Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L (2018) DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome 6:23. https://doi.org/10.1186/s40168-018-0401-z1. Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L (2018) DeepARG: A Deep Learning Approach for Predicting Antibiotic Resistance Genes from Metagenomic Data. Microbiome 6:23. 10.1186/s40168-018-0401-z

Article  PubMed  PubMed Central  Google Scholar 

Borowiec ML (2016) AMAS: a fast tool for alignment manipulation and computing of summary statistics. PeerJ 4:e1660. https://doi.org/10.7717/peerj.16602. Borowiec ML (2016) AMAS: A Fast Tool for Alignment Manipulation and Computing of Summary Statistics. PeerJ 4:e1660. 10.7717/peerj.1660

Article  PubMed  PubMed Central  Google Scholar 

Brenner DJ, Davis BR, Steigerwalt AG, Riddle CF, McWhorter AC, Allen SD, Farmer JJ, Saitoh Y, Fanning GR (1982a) A typical biogroups of Escherichia coli found in clinical specimens and description of Escherichia hermannii sp. nov. J Clin Microbiol 15:703–713. https://doi.org/10.1128/jcm.15.4.703-713.1982

Article  PubMed  PubMed Central  CAS  Google Scholar 

Brenner DJ, McWhorter AC, Leete Knutson JK, Steigerwalt AG (1982b) Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds. J Clin Microbiol 15:1133–1140. https://doi.org/10.1128/jcm.15.6.1133-1140.19824. Brenner DJ, McWhorter AC, Leete Knutson JK, Steigerwalt AG (1982) Escherichia vulneris: A New Species of Enterobacteriaceae Associated with Human Wounds. J Clin Microbiol 15:1133–1140. 10.1128/jcm.15.6.1133-1140.1982

Article  PubMed  PubMed Central  CAS  Google Scholar 

Brown SP, Cornforth DM, Mideo N (2012) Evolution of virulence in opportunistic pathogens: generalism, plasticity, and control. Trends Microbiol 20(7):336–342. https://doi.org/10.1016/j.tim.2012.04.005

Article  PubMed  PubMed Central  CAS  Google Scholar 

Buchfink B, Reuter K, Drost H-K (2021) Sensitive protein alignments at tree-of-life scale using diamond. Nat Methods 18(4):366–368. https://doi.org/10.1038/s41592-021-01101-x

Article  PubMed  PubMed Central  CAS  Google Scholar 

Castellani A, Chalmers AJ (1919) Manual of tropical medicine. Tindall and Cox Publishers, Baillière

Book  Google Scholar 

Clermont O, Gordon DM, Brisse S, Walk ST, Denamur E (2011) Characterization of the cryptic Escherichia lineages: rapid identification and prevalence. Environ Microbiol 13(9):2468–2477. https://doi.org/10.1111/j.1462-2920.2011.02519.x

Article  PubMed  Google Scholar 

De Nies L, Lopes S, Busi BS, Galata V, Heintz-Buschart A, Laczny CC, May P, Wilmes P (2021) PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. Microbiome 9(1):49. https://doi.org/10.1186/s40168-020-00993-9

Article  PubMed  PubMed Central  CAS  Google Scholar 

Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomic. Genome Biol 20(1):238. https://doi.org/10.1186/s13059-019-1832-y

Article  PubMed  PubMed Central  Google Scholar 

European Committee on Antimicrobial Susceptibility Testing (2021) European committee on antimicrobial susceptibility testing breakpoint tables for interpretation of MICs and zone diameters. EUCAST Clinical Breakpoint Tables 12

Farmer JJ, Fanning GR, Davis BR, O’Hara CM, Riddle C, Hickman-Brenner FW, Asbury MA, Lowery VA, Brenner DJ (1985) Escherichia fergusonii and Enterobacter taylorae, Two New Species of Enterobacteriaceae Isolated from Clinical Specimens. J Clin Microbiol 21(1):77–81. https://doi.org/10.1128/jcm.21.1.77-81.198512. Farmer JJ, Fanning GR, Davis BR, O’Hara CM, Riddle C, Hickman-Brenner FW, Asbury MA, Lowery VA, Brenner DJ (1985) Escherichia fergusonii and Enterobacter taylorae, Two New Species of Enterobacteriaceae Isolated from Clinical Specimens. J Clin Microbiol 21 (1):77–81. 10.1128/jcm.21.1.77-81.1985

Article  PubMed  PubMed Central  CAS  Google Scholar 

Gangiredla J, Mammel MK, Barnaba TJ, Tartera C, Gebru ST, Patel IR, Leonard SR et al (2018) Draft genome sequences of Escherichia albertii, Escherichia fergusonii, and strains belonging to six cryptic lineages of Escherichia spp. Genome Announc 6(18):e00271-e318. https://doi.org/10.1128/genomeA.00271-18

Article  PubMed  PubMed Central  Google Scholar 

Huys G, Cnockaert M, Janda JM, Swings J (2003) Escherichia albertii sp. nov., a diarrhoeagenic species isolated from stool specimens of bangladeshi children. Int J Syst Evol Microbiol 53(3):807–10. https://doi.org/10.1099/ijs.0.02475-0

Article  PubMed  CAS  Google Scholar 

Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H et al (2012) Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 158(4):1005–1015. https://doi.org/10.1099/mic.0.055459-0

Article  PubMed  PubMed Central  CAS  Google Scholar 

Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30(4):772–780. https://doi.org/10.1093/molbev/mst010

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kim H-S, Nagore D, Nikaido H (2010) Multidrug efflux pump mdtbc of Escherichia coli is active only as a B 2 C heterotrimer. J Bacteriol 192(5):1377–1386. https://doi.org/10.1128/JB.01448-09

Article  PubMed  CAS  Google Scholar 

Liu S, Jin D, Lan R, Wang Y, Meng Q, Dai H, Lu S, Hu S, Xu J (2015) Escherichia marmotae sp. nov., Isolated from Faeces of Marmota himalayana. https://doi.org/10.1099/ijs.0.000228

Liu S, Feng J, Pu J, Xu X, Lu S, Yang J, Wang Y et al (2019) Genomic and molecular characterisation of Escherichia marmotae from wild rodents in qinghai-tibet plateau as a potential pathogen. Sci Rep-UK 9(1):10619. https://doi.org/10.1038/s41598-019-46831-3

Article  CAS  Google Scholar 

Liu B, Zheng D, Zhou S, Chen L, Yang J (2022) VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 50(D1):D912-917. https://doi.org/10.1093/nar/gkab1107

Article  PubMed  CAS  Google Scholar 

Nguyen L-T, Schmidt HA, Von Haeseler A, Minh BQ (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32(1):268–274. https://doi.org/10.1093/molbev/msu300

Article  PubMed  CAS  Google Scholar 

Okuno M, Arimizu Y, Miyahara S, Wakabayashi Y, Gotoh A, Yoshino S, Harada T et al (2023) Escherichia cryptic clade i is an emerging source of human intestinal pathogens. BMC Biol 21(1):81. https://doi.org/10.1186/s12915-023-01584-4

Article  PubMed  PubMed Central  CAS  Google Scholar 

Rambaut A (2010) FigTree v1. 3.1. (No Title). https://github.com/rambaut/figtree

Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069. https://doi.org/10.1093/bioinformatics/btu153

Article  PubMed  CAS  Google Scholar 

Sivertsen A, Dyrhovden R, Tellevik MR, Bruvold TS, Nybakken E, Skutlaberg DH, Ingerid Skarstein I, Kommedal Ø (2022) Escherichia marmotae – a Human Pathogen Easily Misidentified as Escherichia coli. Microbiol Spectrum 10(2):e02035-e2121. https://doi.org/10.1128/spectrum.02035-21

Article  CAS  Google Scholar 

Souguir M, Châtre P, Drapeau A, François P, Azaiez S, Ncir S, Madec J-Y, Mansour W, Haenni M (2023) Molecular characterization of highly prevalent Escherichia coli and Escherichia marmotae resistant to extended-spectrum cephalosporins in european starlings (Sturnus vulgaris ) in tunisia. Microbiology Spectrum 11(5):e02220-e2223. https://doi.org/10.1128/spectrum.02220-23

Article  PubMed  PubMed Central  CAS  Google Scholar 

Tenaillon O, Skurnik D, Picard B, Denamur E (2010) The population genetics of commensal Escherichia coli. Nat Rev Microbiol 8(3):207–217. https://doi.org/10.1038/nrmicro2298

Article  PubMed  CAS  Google Scholar 

van der Putten BCL, Matamoros S, Mende DR, Scholl ER, COMBAT Consortium†, Schultsz C (2021) Escherichia ruysiae sp. nov., a Novel Gram-Stain-Negative Bacterium, Isolated from a Faecal Sample of an International Traveller. Int J Syst Evol Microbiol 71(2):004609. https://doi.org/10.1099/ijsem.0.004609

Vignaroli C, Di Sante L, Magi G, Luna GM, Di Cesare A, Pasquaroli S, Facinelli B, Biavasco F (2015) Adhesion of marine cryptic Escherichia isolates to human intestinal epithelial cells. ISME J 9(2):508–515. https://doi.org/10.1038/ismej.2014.164

Article  PubMed  CAS  Google Scholar 

Walk ST (2015) The “Cryptic” Escherichia.https://doi.org/10.1128/ecosalplus.esp-0002-2015

Walk ST, Alm EW, Gordon DM, Ram JL, Toranzos GA, Tiedje JM, Whittam TS (2009) Cryptic lineages of the genus Escherichia. Appl Environ Microbiol 75(20):6534–6544. https://doi.org/10.1128/AEM.01262-09