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Parra-Flores J, Holý O, Acuña S, Lepuschitz S, Pietzka A, Contreras-Fernández A, Chavarría-Sepulveda P, Cruz-Córdova A, Xicohtencatl-Cortes J, Mancilla-Rojano J, Castillo A, Ruppitsch W, Forsythe S. Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile. Front Microbiol 2022; 13:884721. [PMID: 35722296 PMCID: PMC9201451 DOI: 10.3389/fmicb.2022.884721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/04/2022] [Indexed: 11/14/2022] Open
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.
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Affiliation(s)
- Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - Ondřej Holý
- Science and Research Centre, Faculty of Health Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Sergio Acuña
- Department of Food Engineering, Universidad del Bío-Bío, Chillán, Chile
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | | | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jetsi Mancilla-Rojano
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.,Faculty of Medicine, Biological Sciences Graduate Program, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandro Castillo
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX, United States
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
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Hasan H, Nasirudeen NA, Ruzlan MAF, Mohd Jamil MA, Ismail NAS, Wahab AA, Ali A. Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers. CHILDREN (BASEL, SWITZERLAND) 2021; 8:1112. [PMID: 34943308 PMCID: PMC8700514 DOI: 10.3390/children8121112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022]
Abstract
Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.
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Affiliation(s)
- Haziqah Hasan
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Nor Ashika Nasirudeen
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Muhammad Alif Farhan Ruzlan
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Muhammad Aiman Mohd Jamil
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Noor Akmal Shareela Ismail
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
| | - Asrul Abdul Wahab
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
| | - Adli Ali
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
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Parra-Flores J, Holý O, Riffo F, Lepuschitz S, Maury-Sintjago E, Rodríguez-Fernández A, Cruz-Córdova A, Xicohtencatl-Cortes J, Mancilla-Rojano J, Troncoso M, Figueroa G, Ruppitsch W, Forsythe S. Profiling the Virulence and Antibiotic Resistance Genes of Cronobacter sakazakii Strains Isolated From Powdered and Dairy Formulas by Whole-Genome Sequencing. Front Microbiol 2021; 12:694922. [PMID: 34276629 PMCID: PMC8278472 DOI: 10.3389/fmicb.2021.694922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Cronobacter sakazakii is an enteropathogen that causes neonatal meningitis, septicemia, and necrotizing enterocolitis in preterm infants and newborns with a mortality rate of 15 to 80%. Powdered and dairy formulas (P-DF) have been implicated as major transmission vehicles and subsequently the presence of this pathogen in P-DF led to product recalls in Chile in 2017. The objective of this study was to use whole genome sequencing (WGS) and laboratory studies to characterize Cronobacter strains from the contaminated products. Seven strains were identified as C. sakazakii, and the remaining strain was Franconibacter helveticus. All C. sakazakii strains adhered to a neuroblastoma cell line, and 31 virulence genes were predicted by WGS. The antibiograms varied between strains. and included mcr-9.1 and bla CSA genes, conferring resistance to colistin and cephalothin, respectively. The C. sakazakii strains encoded I-E and I-F CRISPR-Cas systems, and carried IncFII(pECLA), Col440I, and Col(pHHAD28) plasmids. In summary, WGS enabled the identification of C. sakazakii strains and revealed multiple antibiotic resistance and virulence genes. These findings support the decision to recall the contaminated powdered and dairy formulas from the Chilean market in 2017.
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Affiliation(s)
- Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - Ondrej Holý
- Department of Public Health, Palacký University Olomouc, Olomouc, Czechia
| | | | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | | | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jetsi Mancilla-Rojano
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
- Faculty of Medicine, Biological Sciences Graduate Program, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miriam Troncoso
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Guillermo Figueroa
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
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Abstract
Diarrheal disease is still a major public health concern, as it is still considered an important cause of death in children under five years of age. A few decades ago, the detection of enteropathogenic E. coli was made by detecting the O, H, and K antigens, mostly by agglutination. The recent protocols recommend the molecular methods for diagnosing EPEC, as they can distinguish between typical and atypical EPEC by identifying the presence/absence of specific virulence factors. EPEC are defined as diarrheagenic strains of E. coli that can produce attaching and effacing lesions on the intestinal epithelium while being incapable of producing Shiga toxins and heat-labile or heat-stable enterotoxins. The ability of these strains to produce attaching and effacing lesions enable them to cause localized lesions by attaching tightly to the surface of the intestinal epithelial cells, disrupting the surfaces of the cells, thus leading to the effacement of the microvilli. EPEC are classified on typical and atypical isolates, based on the presence or absence of E. coli adherence factor plasmids. All the EPEC strains are eae positive; typical EPEC strains are eae+, bfpA+, while atypical strains are eae+, bfpA−. No vaccines are currently available to prevent EPEC infections.
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