Abram KZ, Jun S-R, Udaondo Z (2022) Pseudomonas aeruginosa pangenome: core and accessory genes of a highly resourceful opportunistic pathogen. Springer, Cham, pp 3–28
Amato S, Vanik J, Kocka FE (1980) Identification of Pseudomonas aeruginosa with the API-20E system. Can J Microbiol 26:554–555. https://doi.org/10.1139/M80-096
Article PubMed CAS Google Scholar
arpcard (Comprehensive antibiotic resistance database) GitHub [WWW Document], n.d. https://github.com/arpcard. Accessed 11 Feb 2024
Aslanzadeh J (2006) Biochemical profile-based microbial identification systems. Advanced techniques in diagnostic microbiology. Springer, Boston, pp 84–116 https://doi.org/10.1007/0-387-32892-0_6
Blair JM, Piddock LJ (2009) Structure, function and inhibition of RND efflux pumps in gram-negative bacteria: an update. Curr Opin Microbiol 12:512–519. https://doi.org/10.1016/j.mib.2009.07.003
Article PubMed CAS Google Scholar
BLAST+ 2.12.0 Now available with more efficient multithreaded searches - NCBI insights [WWW Document] n.d. https://ncbiinsights.ncbi.nlm.nih.gov/2021/07/09/blast-2-12-0/. Accessed 30 Sept 2024
BLAST: Basic local alignment search tool [WWW Document], n.d. https://blast.ncbi.nlm.nih.gov/Blast.cgi. Accessed 30 Sept 2024
Busse HJ, Denner EBM, Lubitz W (1996) Classification and identification of bacteria: current approaches to an old problem. overview of methods used in bacterial systematics. J Biotechnol 47:3–38. https://doi.org/10.1016/0168-1656(96)01379-X
Article PubMed CAS Google Scholar
Carroll KC, Glanz BD, Borek AP, Burger C, Bhally HS, Henciak S, Flayhart D (2006) Evaluation of the BD phoenix automated microbiology system for identification and antimicrobial susceptibility testing of Enterobacteriaceae. J Clin Microbiol 44:3506–3509. https://doi.org/10.1128/JCM.00994-06
Article PubMed PubMed Central CAS Google Scholar
Chen L, Zheng D, Liu B, Yang J, Jin Q (2016) VFDB 2016: hierarchical and refined dataset for big data analysis - 10 years on. Nucleic Acids Res 44:D694–D697. https://doi.org/10.1093/NAR/GKV1239
Article PubMed CAS Google Scholar
Chromas | Technelysium Pty Ltd [WWW Document], n.d. https://technelysium.com.au/wp/chromas/. Accessed 30 Sept 2024
Clinical and Laboratory Standards Institute (CLSI) 2024 Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically. 12th ed. CLSI standard M07
Clinical and Laboratory Standards Institute (CLSI) 2018 Interpretive criteria for identification of bacteria and fungi by targeted DNA sequencing. 2nd ed. CLSI guideline MM18
Deruelle V, Bouillot S, Job V, Taillebourg E, Fauvarque M-O, Attrée I, Huber P (2021) The bacterial toxin ExoU requires a host trafficking chaperone for transportation and to induce necrosis. Nat Commun 12:4024. https://doi.org/10.1038/s41467-021-24337-9
Article PubMed PubMed Central CAS Google Scholar
Elbehiry A, Marzouk E, Aldubaib M, Moussa I, Abalkhail A, Ibrahem M, Hamada M, Sindi W, Alzaben F, Almuzaini AM, Algammal AM, Rawway M (2022) Pseudomonas species prevalence, protein analysis, and antibiotic resistance: an evolving public health challenge. AMB Express 12:53. https://doi.org/10.1186/S13568-022-01390-1
Article PubMed PubMed Central CAS Google Scholar
Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH, Hoffmann M, Pettengill JB, Prasad AB, Tillman GE, Tyson GH, Klimke W (2021) AMRfinderplus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 11(1):12728. https://doi.org/10.1038/s41598-021-91456-0
Article PubMed PubMed Central CAS Google Scholar
Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ, Tolstoy I, Tyson GH, Zhao S, Hsu CH, McDermott PF, Tadesse DA, Morales C, Simmons M, Tillman G, Wasilenko J, Folster JP, Klimke W (2019) Validating the AMRfinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother. https://doi.org/10.1128/AAC.00483-19
Article PubMed PubMed Central Google Scholar
Fernández-Rodríguez D, Colín-Castro CA, Hernández-Durán M, López-Jácome LE, Franco-Cendejas R (2021) Staphylococcus epidermidis small colony variants, clinically significant quiescent threats for patients with prosthetic joint infection. Microbes Infect 23:104854. https://doi.org/10.1016/j.micinf.2021.104854
Article PubMed CAS Google Scholar
Food and Drug Administration, n.d. Proactive applications of whole genome sequencing technology | FDA [WWW Document]. https://www.fda.gov/food/whole-genome-sequencing-wgs-program/proactive-applications-whole-genome-sequencing-technology?utm_source=chatgpt.com. Accessed 6 Jul 2025
Galar A, Kulldorff M, Rudnick W, O’Brien TF, Stelling J (2013) Biochemical phenotypes to discriminate microbial subpopulations and improve outbreak detection. PLoS ONE 8:e84313
Article PubMed PubMed Central Google Scholar
García-Lara B, Saucedo-Mora MA, Roldán-Sánchez JA, Pérez-Eretza B, Ramasamy M, Lee J, Coria-Jimenez R, Tapia M, Varela-Guerrero V, García-Contreras R (2015) Inhibition of quorum-sensing-dependent virulence factors and biofilm formation of clinical and environmental Pseudomonas aeruginosa strains by ZnO nanoparticles. Lett Appl Microbiol 61:299–305. https://doi.org/10.1111/LAM.12456
Garey KW, Vo QP, Larocco MT, Gentry LO, Tam VH (2008) Prevalence of type III secretion protein exoenzymes and antimicrobial susceptibility patterns from bloodstream isolates of patients with Pseudomonas aeruginosa bacteremia. J Chemother 20:714–720. https://doi.org/10.1179/joc.2008.20.6.714
Article PubMed CAS Google Scholar
Garrido-Sanz D, Arrebola E, Martínez-Granero F, García-Méndez S, Muriel C, Blanco-Romero E, Martín M, Rivilla R, Redondo-Nieto M (2017) Classification of isolates from the Pseudomonas fluorescens complex into phylogenomic groups based in group-specific markers. Front Microbiol 8:413. https://doi.org/10.3389/fmicb.2017.00413
Article PubMed PubMed Central Google Scholar
Girard L, Lood C, Höfte M, Vandamme P, Rokni-Zadeh H, van Noort V, Lavigne R, De Mot R (2021) The ever-expanding Pseudomonas genus: description of 43 new species and partition of the Pseudomonas putida group. Microorganisms 9:1766. https://doi.org/10.3390/microorganisms9081766
Article PubMed PubMed Central CAS Google Scholar
GitHub - arpcard/rgi: Resistance gene identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models. [WWW Document], n.d. https://github.com/arpcard/rgi. Accessed 11 Feb 2024
GitHub - tseemann/abricate: mag_right: Mass screening of contigs for antimicrobial and virulence genes [WWW Document], n.d. https://github.com/tseemann/abricate. Accessed 30 Sept 2024
GitHub - tseemann/snp-dists: Pairwise SNP distance matrix from a FASTA sequence alignment [WWW Document], n.d. https://github.com/tseemann/snp-dists. Accessed 30 Sept 2024
Grohs P, Remaud E, Lath C, Vuong K, Parolini ML, Dannaoui E, Podglajen I (2023) Comparison of the new VITEK MS PRIME system with the matrix-assisted laser desorption ionization biotyper Microflex LT for the identification of microorganisms. Ann Lab Med 43:574–584. https://doi.org/10.3343/ALM.2023.43.6.574
Article PubMed PubMed Central Google Scholar
Hauser AR (2009) The type III secretion system of Pseudomonas aeruginosa: infection by injection. Nat Rev Microbiol 7:654–665. https://doi.org/10.1038/nrmicro2199
Article PubMed PubMed Central CAS Google Scholar
Hernández-Durán M, Colín-Castro CA, Fernández-Rodríguez D, Delgado G, Morales-Espinosa R, Martínez-Zavaleta MG, Shekhar C, Ortíz-Álvarez J, García-Contreras R, Franco-Cendejas R, López-Jácome LE (2024) Inside-out, antimicrobial resistance mediated by efflux pumps in clinical strains of Acinetobacter baumannii isolated from burn wound infections. Braz J Microbiol. https://doi.org/10.1007/s42770-024-01461-4
Article PubMed PubMed Central Google Scholar
Hofmann K, Huptas C, Doll EV, Scherer S, Wenning M (2020) Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate. Int J Syst Evol Microbiol 70:935–943. https://doi.org/10.1099/IJSEM.0.003851
Article PubMed CAS Google Scholar
Holmes B, Willcox WR, Lapage SP (1978) Identification of enterobacteriaceae by the API 20E system. J Clin Pathol 31:22. https://doi.org/10.1136/JCP.31.1.22
Article PubMed PubMed Central CAS Google Scholar
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 9(1):5114. https://doi.org/10.1038/s41467-018-07641-9
Article PubMed PubMed Central CAS Google Scholar
Janda JM, Abbott SL (2002) Bacterial identification for publication: when is enough enough? J Clin Microbiol 40:1887. https://doi.org/10.1128/JCM.40.6.1887-1891.2002
Article PubMed PubMed Central Google Scholar
Janda JM, Abbott SL, Khashe S, Probert W (2001) Biochemical identification and characterization of DNA groups within the Proteus vulgaris complex. J Clin Microbiol 39:1231. https://doi.org/10.1128/JCM.39.4.1231-1234.2001
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