Skip to content
1887

Journal of Medical Microbiology logo Journal of Medical Microbiology

Volume 75, Issue 4

From colonization to invasion: genomic and phenotypic comparison of faecal and bloodstream isolates from the same patients Open Access

Abstract

Gram-negative bloodstream infections (GNBSIs) carry a significant global health burden. and are the two most common causes of healthcare-associated GNBSI, which may arise from gastrointestinal tract (GIT) colonization.

We do not fully understand how GNBSIs arise from GIT colonization.

To understand and genomic and phenotypic adaptations that underpin transition from GIT colonization to invasive bloodstream infection.

This study identified ‘linked’ faecal and blood isolates from children with healthcare-associated GNBSI caused by and . Linked pairs were compared for antimicrobial resistance and biofilm formation and underwent comparative genomic analysis via whole-genome sequencing, comparative average nucleotide identity and core genome single nucleotide polymorphism (SNP) analysis.

Five isolate pairs (three , two ) showed high relatedness, supporting the GIT origin of bloodstream infection. Isolates within pairs had identical virulence genes, whereas phenotypic assays revealed changes in antimicrobial susceptibility, with one pair undergoing changes in resistance gene profiles and increased biofilm formation in four out of five isolates.

This study provides insight into within-host evolution from gastrointestinal colonization to bloodstream invasion in Gram-negative pathogens. Convergence on metabolic adaptation and biofilm formation suggests that these traits may be advantageous in healthcare-associated GNBSI. Further studies involving larger cohorts alongside functional validation of mutations are needed to better understand GNBSI pathogenesis.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance (AMR) , biofilm , bloodstream infection , Escherichia coli , Klebsiella and plasmids
Funding
This study was supported by the:
  • Medical Research Council (Award MR/W030578/1)
    • Principal Award Recipient: AdamP Roberts
  • UK Research and Innovation (Award SIPF 36348)
    • Principal Award Recipient: AdamP Roberts
  • National Institute for Health and Care Research (Award NIHR200632)
    • Principal Award Recipient: AdamP Roberts
  • Medical Research Council (Award MR/W007037/1)
    • Principal Award Recipient: EllieAllman
  • Medical Research Council (Award MR/N013514/1)
    • Principal Award Recipient: RalfhPulmones
© 2026 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/jmm/10.1099/jmm.0.002147
2026-04-08
2026-04-14

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/jmm/75/4/jmm002147.html?itemId=/content/journal/jmm/10.1099/jmm.0.002147&mimeType=html&fmt=ahah

References

  1. Hallmaier-Wacker LK, Andrews A, Nsonwu O, Demirjian A, Hope RJ et al. Incidence and aetiology of infant gram-negative bacteraemia and meningitis: systematic review and meta-analysis. Arch Dis Child 2022; 107:988–994 [View Article] [PubMed]
     [Google Scholar]
  2. Rudd KE, Johnson SC, Agesa KM, Shackelford KA, Tsoi D et al. Global, regional, and national sepsis incidence and mortality, 1990-2017: analysis for the global burden of disease study. Lancet 2020; 395:200–211 [View Article] [PubMed]
     [Google Scholar]
  3. Wagner M, Bonhoeffer J, Erb TO, Glanzmann R, Häcker FM et al. Prospective study on central venous line associated bloodstream infections. Arch Dis Child 2011; 96:827–831 [View Article] [PubMed]
     [Google Scholar]
  4. Kern WV, Rieg S. Burden of bacterial bloodstream infection-a brief update on epidemiology and significance of multidrug-resistant pathogens. Clin Microbiol Infect 2020; 26:151–157 [View Article] [PubMed]
     [Google Scholar]
  5. Lipworth S, Vihta K-D, Davies T, Wright S, Tabirao M et al. Molecular epidemiology and antimicrobial resistance phenotype of paediatric bloodstream infections caused by gram-negative bacteria. Commun Med 2022; 2:101 [View Article] [PubMed]
     [Google Scholar]
  6. WHO bacterial priority pathogens list, 2024: Bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance. Geneva: World Health Organization; 2024
  7. Holmes CL, Anderson MT, Mobley HLT, Bachman MA. Pathogenesis of gram-negative bacteremia. Clin Microbiol Rev 2021; 34:e00234-20 [View Article] [PubMed]
     [Google Scholar]
  8. Jiménez-Rojas V, Villanueva-García D, Miranda-Vega AL, Aldana-Vergara R, Aguilar-Rodea P et al. Gut colonization and subsequent infection of neonates caused by extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae. Front Cell Infect Microbiol 2023; 13:1322874 [View Article] [PubMed]
     [Google Scholar]
  9. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 2011; 17:10 [View Article]
     [Google Scholar]
  10. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  11. Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL et al. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 2021; 12:4188 [View Article] [PubMed]
     [Google Scholar]
  12. Lam MMC, Wick RR, Judd LM, Holt KE, Wyres KL. Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex. Microb Genom 2022; 8:000800 [View Article] [PubMed]
     [Google Scholar]
  13. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  14. R Core TeamR: a language and environment for statistical computing Vienna, Austria: R Foundation for Statistical Computing; 2021
  15. Florensa AF, Kaas RS, Clausen PTLC, Aytan-Aktug D, Aarestrup FM. ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes. Microb Genom 2022; 8:000748 [View Article] [PubMed]
     [Google Scholar]
  16. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and Plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  17. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
     [Google Scholar]
  18. Deatherage DE, Barrick JE. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol Biol 2014; 1151:165–188 [View Article] [PubMed]
     [Google Scholar]
  19. European Committee on Antimicrobial Susceptibility Testing (EUCAST) Disk diffusion manual, version 12.0; 2024
  20. European Committee on Antimicrobial Susceptibility Testing (EUCAST) Breakpoint tables for interpretation of mics and zone diameters, version 14.0; 2024
  21. European Committee on Antimicrobial Susceptibility Testing (EUCAST) Broth microdilution - EUCAST reading guide, version 5.0; 2024
  22. Merritt JH, Kadouri DE, O’Toole GA. Growing and analyzing static biofilms. Curr Protoc Microbiol 2005; Chapter 1:Unit 1B.1 [View Article] [PubMed]
     [Google Scholar]
  23. O’Toole GA. Microtiter dish biofilm formation assay. JoVE 2011; 2011:e2437 [View Article]
     [Google Scholar]
  24. Schwartz DJ, Shalon N, Wardenburg K, DeVeaux A, Wallace MA et al. Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit. Sci Transl Med 2023; 15:eadg5562 [View Article] [PubMed]
     [Google Scholar]
  25. Carl MA, Ndao IM, Springman AC, Manning SD, Johnson JR et al. Sepsis from the gut: the enteric habitat of bacteria that cause late-onset neonatal bloodstream infections. Clin Infect Dis 2014; 58:1211–1218 [View Article] [PubMed]
     [Google Scholar]
  26. Rodriguez-R LM, Conrad RE, Viver T, Feistel DJ, Lindner BG et al. An ANI gap within bacterial species that advances the definitions of intra-species units. mBio 2024; 15:e02696–23 [View Article]
     [Google Scholar]
  27. Vornhagen J, Roberts EK, Unverdorben L, Mason S, Patel A et al. Combined comparative genomics and clinical modeling reveals plasmid-encoded genes are independently associated with Klebsiella infection. Nat Commun 2022; 13:4459 [View Article] [PubMed]
     [Google Scholar]
  28. Ludden C, Coll F, Gouliouris T, Restif O, Blane B et al. Defining nosocomial transmission of Escherichia coli and antimicrobial resistance genes: a genomic surveillance study. Lancet Microbe 2021; 2:e472–e480 [View Article] [PubMed]
     [Google Scholar]
  29. Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR et al. Gastrointestinal carriage is a major reservoir of Klebsiella pneumoniae infection in intensive care patients. Clin Infect Dis 2017; 65:208–215 [View Article] [PubMed]
     [Google Scholar]
  30. Thänert R, Choi J, Reske KA, Hink T, Thänert A et al. Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements. Cell Host Microbe 2022; 30:1034–1047 [View Article]
     [Google Scholar]
  31. Rebelo AR, Bortolaia V, Leekitcharoenphon P, Hansen DS, Nielsen HL et al. One day in Denmark: whole-genome sequence-based analysis of Escherichia coli isolates from clinical settings. J Antimicrob Chemother 2025; 80:1011–1021 [View Article] [PubMed]
     [Google Scholar]
  32. Bush SJ, Foster D, Eyre DW, Clark EL, De Maio N et al. Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines. Gigascience 2020; 9:giaa007 [View Article] [PubMed]
     [Google Scholar]
  33. Jamin C, De Koster S, van Koeveringe S, De Coninck D, Mensaert K et al. Harmonization of whole-genome sequencing for outbreak surveillance of Enterobacteriaceae and Enterococci. Microb Genom 2021; 7:000567 [View Article] [PubMed]
     [Google Scholar]
  34. Wylie KM, Wylie TN, Minx PJ, Rosen DA. Whole-genome sequencing of Klebsiella pneumoniae isolates to track strain progression in a single patient with recurrent urinary tract infection. Front Cell Infect Microbiol 2019; 9:14 [View Article] [PubMed]
     [Google Scholar]
  35. Okusu H, Ma D, Nikaido H. AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants. J Bacteriol 1996; 178:306–308 [View Article] [PubMed]
     [Google Scholar]
  36. 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]
  37. Lv F, Cai J, He Q, Wang W, Luo Y et al. Overexpression of efflux pumps mediate pan resistance of Klebsiella pneumoniae sequence type 11. Microb Drug Resist 2021; 27:1405–1411 [View Article] [PubMed]
     [Google Scholar]
  38. Chowdhury N, Suhani S, Purkaystha A, Begum MK, Raihan T et al. Identification of AcrAB-TolC efflux pump genes and detection of mutation in efflux repressor AcrR from omeprazole responsive multidrug-resistant Escherichia coli isolates causing urinary tract infections. Microbiol Insights 2019; 12:1178636119889629 [View Article] [PubMed]
     [Google Scholar]
  39. Alav I, Sutton JM, Rahman KM. Role of bacterial efflux pumps in biofilm formation. J Antimicrob Chemother 2018; 73:2003–2020 [View Article] [PubMed]
     [Google Scholar]
  40. Tang M, Wei X, Wan X, Ding Z, Ding Y et al. The role and relationship with efflux pump of biofilm formation in Klebsiella pneumoniae. Microb Pathog 2020; 147:104244 [View Article] [PubMed]
     [Google Scholar]
  41. Vuotto C, Longo F, Pascolini C, Donelli G, Balice MP et al. Biofilm formation and antibiotic resistance in Klebsiella pneumoniae urinary strains. J Appl Microbiol 2017; 123:1003–1018 [View Article] [PubMed]
     [Google Scholar]
  42. Hennequin C, Aumeran C, Robin F, Traore O, Forestier C. Antibiotic resistance and plasmid transfer capacity in biofilm formed with a CTX-M-15-producing Klebsiella pneumoniae isolate. J Antimicrob Chemother 2012; 67:2123–2130 [View Article] [PubMed]
     [Google Scholar]
  43. Reza A, Sutton JM, Rahman KM. Effectiveness of efflux pump inhibitors as biofilm disruptors and resistance breakers in gram-negative (ESKAPEE) bacteria. Antibiotics 2019; 8:229 [View Article] [PubMed]
     [Google Scholar]
  44. Nielsen KL, Stegger M, Godfrey PA, Feldgarden M, Andersen PS et al. Adaptation of Escherichia coli traversing from the faecal environment to the urinary tract. Int J Med Microbiol 2016; 306:595–603 [View Article] [PubMed]
     [Google Scholar]
  45. Prieto A, Urcola I, Blanco J, Dahbi G, Muniesa M et al. Tracking bacterial virulence: global modulators as indicators. Sci Rep 2016; 6:25973 [View Article] [PubMed]
     [Google Scholar]
  46. Barrios AFG, Zuo R, Ren D, Wood TK. Hha, YbaJ, and OmpA regulate Escherichia coli K12 biofilm formation and conjugation plasmids abolish motility. Biotechnol Bioeng 2006; 93:188–200 [View Article] [PubMed]
     [Google Scholar]
  47. Bandeira M, Borges V, Gomes JP, Duarte A, Jordao L. Insights on Klebsiella pneumoniae biofilms assembled on different surfaces using phenotypic and genotypic approaches. Microorganisms 2017; 5:16 [View Article] [PubMed]
     [Google Scholar]
  48. Krall LJ, Klein S, Boutin S, Wu CC, Sähr A et al. Invasiveness of Escherichia coli is associated with an IncFII plasmid. Pathogens 2021; 10:1645 [View Article] [PubMed]
     [Google Scholar]
  49. Ueda T, Takahashi H, Uyar E, Ishikawa S, Ogasawara N et al. Functions of the Hha and YdgT proteins in transcriptional silencing by the nucleoid proteins, H-NS and StpA, in Escherichia coli. DNA Research 2013; 20:263–271 [View Article]
     [Google Scholar]
  50. Sharma VK, Bearson BL. Hha controls Escherichia coli O157:H7 biofilm formation by differential regulation of global transcriptional regulators FlhDC and CsgD. Appl Environ Microbiol 2013; 79:2384–2396 [View Article] [PubMed]
     [Google Scholar]
  51. Fang C-T, Yi W-C, Shun C-T, Tsai S-F. DNA adenine methylation modulates pathogenicity of Klebsiella pneumoniae genotype K1. J Microbiol Immunol Infect 2017; 50:471–477 [View Article]
     [Google Scholar]
  52. Desvaux M, Dalmasso G, Beyrouthy R, Barnich N, Delmas J et al. Pathogenicity factors of genomic islands in intestinal and extraintestinal Escherichia coli. Front Microbiol 2020; 11:2065 [View Article] [PubMed]
     [Google Scholar]
  53. Xu W-Y, Li Y-J, Fan C. Different loci and mRNA copy number of the increased serum survival gene of Escherichia coli. Can J Microbiol 2018; 64:147–154 [View Article] [PubMed]
     [Google Scholar]
  54. Chen J-H, Siu LK, Fung C-P, Lin J-C, Yeh K-M et al. Contribution of outer membrane protein K36 to antimicrobial resistance and virulence in Klebsiella pneumoniae. J Antimicrob Chemother 2010; 65:986–990 [View Article] [PubMed]
     [Google Scholar]
  55. Garcia EC, Brumbaugh AR, Mobley HLT. Redundancy and specificity of Escherichia coli iron acquisition systems during urinary tract infection. Infect Immun 2011; 79:1225–1235 [View Article] [PubMed]
     [Google Scholar]
  56. Mann R, Mediati DG, Duggin IG, Harry EJ, Bottomley AL. Metabolic adaptations of uropathogenic E. coli in the urinary tract. Front Cell Infect Microbiol 2017; 7:241 [View Article] [PubMed]
     [Google Scholar]
  57. Krawczyk B, Śledzińska A, Szemiako K, Samet A, Nowicki B et al. Characterisation of Escherichia coli isolates from the blood of haematological adult patients with bacteraemia: translocation from gut to blood requires the cooperation of multiple virulence factors. Eur J Clin Microbiol Infect Dis 2015; 34:1135–1143 [View Article] [PubMed]
     [Google Scholar]
/content/journal/jmm/10.1099/jmm.0.002147
Loading
From colonization to invasion: genomic and phenotypic comparison of faecal and bloodstream isolates from the same patients
J. Med. Microbiol. 75, 002147 (2026); https://doi.org/10.1099/jmm.0.002147
/content/journal/jmm/10.1099/jmm.0.002147
/content/journal/jmm/10.1099/jmm.0.002147
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

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