Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates and Sample Preparation
2.2. DNA Extraction
2.3. WGS and Bioinformatic Analysis
2.4. Detection of Virulence and Antimicrobial Resistance Genes
2.5. Antimicrobial Susceptibility Test
2.6. Detection of Plasmids and Prophages
3. Results and Discussion
3.1. General Features of C. Sakazakii Strains
3.2. Phylogenetic Analysis
3.3. Virulence Factors Identified in the Selected Isolates
3.3.1. Virulence Factors Associated with Environmental Persistence
Adaptation to High Temperature
Adaptation to Acidic Environments, Osmotic Pressure, and Desiccation
3.3.2. Virulence Factors Associated with Invasion and Persistence in the Host Cell
Cell Attachment and Invasion
- 1-Flagellar and chemotaxis proteins
- 2-Outer membrane proteins (OMPs)
- 3-Lipopolysaccharides (LPSs)
- 4-Macrophage survival
- 5-Anti-Toxins
- 6-Utilization of Sialic Acid
- 7-Iron Acquisition System
- 8-Zinc Acquisition System
3.4. Antimicrobial Resistance Genes
3.5. Antibiotic Resistance Profile
3.6. Detection of Plasmids and Mobile Genetic Elements
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Isolates | Antibiotics | MIC * (µg) | Antibiotic Resistance Profile |
---|---|---|---|
CFS1154 | FAZ ** | 8 | R *** |
MIN | 4 | R | |
CFS1155 | MIN | 4 | R |
CFS1156 | FAZ | 8 | R |
MIN | 2 | R | |
CFS1157 | FAZ | 8 | R |
MIN | 4 | R | |
CFS1158 | FAZ | 16 | R |
MIN | 4 | R | |
CFS1159 | FAZ | 8 | R |
MIN | 2 | R | |
CFS1160 | FAZ | 8 | R |
MIN | 2 | R | |
CFS1161 | FAZ | 8 | R |
MIN | 2 | R | |
CFS1169 | FAZ | 8 | R |
MIN | 2 | R | |
CFS1176 | FAZ | 16 | R |
MIN | 2 | R | |
A/S 2 | 8/4 | R | |
CFS1297 | FAZ | 4 | R |
MIN | 4 | R | |
CFS1304 | FAZ | 16 | R |
MIN | 4 | R | |
CIP | 2 | R | |
CFS1322 | FAZ | 8 | R |
MIN | 4 | R | |
TAZ | 2 | I | |
AXO | 1 | S | |
CFS1362 | FAZ | 8 | R |
MIN | 4 | R | |
CFS1328 | FAZ | 8 | R |
MIN | 4 | R | |
CFS1370 | FAZ | 8 | R |
MIN | 4 | R | |
CFS1377 | FAZ | 8 | R |
MIN | 2 | R | |
CFS2786 | AMP | 16 | R |
FAZ | 16 | R | |
C/T | 4 | R | |
CIP | 2 | R | |
MIN | 4 | R | |
CZA | 16/4 | R | |
NIT | 64 | R | |
A/S 2 | 16/8 | R | |
CFS2788 | FAZ | 8 | R |
MIN | 4 | R | |
CIP | 2 | R |
Isolate | Plasmid | %Identity | Query/Template Length | Contig | Position in Contigs | Accession No. |
---|---|---|---|---|---|---|
CFS1156 | Col(pHAD28) | 94.96 | 119/131 | NODE_38_length_3676_cov_857.909693 | 1716...1834 | KU674895 |
CFS1157 | Col(pHAD28) | 94.96 | 119/131 | NODE_41_length_3676_cov_857.909693 | 1716...1834 | KU674895 |
CFS1158 | Col(pHAD28) | 94.96 | 119/131 | NODE_41_length_3676_cov_857.909693 | 1716...1834 | KU674895 |
CFS1160 | Col(pHAD28) | 94.96 | 119/131 | NODE_37_length_3672_cov_866.208737 | 1610...1728 | KU674895 |
CFS1176 | Col(pHAD28) | 94.96 | 119/131 | NODE_106_length_2518_cov_463.535120 | 1949...2067 | KU674895 |
CFS1362 | Col(pHAD28) | 94.96 | 119/131 | NODE_30_length_3676_cov_5.826291 | 1705...1823 | KU674895 |
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Mousavi, Z.E.; Koolman, L.; Macori, G.; Fanning, S.; Butler, F. Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing. Microorganisms 2023, 11, 2749. https://doi.org/10.3390/microorganisms11112749
Mousavi ZE, Koolman L, Macori G, Fanning S, Butler F. Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing. Microorganisms. 2023; 11(11):2749. https://doi.org/10.3390/microorganisms11112749
Chicago/Turabian StyleMousavi, Zeinab Ebrahimzadeh, Leonard Koolman, Guerrino Macori, Séamus Fanning, and Francis Butler. 2023. "Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing" Microorganisms 11, no. 11: 2749. https://doi.org/10.3390/microorganisms11112749