{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T23:56:39Z","timestamp":1787702199931,"version":"build-2784847793"},"reference-count":51,"publisher":"MDPI AG","issue":"22","license":[{"start":{"date-parts":[[2022,11,8]],"date-time":"2022-11-08T00:00:00Z","timestamp":1667865600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Research Directorate of the Universidad del B\u00edo-B\u00edo","award":["195420\/EF"],"award-info":[{"award-number":["195420\/EF"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Foods"],"abstract":"<jats:p>Powdered infant formulas (PIF) are the most used dietary substitutes that are used in order to supplement breastfeeding. However, PIF are not sterile and can be contaminated with different microorganisms. The objective of this study was to genomically characterize Enterobacteriaceae (ENT) and Enterococcus strains that were isolated from PIF. Strains were identified by matrix-assisted laser desorption ionization\u2013time-of-flight mass spectrometry (MALDI-TOF MS) and whole-genome sequencing (WGS). Genomic typing, detection of virulence, and resistance profiles and genes were performed with the Ridom SeqSphere+ software; the comprehensive antibiotic resistance database (CARD) platform; ResFinder and PlasmidFinder tools; and by the disk diffusion method. Nineteen isolates from PIF were analyzed, including ENT such as Kosakonia cowanii, Enterobacter hormaechei, Franconibacter helveticus, Mixta calida, and lactic acid bacteria such as Enterococcus faecium. The strains exhibited resistance to beta-lactams, cephalosporins, and macrolides. Resistance genes such as AcrAB-TolC, marA, msbA, knpEF, oqxAB, fosA, blaACT-7, blaACT-14,qacJ, oqxAB,aac(6\u2019)-Ii, and msr(C); and virulence genes such as astA, cheB, cheR, ompA ompX, terC, ironA, acm, and efaAfm, adem were also detected. All the analyzed strains possessed genes that produced heat-shock proteins, such as IbpA and ClpL. In PIF, the presence of ENT and Enterococcus that are multiresistant to antibiotics\u2014together with resistance and virulence genes\u2014pose a health risk for infants consuming these food products.<\/jats:p>","DOI":"10.3390\/foods11223556","type":"journal-article","created":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T02:34:52Z","timestamp":1667961292000},"page":"3556","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Are Enterobacteriaceae and Enterococcus Isolated from Powdered Infant Formula a Hazard for Infants? A Genomic Analysis"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4835-9747","authenticated-orcid":false,"given":"Julio","family":"Parra-Flores","sequence":"first","affiliation":[{"name":"Department of Nutrition and Public Health, Universidad del B\u00edo-B\u00edo, Chill\u00e1n 3800708, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9346-1612","authenticated-orcid":false,"given":"Adriana","family":"Cabal-Rosel","sequence":"additional","affiliation":[{"name":"Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beatriz","family":"Daza-Prieto","sequence":"additional","affiliation":[{"name":"Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pamela","family":"Chavarria","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Public Health, Universidad del B\u00edo-B\u00edo, Chill\u00e1n 3800708, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9482-8268","authenticated-orcid":false,"given":"Eduard","family":"Maury-Sintjago","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Public Health, Universidad del B\u00edo-B\u00edo, Chill\u00e1n 3800708, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3982-3165","authenticated-orcid":false,"given":"Alejandra","family":"Rodriguez-Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Department of Nutrition and Public Health, Universidad del B\u00edo-B\u00edo, Chill\u00e1n 3800708, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1365-9851","authenticated-orcid":false,"given":"Sergio","family":"Acu\u00f1a","sequence":"additional","affiliation":[{"name":"Department of Food Engineering, Universidad del B\u00edo-B\u00edo, Chill\u00e1n 3800708, Chile"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9940-3333","authenticated-orcid":false,"given":"Werner","family":"Ruppitsch","sequence":"additional","affiliation":[{"name":"Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, 1220 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,11,8]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1159\/000338803","article-title":"Quality and safety aspects of infant nutrition","volume":"60","author":"Koletzko","year":"2012","journal-title":"Ann. Nutr. Metab."},{"key":"ref_2","unstructured":"Editors McSweeney, P., and McNamara, J. (2022). Cronobacter spp. in milk. Book Reference Module in Food Science, Elsevier. [3rd ed.]."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Townsend, S., Hurrell, E., and Forsythe, S. (2008). Virulence studies of Enterobacter sakazakii isolates associated with a neonatal intensive care unit outbreak. BMC Microbiol., 8.","DOI":"10.1186\/1471-2180-8-64"},{"key":"ref_4","unstructured":"Food and Agriculture Organization and World Health Organization (FAO\/WHO) (2004). Enterobacter sakazakii and Other Microorganisms in Powdered Infant Formula: Meeting Report, WHO Press Publisher."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Janda, J.M., and Abbott, S.L. (2021). The Changing Face of the Family Enterobacteriaceae (Order: \u201cEnterobacterales\u201d): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes. Clin. Microbiol. Rev., 34.","DOI":"10.1128\/CMR.00174-20"},{"key":"ref_6","unstructured":"Codex Alimentarius Comission (2008). Food and Agriculture Organization and World Health Organization (FAO\/WHO). Code of Hygienic Practice for Powdered Formulae for Infants and Young Children, WHO Press Publisher. CAC\/RCP 66."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.fm.2004.01.009","article-title":"Isolation of Enterobacter sakazakii and other Enterobacteriaceae from powdered infant formula milk and related products","volume":"21","author":"Iversen","year":"2004","journal-title":"Food Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"534","DOI":"10.4315\/0362-028X.JFP-19-399","article-title":"Microbiological quality of powdered infant formula in Latin America","volume":"83","author":"Cerda","year":"2020","journal-title":"J. Food Prot."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3013","DOI":"10.4315\/0362-028X-69.12.3013","article-title":"Enterobacteriaceae in dehydrated powdered infant formula manufactured in Indonesia and Malaysia","volume":"69","author":"Estuningsih","year":"2006","journal-title":"J. Food Prot."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.ijfoodmicro.2009.08.007","article-title":"Biofilm formation on enteral feeding tubes by Cronobacter sakazakii, Salmonella serovars and other Enterobacteriaceae","volume":"136","author":"Hurrell","year":"2009","journal-title":"Int. J. Food Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/S0168-1605(03)00190-9","article-title":"Occurrence and spread of antibiotic resistances in Enterococcus faecium","volume":"88","author":"Klare","year":"2003","journal-title":"Int. J. Food Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Santos, A., Dos Santos, A., Ito, C., Queiroz, P., de Almeida, J., de Carvalho-J\u00fanior, M., de Oliveira, C., Avelino, M., Wastowski, I., and Gomes, G. (2020). Profile of enterobacteria resistant to beta-lactams. Antibiotics, 9.","DOI":"10.3390\/antibiotics9070410"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Al Mana, H., Sundararaju, S., Tsui, C.K.M., Perez-Lopez, A., Yassine, H., Al Thani, A., Al-Ansari, K., and Eltai, N.O. (2021). Whole-Genome Sequencing for Molecular Characterization of Carbapenem-Resistant Enterobacteriaceae Causing Lower Urinary Tract Infection among Pediatric Patients. Antibiotics, 10.","DOI":"10.3390\/antibiotics10080972"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Pilarczyk-Zurek, M., Strus, M., Adamski, P., and Heczko, P. (2016). The dual role of Escherichia coli in the course of ulcerative colitis. BMC Gastroenterol., 16.","DOI":"10.1186\/s12876-016-0540-2"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2365","DOI":"10.1128\/JCM.00262-14","article-title":"Bacterial whole-genome sequencing revisited: Portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes","volume":"52","author":"Leopold","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Uelze, L., Borowiak, M., Deneke, C., Szab\u00f3, I., Fischer, J., Tausch, S.H., and Malorny, B. (2020). Performance and Accuracy of Four Open-Source Tools for In Silico Serotyping of Salmonella spp. Based on Whole-Genome Short-Read Sequencing Data. Appl. Environ. Microbiol., 86.","DOI":"10.1128\/AEM.02265-19"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nbt.2522","article-title":"Updating benchtop sequencing performance comparison","volume":"31","author":"Sedlazeck","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1005","DOI":"10.1099\/mic.0.055459-0","article-title":"Ribosomal multilocus sequence typing: Universal characterization of bacteria from domain to strain","volume":"158","author":"Jolley","year":"2012","journal-title":"Microbiology"},{"key":"ref_19","unstructured":"Clinical and Laboratory Standards Institute (CLSI) (2020). Performance Standards for Antimicrobial Susceptibility Testing, CLSI. [30th ed.]."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"D694","DOI":"10.1093\/nar\/gkv1239","article-title":"VFDB 2016: Hierarchical and refined dataset for big data analysis\u201410 years on","volume":"44","author":"Chen","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Feldgarden, M., Brover, V., Haft, D.H., Prasad, A.B., Slotta, D.J., Tolstoy, I., Tyson, G.H., Zhao, S., Hsu, C.H., and McDermott, P.F. (2019). Validating the AMRFinder Tool and Resistance Gene Database by Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of Isolates. Antimicrob Agents Chemother., 63, Erratum in Antimicrob Agents Chemother. 2020, 24, 64.","DOI":"10.1128\/AAC.00361-20"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: Expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"2734","DOI":"10.1080\/10408398.2018.1466265","article-title":"Dehydrated foods: Are they microbiologically safe?","volume":"59","author":"Chitrakar","year":"2019","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/j.cofs.2021.06.007","article-title":"Microbial contaminants in powdered infant formula: What is the impact of spray-drying on microbial inactivation?","volume":"42","author":"Lang","year":"2021","journal-title":"Curr. Opin. Food Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3168\/jds.2012-5409","article-title":"Microbiological assessment and evaluation of rehydration instructions on powdered infant formulas, follow-up formulas and infant foods in Malaysia","volume":"96","author":"Hartantyo","year":"2013","journal-title":"J. Dairy Sci."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"109271","DOI":"10.1016\/j.lwt.2020.109271","article-title":"High prevalence of non-faecalis and non-faecium Enterococcus spp. in farmstead cheesehouse and their applicability as hygiene indicators","volume":"126","author":"Kim","year":"2020","journal-title":"LWT"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.jhin.2007.02.013","article-title":"Outbreak of Enterobacter hormaechei septicaemia in newborns caused by contaminated parenteral nutrition in Brazil","volume":"66","author":"Campos","year":"2007","journal-title":"J. Hosp. Infect."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2206","DOI":"10.3389\/fmicb.2018.02206","article-title":"Virulence and Antibiotic Resistance Profiles of Cronobacter sakazakii and Enterobacter spp. Involved in the Diarrheic Hemorrhagic Outbreak in Mexico","volume":"9","author":"Aguirre","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"106650","DOI":"10.1016\/j.ijantimicag.2022.106650","article-title":"Antibiotic resistance in Enterobacter hormaechei","volume":"60","author":"Yeh","year":"2022","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Chavda, K., Westblade, L., Satlin, M., Hemmert, A., Castanheira, M., Jenkins, S., and Kreiswirth, B. (2019). First report of blaVIM-4- and mcr-9-coharboring Enterobacter species isolated from a pediatric patient. mSphere, 4.","DOI":"10.1128\/mSphere.00629-19"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"145","DOI":"10.2147\/IDR.S231366","article-title":"Characterization of blaNDM-1- and blaSHV-12-positive IncX3 plasmid in an Enterobacter hormaechei new sequence type 1000 from China","volume":"13","author":"Li","year":"2020","journal-title":"Infect Drug Resist."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.3201\/eid2406.171648","article-title":"Genomic epidemiology of global carbapenemase-producing Enterobacter spp., 2008\u20132014","volume":"24","author":"Peirano","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/j.resmic.2017.10.005","article-title":"Regulation of the AcrAB-TolC efflux pump in Enterobacteriaceae","volume":"169","author":"Weston","year":"2018","journal-title":"Res. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.jgar.2021.08.014","article-title":"Draft genome sequence of colistin-resistant and extended-spectrum \u03b2-lactamase (ESBL)-producing multidrug-resistant Escherichia coli isolated from poultry meat","volume":"27","author":"Yasir","year":"2021","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"7475","DOI":"10.1038\/s41598-020-64424-3","article-title":"Identification and characterisation of enteroaggregative Escherichia coli subtypes associated with human disease","volume":"10","author":"Ellis","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Ramos, C.P., Kamei, C.Y.I., Viegas, F.M., de Melo Barbieri, J., Cunha, J.L.R., Hounmanou, Y.M.G., Coura, F.M., Santana, J.A., Lobato, F.C.F., and Bojesen, A.M. (2022). Fecal Shedding of Multidrug Resistant Escherichia coli Isolates in Dogs Fed with Raw Meat-Based Diets in Brazil. Antibiotics, 11.","DOI":"10.3390\/antibiotics11040534"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Petrzik, K., Br\u00e1zdov\u00e1, S., and Krawczyk, K. (2021). Novel Viruses That Lyse Plant and Human Strains of Kosakonia cowanii. Viruses, 13.","DOI":"10.3390\/v13081418"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"101527","DOI":"10.1016\/j.bcab.2020.101527","article-title":"Enhanced textile wastewater treatment by a novel biofilm carrier with adsorbed nutrients","volume":"24","author":"Mulinari","year":"2020","journal-title":"Biocatal. Agric. Biotechnol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Berinson, B., Bellon, E., Christner, M., Both, A., Aepfelbacher, M., and Rohde, H. (2020). Identification of Kosakonia cowanii as a rare cause of acute cholecystitis: Case report and review of the literature. BMC Infect Dis., 20.","DOI":"10.1186\/s12879-020-05084-6"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1055\/s-0040-1721448","article-title":"Bacteremia due to Kosakonia cowanii in a preterm neonate","volume":"16","author":"Duployez","year":"2021","journal-title":"J. Pediatr. Infect Dis."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"e1135","DOI":"10.1002\/mbo3.1135","article-title":"Mobile fosfomycin resistance genes in Enterobacteriaceae\u2014An increasing threat","volume":"9","author":"Zurfluh","year":"2020","journal-title":"Microbiologyopen"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1111\/mmi.14606","article-title":"Escherichia coli small heat shock protein IbpA is an aggregation-sensor that self-regulates its own expression at posttranscriptional levels","volume":"115","author":"Miwa","year":"2021","journal-title":"Mol. Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.3389\/fmicb.2017.01109","article-title":"Prevalence and genetic diversity of Enterococcus faecalis isolates from mineral water and spring water in China","volume":"16","author":"Wei","year":"2017","journal-title":"Front Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"112452","DOI":"10.1016\/j.lwt.2021.112452","article-title":"Enterococcus faecalis and Enterococcus faecium in pasteurized milk: Prevalence, genotyping, and characterization of virulence traits","volume":"153","author":"Nasiri","year":"2022","journal-title":"LWT"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"3368","DOI":"10.1021\/acs.biochem.0c00544","article-title":"Significance of individual domains of ClpL: A novel chaperone from Streptococcus mutans","volume":"59","author":"Jana","year":"2020","journal-title":"Biochemistry."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Kim, H.-J., Youn, H.-Y., Kang, H.-J., Moon, J.-S., Jang, Y.-S., Song, K.-Y., and Seo, K.-H. (2022). Prevalence and Virulence Characteristics of Enterococcus faecalis and Enterococcus faecium in Bovine Mastitis Milk Compared to Bovine Normal Raw Milk in South Korea. Animals, 12.","DOI":"10.3390\/ani12111407"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"2700","DOI":"10.3389\/fmicb.2018.02700","article-title":"Resistance of Listeria monocytogenes to Stress Conditions Encountered in Food and Food Processing Environments","volume":"9","author":"Bucur","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.3389\/fmicb.2018.01708","article-title":"Cronobacter sakazakii and microbiological parameters in dairy formulas associated with a food alert in Chile","volume":"9","author":"Contreras","year":"2018","journal-title":"Front. Microbiol."},{"key":"ref_50","unstructured":"World Health Organization (WHO) (2022, September 08). Safe Preparation, Storage and Handling of Powdered Infant Formula. Available online: https:\/\/apps.who.int\/iris\/handle\/10665\/43659."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.ijfoodmicro.2009.08.005","article-title":"International survey of Cronobacter sakazakii and other Cronobacter spp. in follow up formulas and infant foods","volume":"136","author":"Chap","year":"2009","journal-title":"Int. J. Food Microbiol."}],"container-title":["Foods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2304-8158\/11\/22\/3556\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:12:44Z","timestamp":1760145164000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2304-8158\/11\/22\/3556"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,8]]},"references-count":51,"journal-issue":{"issue":"22","published-online":{"date-parts":[[2022,11]]}},"alternative-id":["foods11223556"],"URL":"https:\/\/doi.org\/10.3390\/foods11223556","relation":{},"ISSN":["2304-8158"],"issn-type":[{"value":"2304-8158","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,8]]}}}