichia coli is an aminoglycoside efflux pump. J Bacteriol 2000; 182:1754–1756 [View Article] [PubMed]
     [Google Scholar]
  17. Nishino K, Hayashi-Nishino M, Yamaguchi A. H-NS modulates multidrug resistance of Salmonella enterica serovar Typhimurium by repressing multidrug efflux genes acrEF. Antimicrob Agents Chemother 2009; 53:3541–3543 [View Article] [PubMed]
     [Google Scholar]
  18. Nishino K, Yamaguchi A. Role of histone-like protein H-NS in multidrug resistance of Escherichia coli. J Bacteriol 2004; 186:1423–1429 [View Article] [PubMed]
     [Google Scholar]
  19. Roe AJ, Yull H, Naylor SW, Woodward MJ, Smith DGE et al. Heterogeneous surface expression of EspA translocon filaments by Escherichia coli O157:H7 is controlled at the posttranscriptional level. Infect Immun 2003; 71:5900–5909 [View Article] [PubMed]
     [Google Scholar]
  20. Pianciola L, Rivas M. Genotypic features of clinical and bovine Escherichia coli O157 strains isolated in countries with different associated-disease incidences. Microorganisms 2018; 6:36 [View Article] [PubMed]
     [Google Scholar]
  21. Bruyand M, Mariani-Kurkdjian P, Gouali M, de Valk H, King LA et al. Hemolytic uremic syndrome due to Shiga toxin-producing Escherichia coli infection. Med Mal Infect 2018; 48:167–174 [View Article] [PubMed]
     [Google Scholar]
  22. Butt S, Jenkins C, Godbole G, Byrne L. The epidemiology of Shiga toxin-producing Escherichia coli serogroup O157 in England, 2009-2019. Epidemiol Infect 2022; 150:e52 [View Article] [PubMed]
     [Google Scholar]
  23. Adams NL, Byrne L, Smith GA, Elson R, Harris JP et al. Shiga toxin-producing Escherichia coli O157, England and Wales, 1983-2012. Emerg Infect Dis 2016; 22:590–597 [View Article] [PubMed]
     [Google Scholar]
  24. Connor CH, Zucoloto AZ, Yu I-L, Corander J, McDonald B et al. Multi-drug resistant E. coli displace commensal E. coli from the intestinal tract, a trait associated with elevated levels of genetic diversity in carbohydrate metabolism genes. Microbiology 2022; 2022 [View Article] [PubMed]
     [Google Scholar]
  25. Zhou Z, Alikhan NF, Mohamed K, Fan Y, Agama Study G et al. The enterobase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res 2020; 30:138–152
     [Google Scholar]
  26. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
     [Google Scholar]
  27. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  28. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  31. European Committee for Antimicrobial Susceptibility Testing of the European Society of Clinical M, Infectious D EUCAST definitive document E.DEF 3.1, June 2000: determination of minimum inhibitory concentrations (mics) of antibacterial agents by agar dilution. Clin Microbiol Infect 2000
     [Google Scholar]
  32. Leus IV, Adamiak J, Trinh AN, Smith RD, Smith L et al. Inactivation of AdeABC and AdeIJK efflux pumps elicits specific nonoverlapping transcriptional and phenotypic responses in Acinetobacter baumannii. Mol Microbiol 2020; 114:1049–1065 [View Article] [PubMed]
     [Google Scholar]
  33. Nowak J, Seifert H, Higgins PG. Prevalence of eight resistance-nodulation-division efflux pump genes in epidemiologically characterized Acinetobacter baumannii of worldwide origin. J Med Microbiol 2015; 64:630–635 [View Article] [PubMed]
     [Google Scholar]
  34. Darby EM, Bavro VN, Dunn S, McNally A, Blair JMA. RND pumps across the Acinetobacter genus; AdeIJK is the ancestral efflux system. bioRxiv 2022; 2022: [View Article]
     [Google Scholar]
  35. Naylor SW, Low JC, Besser TE, Mahajan A, Gunn GJ et al. Lymphoid follicle-dense mucosa at the terminal rectum is the principal site of colonization of enterohemorrhagic Escherichia coli O157:H7 in the bovine host. Infect Immun 2003; 71:1505–1512 [View Article] [PubMed]
     [Google Scholar]
  36. Sauder AB, Kendall MM. After the fact(or): posttranscriptional gene regulation in enterohemorrhagic Escherichia coli O157:H7. J Bacteriol 2018; 200:19 [View Article] [PubMed]
     [Google Scholar]
  37. Ma D, Cook DN, Alberti M, Pon NG, Nikaido H et al. Genes acrA and acrB encode a stress-induced efflux system of Escherichia coli. Mol Microbiol 1995; 16:45–55 [View Article] [PubMed]
     [Google Scholar]
  38. Hirakawa H, Inazumi Y, Masaki T, Hirata T, Yamaguchi A. Indole induces the expression of multidrug exporter genes in Escherichia coli. Mol Microbiol 2005; 55:1113–1126 [View Article] [PubMed]
     [Google Scholar]
  39. Teelucksingh T, Thompson LK, Cox G. The Evolutionary conservation of Escherichia coli drug efflux pumps supports physiological functions. J Bacteriol 2020; 202:22 [View Article] [PubMed]
     [Google Scholar]
  40. Jerse AE, Simms AN, Crow ET, Snyder LA et al. A gonococcal efflux pump system enhances bacterial survival in A female mouse model of genital tract infection. Infect Immun 2003; 71:5576–5582 [View Article] [PubMed]
     [Google Scholar]
  41. Bina XR, Howard MF, Taylor-Mulneix DL, Ante VM, Kunkle DE et al. The Vibrio cholerae RND efflux systems impact virulence factor production and adaptive responses via periplasmic sensor proteins. PLoS Pathog 2018; 14:e1006804 [View Article] [PubMed]
     [Google Scholar]
  42. Nishino K, Latifi T, Groisman EA. Virulence and drug resistance roles of multidrug efflux systems of Salmonella enterica serovar Typhimurium. Mol Microbiol 2006; 59:126–141 [View Article] [PubMed]
     [Google Scholar]
  43. Wang-Kan X, Blair JMA, Chirullo B, Betts J, La Ragione RM et al. Lack of AcrB efflux function confers loss of virulence on Salmonella enterica serovar Typhimurium. mBio 2017; 8:e00968-17 [View Article] [PubMed]
     [Google Scholar]
  44. Blair JMA, Smith HE, Ricci V, Lawler AJ, Thompson LJ et al. Expression of homologous RND efflux pump genes is dependent upon AcrB expression: implications for efflux and virulence inhibitor design. J Antimicrob Chemother 2015; 70:424–431 [View Article] [PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.001324
Loading
E. coli ST11 (O157:H7) does not encode a functional AcrF efflux pump
Microbiology 169, 001324 (2023); https://doi.org/10.1099/mic.0.001324
/content/journal/micro/10.1099/mic.0.001324
/content/journal/micro/10.1099/mic.0.001324
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error