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Updated: Sep 7, 2025
Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples
Published on: October 25, 2018
Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in
Julio Parra-Flores1, Ondřej Holý2, Sergio Acuña3
1Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile.
Insights
Cronobacter and Salmonella were found in powdered infant formula (PIF) in Chile, posing a health risk to infants. Enhanced sanitary practices are crucial for PIF production and retail surveillance to prevent contamination.
Area of Science:
- Food Microbiology
- Public Health Microbiology
- Bacterial Pathogenesis
Background:
- Powdered infant formula (PIF) is a critical nutrition source for infants globally.
- Contamination of PIF with foodborne pathogens like Cronobacter and Salmonella poses a significant public health risk.
- Previous surveillance for these pathogens in PIF in Chile has been limited.
Purpose of the Study:
- To characterize Cronobacter and Salmonella strains isolated from PIF sold in Chile.
- To identify antibiotic resistance and virulence factors in these bacterial isolates.
- To assess the potential health risks associated with Cronobacter and Salmonella in PIF.
Main Methods:
- Whole Genome Sequencing (WGS) for bacterial identification and characterization.
- Multilocus Sequence Typing (MLST) including ribosomal MLST (rMLST) and core genome MLST (cgMLST).
- Detection of antibiotic resistance genes and virulence-associated genes.
Main Results:
- Identified Cronobacter sakazakii (ST1, ST31) and Cronobacter malonaticus (ST60), and Salmonella Typhimurium (ST19).
- Detected cephalothin resistance in Cronobacter and oxacillin/ampicillin resistance in Salmonella, with numerous associated resistance genes.
- Identified extensive virulence factors in both pathogens, including genes for adherence, invasion, and toxin production.
- Characterized CRISPR-Cas systems and plasmids in both Cronobacter and Salmonella isolates.
Conclusions:
- Cronobacter and Salmonella strains found in PIF possess antibiotic resistance and virulence factors.
- The presence of these pathogens in PIF represents a health risk for infants under six months.
- Reinforcement of sanitary practices in PIF production and retail surveillance is recommended.
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, bla , and bla . 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.
