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

Abstract

This study characterized five Cronobacter spp. and six Salmonella 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 Cronobacter sakazakii sequence type (ST) ST1 and ST31 (serotypes O:1 and O:2) and one strain of Cronobacter malonaticus ST60 (O:1) were identified. All Salmonella strains were identified as Salmonella Typhimurium ST19 (serotype O:4) by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST (cgMLST). The C. sakazakii and C. malonaticus isolates were resistant to cephalothin, whereas the Salmonella isolates were resistant to oxacillin and ampicillin. Nineteen antibiotic resistance genes were detected in the C. sakazakii and C. malonaticus isolates; the most prevalent were mcr-9.1, blaCSA, and blaCMA. In Salmonella, 30 genes encoding for aminoglycoside and cephalosporin resistance were identified, including aac(6′)-Iaa, β-lactamases ampH, ampC1, and marA. In the Cronobacter 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 Salmonella 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 C. sakazakii and C. malonaticus strains harbored I-E and I-F CRISPR-Cas systems and carried Col(pHHAD28) and IncFIB(pCTU1) plasmids, respectively. The Salmonella strains harbored type I-E CRISPR-Cas systems and carried IncFII(S) plasmids. The presence of C. sakazakii and Salmonella 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.

Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing

“…However, C. sakazakii is able to utilize sialic acid enhance its ability to cause systematic infections [36]. NanA has been identified as an antitoxin-encoding gene in C. sakazakii in multiple research works [4,5,38] and was also found in the current study.…”

“…OmpA has been reported as an important cellular adhesion factor in Cronobacter spp. to epithelial and endothelial cells of human and animal origin [5,28,36]. In addition, ompA has also been mentioned as a stress-response-encoding gene, especially osmotic stress [38].…”

“…RelB is an anti-toxin coding gene identified in all the isolates. Antitoxins are generally low-molecular-weight proteins that limit the toxin activity in the host cell by forming nontoxic toxin-antitoxin complexes (TA), shielding toxin targets, or specifically degrading toxin mRNAs [5]. A few reports have identified the possible presence of toxins associated with C. sakazakii [1].…”

“…Therefore, neonates and low-birthweight infants are the most susceptible population group since they could become infected through the consumption of PIF, or through contaminated bottles and appliances used for PIF preparation. The clinical profiles are mainly severe infantile septicemia, necrotizing enterocolitis, meningitis, and serious neurological sequelae [1,2,5].…”

“…The analysis of the complete genome of the Cronobacter strains isolated from PIF manufacturing plants enables us to identify new strains, taxonomic relationships, and genes associated with virulence and antibiotic resistance [5]. In recent years, WGS (wholegenome sequencing) has enabled researchers to perform extensive profiling and genotyping, such as multilocus sequence typing (MLST), and complete analysis of the pathogenesis process of C. sakazakii isolated from PIF plants is therefore possible.…”