{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T04:50:30Z","timestamp":1789015830916,"version":"build-2803163510"},"reference-count":48,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2020,3,7]],"date-time":"2020-03-07T00:00:00Z","timestamp":1583539200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Non-Escherichia coli Enterobacterales (NECE) can colonize the human gut and may present virulence determinants and phenotypes that represent severe heath concerns. Most information is available for virulent NECE strains, isolated from patients with an ongoing infection, while the commensal NECE population of healthy subjects is understudied. In this study, 32 NECE strains were isolated from the feces of 20 healthy adults. 16S rRNA gene sequencing and mass spectrometry attributed the isolates to Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae, Enterobacter aerogenes, Enterobacter kobei, Citrobacter freundii, Citrobacter amalonaticus, Cronobacter sp., and Hafnia alvei, Morganella morganii, and Serratia liquefaciens. Multiplex PCR revealed that K. pneumoniae harbored virulence genes for adhesins (mrkD, ycfM, and kpn) and enterobactin (entB) and, in one case, also for yersiniabactin (ybtS, irp1, irp2, and fyuA). Virulence genes were less numerous in the other NECE species. Biofilm formation was spread across all the species, while curli and cellulose were mainly produced by Citrobacter and Enterobacter. Among the most common antibiotics, amoxicillin-clavulanic acid was the sole against which resistance was observed, only Klebsiella strains being susceptible. The NECE inhabiting the intestine of healthy subjects have traits that may pose a health threat, taking into account the possibility of horizontal gene transfer.<\/jats:p>","DOI":"10.3390\/ijms21051847","type":"journal-article","created":{"date-parts":[[2020,3,9]],"date-time":"2020-03-09T05:37:34Z","timestamp":1583732254000},"page":"1847","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":47,"title":["Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of Non-Escherichia coli Enterobacterales from the Gut Microbiota of Healthy Subjects"],"prefix":"10.3390","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2350-8902","authenticated-orcid":false,"given":"Alberto","family":"Amaretti","sequence":"first","affiliation":[{"name":"Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy"},{"name":"Biogest-Siteia, University of Modena and Reggio Emilia, Modena, Viale Amendola 2, 42122 Reggio Emilia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Righini","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francesco","family":"Candeliere","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eliana","family":"Musmeci","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8101-9835","authenticated-orcid":false,"given":"Francesca","family":"Bonvicini","sequence":"additional","affiliation":[{"name":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanna Angela","family":"Gentilomi","sequence":"additional","affiliation":[{"name":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna, Via Massarenti 9, 40138 Bologna, Italy"},{"name":"Unit of Microbiology, Alma Mater Studiorum-University of Bologna, S. Orsola-Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maddalena","family":"Rossi","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy"},{"name":"Biogest-Siteia, University of Modena and Reggio Emilia, Modena, Viale Amendola 2, 42122 Reggio Emilia, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0944-6677","authenticated-orcid":false,"given":"Stefano","family":"Raimondi","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2020,3,7]]},"reference":[{"key":"ref_1","first-page":"3","article-title":"E. coli as an all-rounder: The thin line between commensalism and pathogenicity","volume":"358","author":"Leimbach","year":"2013","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Manges, A.R., Geum, H.M., Guo, A., Edens, T.J., Fibke, C.D., and Pitout, J.D.D. (2019). Global extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Clin. Microbiol. Rev., 32.","DOI":"10.1128\/CMR.00135-18"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The Clermont Escherichia coli phylo-typing method revisited: Improvement of specificity and detection of new phylo-groups","volume":"5","author":"Clermont","year":"2013","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1128\/CMR.00022-13","article-title":"Recent advances in understanding enteric pathogenic Escherichia coli","volume":"26","author":"Croxen","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Raimondi, S., Righini, L., Candeliere, F., Musmeci, E., Bonvicini, F., Gentilomi, G., Star\u010di\u010d Erjavec, M., Amaretti, A., and Rossi, M. (2019). Antibiotic resistance, virulence factors, phenotyping, and genotyping of E. coli isolated from the feces of healthy subjects. Microorganisms, 7.","DOI":"10.3390\/microorganisms7080251"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/s13099-019-0290-0","article-title":"Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: Recent reports","volume":"11","author":"Sarowska","year":"2019","journal-title":"Gut Pathog."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"4","DOI":"10.3389\/fcimb.2018.00004","article-title":"Colonization, Infection, and the accessory genome of Klebsiella pneumoniae","volume":"8","author":"Martin","year":"2018","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_8","first-page":"392","article-title":"Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment","volume":"6","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"233","DOI":"10.3389\/fcimb.2018.00233","article-title":"Genetic diversity, multidrug resistance, and virulence of Citrobacter freundii from diarrheal patients and healthy individuals","volume":"8","author":"Liu","year":"2018","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Gajd\u00e1cs, M., and Urb\u00e1n, E. (2019). Resistance Trends and epidemiology of citrobacter-enterobacter-serratia in urinary tract infections of inpatients and outpatients (RECESUTI): A 10-year survey. Medicina (Kaunas), 55.","DOI":"10.3390\/medicina55060285"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"483","DOI":"10.3389\/fcimb.2017.00483","article-title":"Antimicrobial resistance of hypervirulent Klebsiella pneumoniae: Epidemiology, hypervirulence-associated determinants, and resistance mechanisms","volume":"7","author":"Lee","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.bjm.2018.04.009","article-title":"Detection of virulence and \u03b2-lactamase encoding genes in Enterobacter aerogenes and Enterobacter cloacae clinical isolates from Brazil","volume":"49","author":"Azevedo","year":"2018","journal-title":"Braz. J. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S0928-8244(03)00276-1","article-title":"Yersiniabactin and other siderophores produced by clinical isolates of Enterobacter spp. and Citrobacter spp.","volume":"40","author":"Mokracka","year":"2004","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.3389\/fmicb.2019.02774","article-title":"Comparative genomic analysis of Citrobacter and key genes essential for the pathogenicity of Citrobacter koseri","volume":"10","author":"Yuan","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1139\/w11-063","article-title":"Virulence traits in Cronobacter species isolated from different sources","volume":"57","author":"Cruz","year":"2011","journal-title":"Can. J. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"4151","DOI":"10.1128\/IAI.71.7.4151-4158.2003","article-title":"Production of cellulose and curli fimbriae by members of the family Enterobacteriaceae isolated from the human gastrointestinal tract","volume":"71","author":"Zogaj","year":"2003","journal-title":"Infect. Immun."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Tursi, S.A., and T\u00fckel, \u00c7. (2018). Curli-containing enteric biofilms inside and out: Matrix composition, immune recognition, and disease implications. Microbiol. Mol. Biol. Rev., 82.","DOI":"10.1128\/MMBR.00028-18"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1097\/PAT.0000000000000237","article-title":"Resistance mechanisms in Enterobacteriaceae","volume":"47","author":"Partridge","year":"2015","journal-title":"Pathology"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.patbio.2012.10.004","article-title":"Virulence profiles and antibiotic susceptibility patterns of Klebsiella pneumoniae strains isolated from different clinical specimens","volume":"61","author":"Messai","year":"2013","journal-title":"Pathol. Biol. (Paris)"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"4377","DOI":"10.1128\/JCM.02316-14","article-title":"Multiplex PCR for detection of seven virulence factors and K1\/K2 capsular serotypes of Klebsiella pneumoniae","volume":"52","author":"Compain","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Johnson, J.R., Porter, S., Johnston, B., Kuskowski, M.A., Spurbeck, R.R., Mobley, H.L., and Williamson, D.A. (2015). Host characteristics and bacterial traits predict experimental virulence for Escherichia coli bloodstream isolates from patients with urosepsis. Open Forum Infect. Dis., 2.","DOI":"10.1093\/ofid\/ofv083"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1093\/infdis\/130.4.402","article-title":"Prevalence and characteristics of Klebsiella species: Relation to association with a hospital environment","volume":"130","author":"Davis","year":"1974","journal-title":"J. Infect. Dis."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1016\/j.micinf.2008.07.040","article-title":"Host and microbiota factors that control Klebsiella pneumoniae mucosal colonization in mice","volume":"10","author":"Lau","year":"2008","journal-title":"Microbes Infect."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1056\/NEJMoa1306801","article-title":"Multistate point-prevalence survey of health care-associated infections","volume":"370","author":"Magill","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e22838","DOI":"10.1002\/jcla.22838","article-title":"Prevalence of pks gene cluster and characteristics of Klebsiella pneumoniae-induced bloodstream infections","volume":"33","author":"Lan","year":"2019","journal-title":"J. Clin. Lab. Anal."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1128\/IAI.00372-06","article-title":"Yersiniabactin is a virulence factor for Klebsiella pneumoniae during pulmonary infection","volume":"75","author":"Lawlor","year":"2007","journal-title":"Infect. Immun."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1268","DOI":"10.1086\/315831","article-title":"High-pathogenicity island of Yersinia pestis in Enterobacteriaceae isolated from blood cultures and urine samples: Prevalence and functional expression","volume":"182","author":"Schubert","year":"2000","journal-title":"J. Infect. Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1016\/j.ijmm.2004.06.026","article-title":"The Yersinia high-pathogenicity island (HPI): Evolutionary and functional aspects","volume":"294","author":"Schubert","year":"2004","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1038\/s41591-018-0145-0","article-title":"Learning from bacterial competition in the host to develop antimicrobials","volume":"24","author":"Raffatellu","year":"2018","journal-title":"Nat. Med."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1084\/jem.20030857","article-title":"A novel virulence gene in Klebsiella pneumoniae strains causing primary liver abscess and septic metastatic complications","volume":"199","author":"Fang","year":"2004","journal-title":"J. Exp. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1086\/503420","article-title":"Association between rmpA and magA genes and clinical syndromes caused by Klebsiella pneumoniae in Taiwan","volume":"42","author":"Yu","year":"2006","journal-title":"Clin. Infect. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/nrgastro.2013.35","article-title":"The gastrointestinal mucus system in health and disease","volume":"10","author":"Johansson","year":"2013","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/nrmicro3432","article-title":"Urinary tract infections: Epidemiology, mechanisms of infection and treatment options","volume":"13","author":"Walker","year":"2015","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1093\/femsre\/fuv015","article-title":"Giving structure to the biofilm matrix: An overview of individual strategies and emerging common themes","volume":"39","author":"Hobley","year":"2015","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Martin, R.M., Cao, J., Brisse, S., Passet, V., Wu, W., Zhao, L., Malani, P.N., Rao, K., and Bachman, M.A. (2016). Molecular epidemiology of colonizing and infecting isolates of Klebsiella pneumoniae. mSphere, 1.","DOI":"10.1128\/mSphere.00261-16"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1093\/cid\/cix270","article-title":"Gastrointestinal carriage is a major reservoir of Klebsiella pneumoniae infection in intensive care patients","volume":"65","author":"Gorrie","year":"2017","journal-title":"Clin. Infect. Dis."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Gajd\u00e1cs, M., B\u00e1tori, Z., \u00c1br\u00f3k, M., L\u00e1z\u00e1r, A., and Buri\u00e1n, K. (2020). Characterization of resistance in gram-negative urinary isolates using existing and novel indicators of clinical relevance: A 10-year data analysis. Life (Basel), 10.","DOI":"10.1038\/s41598-020-74834-y"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.arcped.2018.09.013","article-title":"Klebsiella pneumoniae and Klebsiella oxytoca meningitis in infants. Epidemiological and clinical features","volume":"26","author":"Carrie","year":"2019","journal-title":"Arch. Pediatr."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"12321","DOI":"10.1038\/s41598-018-30569-5","article-title":"Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction","volume":"8","author":"Brossel","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Gajd\u00e1cs, M., \u00c1br\u00f3k, M., L\u00e1z\u00e1r, A., and Buri\u00e1n, K. (2019). Comparative epidemiology and resistance trends of common urinary pathogens in a tertiary-care hospital: A 10-year surveillance study. Medicina (Kaunas), 55.","DOI":"10.3390\/medicina55070356"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"11192","DOI":"10.1038\/s41598-018-29229-5","article-title":"Gut bacterial microbiota and its resistome rapidly recover to basal state levels after short-term amoxicillin-clavulanic acid treatment in healthy adults","volume":"8","author":"MacPherson","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1111\/j.1469-0691.2011.03703.x","article-title":"EUCAST expert rules in antimicrobial susceptibility testing","volume":"19","author":"Leclercq","year":"2013","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1093\/molbev\/msj125","article-title":"Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: Evolution and implications for ERIC-PCR","volume":"23","author":"Wilson","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.anaerobe.2015.10.006","article-title":"Comparison of culture-dependent and independent approaches to characterize fecal bifidobacteria and lactobacilli","volume":"38","author":"Quartieri","year":"2016","journal-title":"Anaerobe"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.ijfoodmicro.2018.09.017","article-title":"Microbiota of sliced cooked ham packaged in modified atmosphere throughout the shelf life: Microbiota of sliced cooked ham in MAP","volume":"16","author":"Raimondi","year":"2019","journal-title":"Int. J. Food Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1128\/JCM.01811-12","article-title":"Typing of nosocomial outbreaks of Acinetobacter baumannii by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry","volume":"51","author":"Mencacci","year":"2013","journal-title":"J. Clin. Microbiol."},{"key":"ref_47","first-page":"10","article-title":"N-Acetyl-glucosamine influences the biofilm formation of Escherichia coli","volume":"22","author":"Sicard","year":"2018","journal-title":"Gut Pathog."},{"key":"ref_48","first-page":"1448","article-title":"Biofilm-forming abilities of shiga toxin-producing Escherichia coli isolates associated with human infections","volume":"28","author":"Vogeleer","year":"2015","journal-title":"Appl. Environ. Microbiol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/21\/5\/1847\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T09:05:06Z","timestamp":1760173506000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/21\/5\/1847"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3,7]]},"references-count":48,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2020,3]]}},"alternative-id":["ijms21051847"],"URL":"https:\/\/doi.org\/10.3390\/ijms21051847","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,7]]}}}