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Volume 11, Issue 2

Phenotypic and genetic heterogeneity of in the course of an animal chronic infection Open Access

Abstract

is a nosocomial pathogen associated with various infections, including urinary tract infections (UTIs). In the course of an infection, is known to rapidly become resistant to antibiotic therapy, but much less is known about possible adaptation without antibiotic pressure. Through a retrospective study, we investigated within-host genetic diversity during a subclinical 5-year UTI in an animal–patient after withdrawal of colistin treatment. We conducted whole-genome sequencing and phenotypic assays on 17 clonally related isolates from the Sequence Type 25 lineage. Phylogenomic analysis revealed their proximity with animal and human strains from the same country suggesting zoonotic transmission (France). In this case study, the clonally related strains presented variations in genome sizes and nucleotide sequences. Over the course of the infection, underwent genome reduction through insertion sequence (IS) recombination, phage excision or plasmid curing. Alongside this global genome reduction, we observed an expansion of IS, initially located on the endogenous large plasmid. Genetic variations were mainly located in biofilm formation and metabolism genes. We observed repeated variations affecting three biofilm genes and two adhesion operons associated with weak biofilm-forming capacity. Conversely, only two metabolic genes were recurrently affected, and phenotypic assays indicated a rather stable metabolism profile between the isolates suggesting minor adaptations to its host. Lastly, an overall decreased antibiotic resistance – expected in the absence of antibiotic treatment – contrasted with a conserved colistin resistance due to a mutation among the isolates.

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  • Accepted:
  • Published Online:
Keyword(s): Acinetobacter baumannii , host infection , mobile genetic elements , multidrug resistance and whole-genome sequencing
Funding
This study was supported by the:
  • VetAgro Sup (Award PhD Funding)
    • Principal Award Recipient: Maria-HalimaLaaberki
  • Fondation pour la Recherche Médicale (FR) (Award PhD funding)
    • Principal Award Recipient: AlexandreChassard
  • Agence Nationale de la Recherche (FR) (Award ANR-11-IDEX-0007)
    • Principal Award Recipient: XavierCharpentier
  • Agence Nationale de la Recherche (FR) (Award ANR-11-LABX-0048)
    • Principal Award Recipient: XavierCharpentier
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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References

  1. Nocera FP, Attili A-R, De Martino L. Acinetobacter baumannii: Its clinical significance in human and veterinary medicine. Pathogens 2021; 10:127 [View Article]
     [Google Scholar]
  2. van der Kolk JH, Endimiani A, Graubner C, Gerber V, Perreten V. Acinetobacter in veterinary medicine, with an emphasis on Acinetobacter baumannii. J Glob Antimicrob Resist 2019; 16:59–71 [View Article] [PubMed]
     [Google Scholar]
  3. Sun R-X, Song P, Walline J, Wang H, Xu Y-C et al. Morbidity and mortality risk factors in emergency department patients with Acinetobacter baumannii bacteremia. World J Emerg Med 2020; 11:164–168 [View Article] [PubMed]
     [Google Scholar]
  4. Iacono M, Villa L, Fortini D, Bordoni R, Imperi F et al. Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob Agents Chemother 2008; 52:2616–2625 [View Article] [PubMed]
     [Google Scholar]
  5. Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis 2018; 18:318–327 [View Article]
     [Google Scholar]
  6. Lupo A, Châtre P, Ponsin C, Saras E, Boulouis H-J et al. Clonal spread of Acinetobacter baumannii sequence type 25 carrying blaoxa-23 in companion animals in france. Antimicrob Agents Chemother 2016; 61:01881–16 [View Article]
     [Google Scholar]
  7. Maragakis LL, Perl TM. Acinetobacter baumannii: epidemiology, antimicrobial resistance, and treatment options. Clin Infect Dis 2008; 46:1254–1263 [View Article] [PubMed]
     [Google Scholar]
  8. Bordenave S, Goñi-Urriza MS, Caumette P, Duran R. Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat. Appl Environ Microbiol 2007; 73:6089–6097 [View Article]
     [Google Scholar]
  9. Sarma PM, Bhattacharya D, Krishnan S, Lal B. Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons. Can J Microbiol 2004; 50:405–414 [View Article] [PubMed]
     [Google Scholar]
  10. Eveillard M, Kempf M, Belmonte O, Pailhoriès H, Joly-Guillou M-L. Reservoirs of Acinetobacter baumannii outside the hospital and potential involvement in emerging human community-acquired infections. Int J Infect Dis 2013; 17:e802–e805 [View Article]
     [Google Scholar]
  11. Wilharm G, Skiebe E, Łopińska A, Higgins PG, Weber K et al. On the ecology of Acinetobacter baumannii – jet stream rider and opportunist by nature. Microbiology 2024 [View Article]
     [Google Scholar]
  12. Sykes EME, Mateo-Estrada V, Engelberg R, Muzaleva A, Zhanel G et al. Phylogenomic and phenotypic analyses highlight the diversity of antibiotic resistance and virulence in both human and non-human Acinetobacter baumannii. mSphere 2024; 9:e0074123 [View Article] [PubMed]
     [Google Scholar]
  13. Tobin LA, Jarocki VM, Kenyon J, Drigo B, Donner E et al. Genomic analysis of diverse environmental Acinetobacter isolates identifies plasmids, antibiotic resistance genes, and capsular polysaccharides shared with clinical strains. Appl Environ Microbiol 2024; 90:e0165423 [View Article] [PubMed]
     [Google Scholar]
  14. Mateo-Estrada V, Tyrrell C, Evans BA, Aguilar-Vera A, Drissner D et al. Acinetobacter baumannii from grass: novel but non-resistant clones. Microb Genom 2023; 9:mgen001054 [View Article] [PubMed]
     [Google Scholar]
  15. Hawkey J, Ascher DB, Judd LM, Wick RR, Kostoulias X et al. Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. Microb Genom 2018; 4:e000165 [View Article] [PubMed]
     [Google Scholar]
  16. Kim M, Park J, Park W. Genomic and phenotypic analyses of multidrug-resistant Acinetobacter baumannii NCCP 16007 isolated from a patient with a urinary tract infection. Virulence 2021; 12:150–164 [View Article] [PubMed]
     [Google Scholar]
  17. Zhang J, Xie J, Li H, Wang Z, Yin Y et al. Genomic and phenotypic evolution of tigecycline-resistant Acinetobacter baumannii in critically ill patients. Microbiol Spectr 2022; 10:e0159321 [View Article]
     [Google Scholar]
  18. Wright MS, Iovleva A, Jacobs MR, Bonomo RA, Adams MD. Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment. Genome Med 2016; 8:26
     [Google Scholar]
  19. Li H, Zhang J, Wang Z, Yin Y, Gao H et al. Evolution of Acinetobacter baumannii in clinical bacteremia patients. IDR 2021; Volume 14:3553–3562 [View Article]
     [Google Scholar]
  20. Penesyan A, Nagy SS, Kjelleberg S, Gillings MR, Paulsen IT. Rapid microevolution of biofilm cells in response to antibiotics. NPJ Biofilms Microbiomes 2019; 5:34 [View Article] [PubMed]
     [Google Scholar]
  21. Lila ASA, Rajab AAH, Abdallah MH, Rizvi SMD, Moin A et al. Biofilm lifestyle in recurrent urinary tract infections. Life 2023; 13:148 [View Article]
     [Google Scholar]
  22. Di Venanzio G, Moon KH, Weber BS, Lopez J, Ly PM et al. Multidrug-resistant plasmids repress chromosomally encoded T6SS to enable their dissemination. Proc Natl Acad Sci U S A 2019; 116:1378–1383 [View Article] [PubMed]
     [Google Scholar]
  23. Di Venanzio G, Flores-Mireles AL, Calix JJ, Haurat MF, Scott NE et al. Urinary tract colonization is enhanced by a plasmid that regulates uropathogenic Acinetobacter baumannii chromosomal genes. Nat Commun 2019; 10:2763 [View Article] [PubMed]
     [Google Scholar]
  24. Benomar S, Di Venanzio G, Feldman MF. Plasmid-encoded H-NS controls extracellular matrix composition in a modern Acinetobacter baumannii urinary isolate. J Bacteriol 2021; 203: [View Article]
     [Google Scholar]
  25. Kopecny L, Palm CA, Drobatz KJ, Balsa IM, Culp WTN. Risk factors for positive urine cultures in cats with subcutaneous ureteral bypass and ureteral stents (2010-2016). J Vet Intern Med 2019; 33:178–183 [View Article] [PubMed]
     [Google Scholar]
  26. De Coster W, Rademakers R. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics 2023; 39:btad311 [View Article] [PubMed]
     [Google Scholar]
  27. Andrew S. Babraham bioinformatics - FastQC: a quality control tool for high throughput sequence data; 2010 https://www.bioinformatics.babraham.ac.uk/projects/fastqc
  28. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
     [Google Scholar]
  30. Gallagher LA, Ramage E, Weiss EJ, Radey M, Hayden HS et al. Resources for genetic and genomic analysis of emerging pathogen Acinetobacter baumannii. J Bacteriol 2015; 197:2027–2035 [View Article] [PubMed]
     [Google Scholar]
  31. Hamidian M, Ambrose SJ, Hall RM. A large conjugative Acinetobacter baumannii plasmid carrying the sul2 sulphonamide and strAB streptomycin resistance genes. Plasmid 2016; 87–88:43–50 [View Article]
     [Google Scholar]
  32. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: bigsdb software, the pubmlst.org website and their applications. Wellcome Open Res 2018; 3:124
     [Google Scholar]
  33. Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S. The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One 2010; 5:e10034 [View Article]
     [Google Scholar]
  34. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
     [Google Scholar]
  35. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [View Article]
     [Google Scholar]
  36. Florensa AF, Kaas RS, Clausen P, 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]
  37. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–6 [View Article] [PubMed]
     [Google Scholar]
  38. Godeux A-S, Svedholm E, Barreto S, Potron A, Venner S et al. Interbacterial transfer of carbapenem resistance and large antibiotic resistance islands by natural transformation in pathogenic Acinetobacter. mBio 2022; 13:e02631–21 [View Article]
     [Google Scholar]
  39. Derelle R, von Wachsmann J, Mäklin T, Hellewell J, Russell T et al. Seamless, rapid and accurate analyses of outbreak genomic data using Split K-mer Analysis (SKA. Bioinformatics 2024 [View Article]
     [Google Scholar]
  40. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 2015; 43:e15 [View Article] [PubMed]
     [Google Scholar]
  41. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article]
     [Google Scholar]
  42. Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 2024; 52:W78–W82 [View Article]
     [Google Scholar]
  43. Moustafa AM, Planet PJ. WhatsGNU: a tool for identifying proteomic novelty. Genome Biol 2020; 21:58 [View Article] [PubMed]
     [Google Scholar]
  44. Yu G. Using ggtree to visualize data on tree-like structures. Curr Protoc Bioinform 2020; 69:e96 [View Article] [PubMed]
     [Google Scholar]
  45. Seemann T. Snippy: fast bacterial variant calling from NGS reads; 2015
  46. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [View Article] [PubMed]
     [Google Scholar]
  47. Brown D, Cantón R, Dubreuil L, Gatermann S, Giske C et al. Widespread implementation of EUCAST breakpoints for antibacterial susceptibility testing in Europe. Euro Surveill 2015; 20:21008 [View Article]
     [Google Scholar]
  48. Tomaras AP, Dorsey CW, Edelmann RE, Actis LAY. Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system. Microbiology 2003; 149:3473–3484 [View Article] [PubMed]
     [Google Scholar]
  49. Repizo GD, Gagné S, Foucault-Grunenwald M-L, Borges V, Charpentier X et al. Differential Role of the T6SS in Acinetobacter baumannii Virulence. PLoS One 2015; 10:e0138265 [View Article] [PubMed]
     [Google Scholar]
  50. Hamidian M, Hall RM. The resistance gene complement of D4, a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate, resides in two genomic islands and a plasmid. J Antimicrob Chemother 2016; 71:1730–1732 [View Article]
     [Google Scholar]
  51. Lupo A, Valot B, Saras E, Drapeau A, Robert M et al. Multiple host colonization and differential expansion of multidrug-resistant ST25-acinetobacter baumannii clades. Sci Rep 2023; 13:21854
     [Google Scholar]
  52. Castillo-Ramírez S. Zoonotic Acinetobacter baumannii: the need for genomic epidemiology in a One Health context. Lancet Microbe 2022; 3:e895–e896 [View Article]
     [Google Scholar]
  53. Rafei R, Koong J, Osman M, Al Atrouni A, Hamze M et al. Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways. FEMS Microbes 2022; 3:xtac027 [View Article] [PubMed]
     [Google Scholar]
  54. Tamadonfar KO, Di Venanzio G, Pinkner JS, Dodson KW, Kalas V et al. Structure–function correlates of fibrinogen binding by Acinetobacter adhesins critical in catheter-associated urinary tract infections. Proc Natl Acad Sci USA 2023; 120: [View Article]
     [Google Scholar]
  55. Pakharukova N, Tuittila M, Paavilainen S, Malmi H, Parilova O et al. Structural basis for Acinetobacter baumannii biofilm formation. Proc Natl Acad Sci USA 2018; 115:5558–5563 [View Article] [PubMed]
     [Google Scholar]
  56. Choi AHK, Slamti L, Avci FY, Pier GB, Maira-Litrán T. The pgaABCD locus of Acinetobacter baumannii encodes the production of poly-beta-1-6-N-acetylglucosamine, which is critical for biofilm formation. J Bacteriol 2009; 191:5953–5963 [View Article] [PubMed]
     [Google Scholar]
  57. Loehfelm TW, Luke NR, Campagnari AA. Identification and characterization of an Acinetobacter baumannii biofilm-associated protein. J Bacteriol 2008; 190:1036–1044 [View Article] [PubMed]
     [Google Scholar]
  58. Sahu PK, Iyer PS, Barage SH, Sonawane KD, Chopade BA. Characterization of the algC gene expression pattern in the multidrug resistant Acinetobacter baumannii AIIMS 7 and correlation with biofilm development on abiotic surface. Sci World J 2014; 2014:1–14 [View Article]
     [Google Scholar]
  59. Kim Y, Xu W, Barrs V, Beatty J, Kenéz Á. In-depth characterisation of the urine metabolome in cats with and without urinary tract diseases. Metabolomics 2022; 18:19 [View Article] [PubMed]
     [Google Scholar]
  60. Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR et al. The human urine metabolome. PLoS One 2013; 8:e73076 [View Article] [PubMed]
     [Google Scholar]
  61. Jørgensen CM, Hammer K, Jensen PR, Martinussen J. Expression of the pyrG gene determines the pool sizes of CTP and dCTP in Lactococcus lactis. Eur J Biochem 2004; 271:2438–2445 [View Article] [PubMed]
     [Google Scholar]
  62. Cremin P, Kasim-Karakas S, Waterhouse AL. LC/ES-MS detection of hydroxycinnamates in human plasma and urine. J Agric Food Chem 2001; 49:1747–1750 [View Article] [PubMed]
     [Google Scholar]
  63. Alteri CJ, Smith SN, Mobley HLT. Fitness of Escherichia coli during urinary tract infection requires gluconeogenesis and the TCA Cycle. PLoS Pathog 2009; 5:e1000448 [View Article]
     [Google Scholar]
  64. EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) Scientific Opinion on the safety and efficacy of malic acid and a mixture of sodium and calcium malate when used as technological additives for all animal species. EFS2 2014; 12:3563 [View Article]
     [Google Scholar]
  65. Pournaras S, Poulou A, Dafopoulou K, Chabane YN, Kristo I et al. Growth retardation, reduced invasiveness, and impaired colistin-mediated cell death associated with colistin resistance development in Acinetobacter baumannii. Antimicrob Agents Chemother 2014; 58:828–832 [View Article] [PubMed]
     [Google Scholar]
  66. Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. The dynamics of molecular evolution over 60,000 generations. Nature 2017; 551:45–50 [View Article] [PubMed]
     [Google Scholar]
  67. Schneider D, Lenski RE. Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol 2004; 155:319–327 [View Article] [PubMed]
     [Google Scholar]
  68. Murray GGR, Charlesworth J, Miller EL, Casey MJ, Lloyd CT et al. Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence. Mol Biol Evol 2021; 38:1570–1579 [View Article] [PubMed]
     [Google Scholar]
  69. Sastre-Dominguez J, DelaFuente J, Toribio-Celestino L, Herencias C, Herrador-Gómez P et al. Plasmid-encoded insertion sequences promote rapid adaptation in clinical enterobacteria. Nat Ecol Evol 2024; 8:2097–2112 [View Article] [PubMed]
     [Google Scholar]
  70. Snitkin ES, Zelazny AM, Gupta J. NISC Comparative Sequencing Program Palmore TN et al. Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment. Genome Res 2013; 23:1155–1162 [View Article] [PubMed]
     [Google Scholar]
  71. Hevia A, Delgado S, Sánchez B, Margolles A. Molecular players involved in the interaction between beneficial bacteria and the immune system. Front Microbiol 2015; 6:1285 [View Article] [PubMed]
     [Google Scholar]
  72. Kalu M, Tan K, Algorri M, Jorth P, Wong-Beringer A. In-human multiyear evolution of carbapenem-resistant Klebsiella pneumoniae causing chronic colonization and intermittent urinary tract infections: a case study. mSphere 2022; 7:e0019022 [View Article] [PubMed]
     [Google Scholar]
  73. Chaguza C, Senghore M, Bojang E, Gladstone RA, Lo SW et al. Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation. Nat Commun 2020; 11:3442 [View Article] [PubMed]
     [Google Scholar]
  74. Gabrielaite M, Johansen HK, Molin S, Nielsen FC, Marvig RL. Gene loss and acquisition in lineages of Pseudomonas aeruginosa evolving in cystic fibrosis patient airways. mBio 2020; 11:e02359-20 [View Article] [PubMed]
     [Google Scholar]
  75. Barker CR, Painset A, Swift C, Jenkins C, Godbole G et al. Microevolution of Campylobacter jejuni during long-term infection in an immunocompromised host. Sci Rep 2020; 10:10109 [View Article] [PubMed]
     [Google Scholar]
  76. Ley SD, de Vos M, Van Rie A, Warren RM. Deciphering within-host microevolution of Mycobacterium tuberculosis through whole-genome sequencing: The phenotypic impact and way forward. Microbiol Mol Biol Rev 2019; 83:00062–18 [View Article] [PubMed]
     [Google Scholar]
  77. Kim SJ, Kim Y-J, Ko KS. Genomic analysis of consecutive Acinetobacter baumannii strains from a single patient. Front Microbiol 2018; 9:2840 [View Article] [PubMed]
     [Google Scholar]
  78. Yamada N, Kamoshida G, Shiraishi T, Yamaguchi D, Matsuoka M et al. PmrAB, the two-component system of Acinetobacter baumannii, controls the phosphoethanolamine modification of lipooligosaccharide in response to metal ions. J Bacteriol 2024; e0043523:
     [Google Scholar]
  79. Lan F, Demaree B, Ahmed N, Abate AR. Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding. Nat Biotechnol 2017; 35:640–646 [View Article] [PubMed]
     [Google Scholar]
/content/journal/mgen/10.1099/mgen.0.001352
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Phenotypic and genetic heterogeneity of Acinetobacter baumannii in the course of an animal chronic infection
M Gen 11, 001352 (2025); https://doi.org/10.1099/mgen.0.001352
/content/journal/mgen/10.1099/mgen.0.001352
/content/journal/mgen/10.1099/mgen.0.001352
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