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PreprintCited by 9Infections and bacterial resistanceBacterial biofilms and quorum sensingAntibiotic Resistance in Bacteria

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Achromobacter xylosoxidans isolates exhibit genome diversity, variable virulence, high levels of antibiotic resistance and potential intrahost evolution

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Acharya, Pooja, Lloyd, Cameron, Lam, Ngoc Thien, Kumke, Jessica, Ray, Sreejana, Yanira Muñoz Ramirez, Zilia, Das, Sanchita, Lam, Hanh Ngoc·2025·mSphere
DOI 10.1101/2025.07.29.667465PMC PMC12931269

Preprint — published as 10.1128/msphere.00870-25 · Paper page

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Abstract

2. Abstract: Achromobacter xylosoxidans is an emerging pathogen characterized by high levels of antibiotic resistance and increasing infection rates worldwide. This motile, opportunistic pathogen is widely distributed in the environment and can cause various infections, including pneumonia, bacteremia, endocarditis, meningitis, and others. In this study, we analyzed the population structure, antibiotic resistance profiles, and virulence factors of over 200 publicly available genomes. Core genome analysis revealed that A. xylosoxidans is highly adaptable, possessing a relatively small core genome. Antibiotic susceptibility testing of isolates from the United States revealed high resistance to multiple antibiotics. Our data show that imipenem/relebactam (IMR) is as effective against A. xylosoxidans as imipenem (IMI) alone, indicating that relebactam does not inhibit β-lactamase activity in Achromobacter. The species features multiple secretion systems, including the Type III secretion system (T3SS) of the YscN family, which is similar to those found in Bordetella pertussis and Pseudomonas aeruginosa . Isolates collected from the same patients showed changes in cytotoxicity, flagella motility, biofilm and antibiotic resistance suggesting its dynamic adaptation to host environment. Intra-host evolved isolates, NIH-010, NIH-016 and NIH-018 demonstrated the loss of flagellar motility and variable cytotoxicity while exhibiting increased antibiotic resistance and enhanced biofilm formation. Sequence analysis suggests that NIH-016-3 has tyrosine to histidine mutation at position 330 near the FlhF Guanosine triphosphate (GTP)-binding domain that may affect flagellar assembly. Interestingly, virulence assays showed significant variation in the ability of different A. xylosoxidans isolates to induce cell death in in vitro models, suggesting its dynamic adaptation to host environment. 3. Importance: This study provides a comprehensive examination of Achromobacter xylosoxidans , an emerging pathogen of global concern due to its high antibiotic resistance and increasing clinical relevance. By analyzing over 200 genomes, we offer critical insights into the population structure, resistance mechanisms, and virulence factors of this species. The identification of a small core genome underscores its potential for genomic plasticity. The existence of multiple secretion systems highlights the great capacity of A. xylosoxidans as a pathogen. Variations in virulence among A. xylosoxidans isolates indicate the complexity of this pathogen underscoring the need for further studies on its virulence mechanisms. Evolution within the host includes the loss of motility-associated systems and enhanced antibiotic resistance and biofilm formation. This work showed that A. xylosoxidans are resistant to relebactam when combined with imipenem a combination effective in other bacteria. These findings emphasize the urgent need for targeted therapeutic strategies to combat this opportunistic pathogen.

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Research works printed but not linked: 106

  1. 10.1016/j.micres.2022.127140 · DOI
  2. 10.1093/gbe/evx061 · DOI
  3. 10.1111/j.1348-0421.1971.tb00607.x · DOI
  4. 10.1513/AnnalsATS.201406-288FR · DOI
  5. 10.1371/journal.pone.0068484 · DOI
  6. 2021, What is the role of Achromobacter species in patients with cystic fibrosis?, Front Biosci (Landmark Ed, 26, 1613, 10.52586/5054 · DOI
  7. Tetart M , Wallet F , Kyheng M , Leroy S , Perez T , Le Rouzic O , et al. Impact of Achromobacter xylosoxidans isolation on the respiratory function of adult patients with cystic fibrosis. ERJ Open Res. 2019;5(4). · DOI
  8. 10.1513/AnnalsATS.201701-071OC · DOI
  9. 10.3390/pathogens8010014 · DOI
  10. 2023, Identification of Virulence Factors Involved in a Murine Model of Severe Achromobacter xylosoxidans Infection, Infect Immun, 91, e0003723, 10.1128/iai.00037-23 · DOI
  11. 2023, The Achromobacter type 3 secretion system drives pyroptosis and immunopathology via independent activation of NLRC4 and NLRP3 inflammasomes, Cell Rep, 42, 113012, 10.1016/j.celrep.2023.113012 · DOI
  12. 2022, The In Vitro Replication Cycle of Achromobacter xylosoxidans and Identification of Virulence Genes Associated with Cytotoxicity in Macrophages, Microbiol Spectr, 10, e0208322, 10.1128/spectrum.02083-22 · DOI
  13. 10.1007/s00253-013-5018-3 · DOI
  14. Pickrum AM , DeLeon O , Dirck A , Tessmer MH , Riegert MO , Biller JA , et al. Achromobacter xylosoxidans Cellular Pathology Is Correlated with Activation of a Type III Secretion System. Infect Immun. 2020;88(7). · DOI
  15. 2022, Characterization of the Achromobacter xylosoxidans Type VI Secretion System and Its Implication in Cystic Fibrosis, Front Cell Infect Microbiol, 12, 859181, 10.3389/fcimb.2022.859181 · DOI
  16. 10.1152/physiol.00011.2005 · DOI
  17. 10.1371/journal.pone.0045892 · DOI
  18. 10.1007/978-3-031-08491-1_8 · DOI
  19. 10.1007/s00253-013-5018-3 · DOI
  20. 2020, Clinical features, laboratory characteristics, and outcomes of patients hospitalized with coronavirus disease 2019 (COVID-19): Early report from the United States, Diagnosis (Berl, 7, 91, 10.1515/dx-2020-0046 · DOI · Paper page
  21. 10.1111/1462-2920.14468 · DOI
  22. Isler B , Kidd TJ , Stewart AG , Harris P , Paterson DL. Achromobacter Infections and Treatment Options. Antimicrob Agents Chemother. 2020;64(11). · DOI
  23. 10.1513/AnnalsATS.201406-288FR · DOI
  24. 10.1128/AAC.04260-14 · DOI
  25. 10.15252/emmm.201910264 · DOI
  26. 10.1371/journal.pcbi.1007608 · DOI
  27. 10.1038/s41467-018-06634-y · DOI
  28. Nguyen M , Long SW , McDermott PF , Olsen RJ , Olson R , Stevens RL , et al. Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella. J Clin Microbiol. 2019;57(2). · DOI · Paper page
  29. 2025, Comparative phenotypic and genotypic antimicrobial susceptibility surveillance in Achromobacter spp. through whole genome sequencing, Microbiol Spectr, 13, e0252724, 10.1128/spectrum.02527-24 · DOI
  30. 10.1093/nar/gkab902 · DOI
  31. Kalantar KL , Carvalho T , de Bourcy CFA , Dimitrov B , Dingle G , Egger R , et al. IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience. 2020;9(10). · DOI · Paper page
  32. Bador J , Neuwirth C , Grangier N , Muniz M , Germe L , Bonnet J , et al. Role of AxyZ Transcriptional Regulator in Overproduction of AxyXY-OprZ Multidrug Efflux System in Achromobacter Species Mutants Selected by Tobramycin. Antimicrob Agents Chemother. 2017;61(8). · DOI
  33. Rees VE , Deveson Lucas DS , Lopez-Causape C , Huang Y , Kotsimbos T , Bulitta JB , et al. Characterization of Hypermutator Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis in Australia. Antimicrob Agents Chemother. 2019;63(4). · DOI
  34. 10.1016/j.molcel.2018.10.015 · DOI
  35. 10.1146/annurev.biochem.73.011303.073626 · DOI · Paper page
  36. 10.1016/j.micres.2015.01.004 · DOI
  37. 2022, Conquering the host: Bordetella spp. and Pseudomonas aeruginosa molecular regulators in lung infection, Front Microbiol, 13, 983149, 10.3389/fmicb.2022.983149 · DOI
  38. 10.2217/fmb-2020-0301 · DOI
  39. 2022, Treatment of Pseudomonas aeruginosa infectious biofilms: Challenges and strategies, Front Microbiol, 13, 955286, 10.3389/fmicb.2022.955286 · DOI
  40. Nielsen SM , Penstoft LN , Norskov-Lauritsen N. Motility , Biofilm Formation and Antimicrobial Efflux of Sessile and Planktonic Cells of Achromobacter xylosoxidans. Pathogens. 2019;8(1). · DOI
  41. 10.1038/s41467-019-10201-4 · DOI
  42. 10.1128/JB.00119-09 · DOI
  43. 10.1016/j.mib.2015.07.017 · DOI
  44. 10.1128/IAI.66.1.43-51.1998 · DOI · Paper page
  45. 10.1128/JB.01677-06 · DOI
  46. 2022, Adaptation and Evolution of Pathogens in the Cystic Fibrosis Lung, J Pediatric Infect Dis Soc, 11, S23, 10.1093/jpids/piac073 · DOI
  47. 10.1128/JB.02013-12 · DOI
  48. 2023, The Vibrio Polar Flagellum: Structure and Regulation, Adv Exp Med Biol, 1404, 77, 10.1007/978-3-031-22997-8_5 · DOI
  49. 10.1093/nar/gkae1082 · DOI
  50. 10.1073/pnas.0702570104 · DOI
  51. 10.1111/mmi.14482 · DOI
  52. 10.1128/JB.00884-09 · DOI
  53. 10.1016/j.mimet.2020.105889 · DOI
  54. 10.1186/s12864-016-2364-4 · DOI
  55. 2022, Pseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen, Adv Exp Med Biol, 1386, 3, 10.1007/978-3-031-08491-1_1 · DOI
  56. 10.1128/JB.186.23.7926-7935.2004 · DOI
  57. 10.1128/AAC.00341-11 · DOI
  58. 10.1128/AAC.01243-12 · DOI
  59. Magallon A , Bador J , Garrigos T , Demeule C , Chapelle A , Varin V , et al. Description of Two Resistance-Nodulation-Cell Division Efflux Systems Involved in Acquired Antibiotic Resistance: AxySUV in Achromobacter xylosoxidans and AinCDJ in Achromobacter insuavis. Antibiotics (Basel). 2025;14(6). · DOI
  60. Ventero MP , Haro-Moreno JM , Molina-Pardines C , Sanchez-Bautista A , Garcia-Rivera C , Boix V , et al. Role of Relebactam in the Antibiotic Resistance Acquisition in Pseudomonas aeruginosa: In Vitro Study. Antibiotics (Basel). 2023;12(11). · DOI
  61. 2025, Activity of imipenem/relebactam against KPC-producing Klebsiella pneumoniae and the possible role of Ompk36 mutation in determining resistance: an Italian retrospective analysis, Ann Clin Microbiol Antimicrob, 24, 23, 10.1186/s12941-025-00792-w · DOI
  62. 10.1080/09687860500042013 · DOI
  63. 2019, Architecture, Function, and Substrates of the Type II Secretion System, EcoSal Plus, 8, 227
  64. 1987, Neisseria gonorrhoeae IgA protease, Secretion and implications for pathogenesis. Antonie Van Leeuwenhoek, 53, 479
  65. 10.1046/j.1365-2958.2003.03674.x · DOI
  66. 10.1128/JB.185.13.3735-3744.2003 · DOI
  67. Tassinari M , Rudzite M , Filloux A , Low HH. Assembly mechanism of a Tad secretion system secretin-pilotin complex. Nature Communications. 2023;14(1). · DOI
  68. 2019, Structure and Activity of the Type VI Secretion System, Microbiology Spectrum, 7, 329
  69. 2024, The prevalence and mechanisms of heteroresistance to ceftazidime/avibactam in KPC-producing Klebsiella pneumoniae, J Antimicrob Chemother, 79, 1865, 10.1093/jac/dkae174 · DOI
  70. Khademi SMH , Gabrielaite M , Paulsson M , Knulst M , Touriki E , Marvig RL , et al. Genomic and Phenotypic Evolution of Achromobacter xylosoxidans during Chronic Airway Infections of Patients with Cystic Fibrosis. mSystems. 2021;6(3). · DOI
  71. 10.1080/21505594.2024.2316439 · DOI
  72. 10.1046/j.1365-2958.2000.01785.x · DOI
  73. 10.1111/j.1462-5822.2004.00466.x · DOI
  74. 2024, Evidence for intracellular Pseudomonas aeruginosa, J Bacteriol, 206, e0010924, 10.1128/jb.00109-24 · DOI
  75. 10.1128/mBIO.01506-14 · DOI
  76. Guerra RM , Maleno FD , Figueras MJ , Pujol-Bajador I , Fernandez-Bravo A. Potential Pathogenicity of Aeromonas spp. Recovered in River Water, Soil, and Vegetation from a Natural Recreational Area. Pathogens. 2022;11(11). · DOI
  77. Tessmer MH , Anderson DM , Pickrum AM , Riegert MO , Frank DW. Identification and Verification of Ubiquitin-Activated Bacterial Phospholipases. J Bacteriol. 2019;201(4). · DOI
  78. 10.1002/pro.3682 · DOI
  79. 10.1098/rspb.2020.2272 · DOI
  80. 10.1038/nrmicro.2015.13 · DOI
  81. Uruen C , Chopo-Escuin G , Tommassen J , Mainar-Jaime RC , Arenas J. Biofilms as Promoters of Bacterial Antibiotic Resistance and Tolerance. Antibiotics (Basel). 2020;10(1). · DOI · Paper page
  82. 10.1016/j.chom.2019.06.002 · DOI · Paper page
  83. Sandri A , Veschetti L , Saitta GM , Passarelli Mantovani R , Carelli M , Burlacchini G , et al. Achromobacter spp. Adaptation in Cystic Fibrosis Infection and Candidate Biomarkers of Antimicrobial Resistance. Int J Mol Sci. 2022;23(16). · DOI
  84. 10.1371/journal.pone.0038925 · DOI
  85. 10.1128/JB.01438-13 · DOI
  86. 10.1111/j.1462-2920.2011.02657.x · DOI · Paper page
  87. 10.1093/bioinformatics/btu170 · DOI · Paper page
  88. 10.1089/cmb.2012.0021 · DOI · Paper page
  89. 10.1093/bioinformatics/btt086 · DOI · Paper page
  90. 10.1101/gr.186072.114 · DOI · Paper page
  91. 10.1073/pnas.0906412106 · DOI
  92. 10.1093/bioinformatics/btu153 · DOI · Paper page
  93. 10.1186/s13059-020-02090-4 · DOI
  94. Hall BG , Nisbet J. Building Phylogenetic Trees From Genome Sequences With kSNP4. Mol Biol Evol. 2023;40(11). · DOI
  95. 10.1093/bioinformatics/btu033 · DOI · Paper page
  96. 10.1093/nar/gkae268 · DOI · Paper page
  97. 2016, SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments, Microb Genom, 2, e000056
  98. 10.1093/molbev/msaa015 · DOI · Paper page
  99. 10.1093/molbev/msu082 · DOI
  100. 10.1016/j.ajhg.2009.01.005 · DOI · Paper page
  101. 10.1371/journal.pgen.1002453 · DOI · Paper page
  102. 10.1093/molbev/mst055 · DOI
  103. 10.1038/srep23080 · DOI
  104. 10.1093/molbev/mst010 · DOI · Paper page
  105. 10.1109/tsmc.1979.4310076 · DOI · Paper page
  106. 10.1093/bioinformatics/btu031 · DOI · Paper page

Metadata

Authors
Acharya, P., Lloyd, C., Lam, N. T., Kumke, J., Ray, S., Yanira Muñoz Ramirez, Z., Das, S., & Lam, H. N.
Affiliations
  • Virginia Tech (US)
  • Ton Duc Thang University (VN)
  • National Institutes of Health (US)
  • Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus II Circuito Universitario s/n, Chihuahua, Mexico
Corresponding author
Lam, Hanh Ngoc
ORCID
Venue
mSphere
Publisher
openRxiv
Published
2025-07-29
Volume
11
Issue
2
Pages
e0087025-e0087025
ISSN
2379-5042 (ISSN-L)
DOI
10.1101/2025.07.29.667465
PMC
PMC12931269
OpenAlex
W7127336502
Cited by
9
References
1
Citations by year
2026: 9
FWCI
38.87
Type
journal article
Language
en
Open access
Licence
Locations
  • mSphere (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed Central (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
NIAID (R00AI139281)
Topics
  • Health Sciences › Medicine › Microbiology (medical) › Infections and bacterial resistance
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bacterial biofilms and quorum sensing
  • Health Sciences › Medicine › Microbiology (medical) › Antibiotic Resistance in Bacteria
Keywords
antibiotic resistance, virulence factors, population structure, core genome, flagellar motility, biofilm formation, cytotoxicity, type III secretion system, imipenem resistance, relebactam, secretion systems, genome plasticity, host adaptation, clinical isolates

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CoChat. (2026). Citation check: Achromobacter xylosoxidans isolates exhibit genome diversity, variable virulence, high levels of antibiotic resistance and potential intrahost evolution. https://app.cochat.ai/papers/10.1101/2025.07.29.667465
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Acharya, P., Lloyd, C., Lam, N. T., Kumke, J., Ray, S., Yanira Muñoz Ramirez, Z., Das, S., & Lam, H. N. (2025). Achromobacter xylosoxidans isolates exhibit genome diversity, variable virulence, high levels of antibiotic resistance and potential intrahost evolution. mSphere. https://doi.org/10.1101/2025.07.29.667465

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