AUTHOR=Parra-Flores Julio , Holý Ondřej , Acuña Sergio , Lepuschitz Sarah , Pietzka Ariane , Contreras-Fernández Alejandra , Chavarría-Sepulveda Pamela , Cruz-Córdova Ariadnna , Xicohtencatl-Cortes Juan , Mancilla-Rojano Jetsi , Castillo Alejandro , Ruppitsch Werner , Forsythe Stephen 

TITLE=Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile

JOURNAL=Frontiers in Microbiology

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.884721

DOI=10.3389/fmicb.2022.884721

ISSN=1664-302X

ABSTRACT=<p>This study characterized five <italic>Cronobacter</italic> spp. and six <italic>Salmonella</italic> spp. strains that had been isolated from 155 samples of powdered infant formula (PIF) sold in Chile and manufactured in Chile and Mexico in 2018–2020. Two strains of <italic>Cronobacter sakazakii</italic> sequence type (ST) ST1 and ST31 (serotypes O:1 and O:2) and one strain of <italic>Cronobacter malonaticus</italic> ST60 (O:1) were identified. All <italic>Salmonella</italic> strains were identified as <italic>Salmonella</italic> Typhimurium ST19 (serotype O:4) by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST (cgMLST). The <italic>C. sakazakii</italic> and <italic>C. malonaticus</italic> isolates were resistant to cephalothin, whereas the <italic>Salmonella</italic> isolates were resistant to oxacillin and ampicillin. Nineteen antibiotic resistance genes were detected in the <italic>C. sakazakii</italic> and <italic>C. malonaticus</italic> isolates; the most prevalent were mcr-9.1, <italic>bla<sub>CSA</sub></italic>, and <italic>bla<sub>CMA</sub></italic>. In <italic>Salmonella</italic>, 30 genes encoding for aminoglycoside and cephalosporin resistance were identified, including <italic>aac(6′)-Iaa</italic>, β-<italic>lactamases ampH</italic>, <italic>ampC1</italic>, and <italic>marA</italic>. In the <italic>Cronobacter</italic> isolates, 32 virulence-associated genes were detected by WGS and clustered as flagellar proteins, outer membrane proteins, chemotaxis, hemolysins, invasion, plasminogen activator, colonization, transcriptional regulator, survival in macrophages, use of sialic acid, and toxin-antitoxin genes. In the <italic>Salmonella</italic> strains, 120 virulence associated genes were detected, adherence, magnesium uptake, resistance to antimicrobial peptides, secretion system, stress protein, toxin, resistance to complement killing, and eight pathogenicity islands. The <italic>C. sakazakii</italic> and <italic>C. malonaticus</italic> strains harbored I-E and I-F CRISPR-Cas systems and carried Col(pHHAD28) and IncFIB(pCTU1) plasmids, respectively. The <italic>Salmonella</italic> strains harbored type I-E CRISPR-Cas systems and carried IncFII(S) plasmids. The presence of <italic>C. sakazakii</italic> and <italic>Salmonella</italic> in PIF is a health risk for infants aged less than 6 months. For this reason, sanitary practices should be reinforced for its production and retail surveillance.</p>