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Garrido-Palazuelos LI, Aguirre-Sánchez JR, Castro-Del Campo N, López-Cuevas O, González-Torres B, Chaidez C, Medrano-Félix JA. Genomic characteristics of Salmonella Montevideo and Pomona: impact of isolation source on antibiotic resistance, virulence and metabolic capacity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-16. [PMID: 38576268 DOI: 10.1080/09603123.2024.2336597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Salmonella enterica is known for its disease-causing serotypes, including Montevideo and Pomona. These serotypes have been found in various environments, including river water, sediments, food, and animals. However, the global spread of these serotypes has increased, leading to many reported infections and outbreaks. The goal of this study was the genomic analysis of 48 strains of S. Montevideo and S. Pomona isolated from different sources, including clinical. Results showed that environmental strains carried more antibiotic resistance genes than the clinical strains, such as genes for resistance to aminoglycosides, chloramphenicol, and sulfonamides. Additionally, the type 4 secretion system, was only found in environmental strains. .Also many phosphotransferase transport systems were identified and the presence of genes for the alternative pathway Entner-Doudoroff. The origin of isolation may have a significant impact on the ability of Salmonella isolates to adapt and survive in different environments, leading to genomic flexibility and a selection advantage.
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Affiliation(s)
- Lennin Isaac Garrido-Palazuelos
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Roberto Aguirre-Sánchez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Osvaldo López-Cuevas
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Berenice González-Torres
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Cristóbal Chaidez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Andrés Medrano-Félix
- Investigadoras e investigadores por México Centro de Investigación En Alimentación y Desarrollo A.C. Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán, México
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Wang J, Li Q, Jiang Y, Wang Z, Jiao X. fosA7: a silent fosfomycin resistance gene in Salmonella? THE LANCET. MICROBE 2024; 5:e211. [PMID: 38008104 DOI: 10.1016/s2666-5247(23)00342-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/11/2023] [Indexed: 11/28/2023]
Affiliation(s)
- Jing Wang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Centre for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Qiuchun Li
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Centre for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yue Jiang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Centre for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhenyu Wang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Centre for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Centre for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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Zhang K, Wang Z, Wang P, Xu H, Jiao X, Li Q. Prevalence and genetic characteristics of Salmonella enterica serovar Meleagridis from animals and humans. Vet Microbiol 2024; 290:109993. [PMID: 38278043 DOI: 10.1016/j.vetmic.2024.109993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/28/2024]
Abstract
Salmonella enterica serovar Meleagridis (S. Meleagridis) is a non-typhoidal Salmonella serotype commonly found in food and humans. In this study, we investigated 61 Chinese S. Meleagridis isolates from various sources, predominantly from pigs and pig products. Additionally, the serotype was also identified in samples from human infections. Whole-genome sequencing analysis of these isolates, combined with 10 isolates from other countries, demonstrated that the Chinese isolates formed a distinct Cluster C, further divided into two subclusters (Cluster C-1 and Cluster C-2) based on cgMLST analysis. CRISPR typing divided the 61 isolates into three CRISPR types (MCT1, MCT2, MCT3), belonging to Cluster I (96.7%, 59/61) and Cluster II (3.3%, 2/61), which corresponded to Cluster C-2 and Cluster C-1, respectively. Among the 48 identified spacers, the spacer SoeB5 was the only target differentiating MCT1 and MCT2 isolates of Cluster I. MelB12 and MelB13, identified in US and Denmark isolates, were not found among the 61 Chinese isolates. Examination of antimicrobial resistance gene profiles and their genetic contexts uncovered the presence of IncR plasmids in 43 (70.5%, 43/61) isolates within Cluster C, conferring resistance to tetracycline and trimethoprim/sulfamethoxazole. Homology analysis of spacers showed that 12 spacers exhibited similarity to sequences in phages or plasmids. Additionally, five spacers showed homology to sequences in plasmids from other Salmonella serotypes, suggesting their potential role in helping S. Meleagridis resist against Salmonella isolates carrying similar plasmids. The comprehensive analysis of CRISPR, cgMLST, and antimicrobial resistance in S. Meleagridis highlights the pig reservoir as a crucial factor in the evolution and transmission of this serotype to humans.
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Affiliation(s)
- Kai Zhang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Zhenyu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Pengyu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Haiyan Xu
- Nantong Center for Disease Control and Prevention, Nantong 226007, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Qiuchun Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China.
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Archer EW, Chisnall T, Tano-Debrah K, Card RM, Duodu S, Kunadu APH. Prevalence and genomic characterization of Salmonella isolates from commercial chicken eggs retailed in traditional markets in Ghana. Front Microbiol 2023; 14:1283835. [PMID: 38029182 PMCID: PMC10646427 DOI: 10.3389/fmicb.2023.1283835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Salmonella enterica are important foodborne bacterial pathogens globally associated with poultry. Exposure to Salmonella-contaminated eggs and egg-related products is a major risk for human salmonellosis. Presently, there is a huge data gap regarding the prevalence and circulating serovars of Salmonella in chicken eggs sold in Ghana. In this study, 2,304 eggs (pools of six per sample unit) collected from informal markets in Accra, Kumasi and Tamale, representing the three ecological belts across Ghana, were tested for Salmonella. Antimicrobial susceptibility testing and Whole Genome Sequencing (WGS) of the isolates were performed using standard microdilution protocols and the Illumina NextSeq platform, respectively. The total prevalence of Salmonella was 5.5% with a higher rate of contamination in eggshell (4.9%) over egg content (1.8%). The serovars identified were S. Ajiobo (n = 1), S. Chester (n = 6), S. Hader (n = 7), S. enteritidis (n = 2); and S. I 4:b:- (n = 8). WGS analysis revealed varied sequence types (STs) that were serovar specific. The S. I 4:b:- isolates had a novel ST (ST8938), suggesting a local origin. The two S. enteritidis isolates belonged to ST11 and were identified with an invasive lineage of a global epidemic clade. All isolates were susceptible to ampicillin, azithromycin, cefotaxime, ceftazidime, gentamicin, meropenem, and tigecycline. The phenotypic resistance profiles to seven antimicrobials: chloramphenicol (13%), ciprofloxacin (94%), and nalidixic acid (94%), colistin (13%), trimethoprim (50%) sulfamethoxazole (50%) and tetracycline (50%) corresponded with the presence of antimicrobial resistance (AMR) determinants including quinolones (gyrA (D87N), qnrB81), aminoglycosides (aadA1), (aph(3")-Ib aph(6)-Id), tetracyclines (tet(A)), phenicols (catA1), trimethoprim (dfrA14 and dfrA1). The S. enteritidis and S. Chester isolates were multidrug resistant (MDR). Several virulence factors were identified, notably cytolethal distending toxin (cdtB gene), rck, pef and spv that may promote host invasion and disease progression in humans. The findings from this study indicate the presence of multidrug resistant and virulent strains of Salmonella serovars in Ghanaian chicken eggs, with the potential to cause human infections. This is a critical baseline information that could be used for Salmonella risk assessment in the egg food chain to mitigate potential future outbreaks.
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Affiliation(s)
- Edward W. Archer
- Nutrition and Food Science Department, University of Ghana, Accra, Ghana
- Food and Drug Authority, Food Safety Management Department, Accra, Ghana
| | - Tom Chisnall
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Kwaku Tano-Debrah
- Nutrition and Food Science Department, University of Ghana, Accra, Ghana
| | | | - Samuel Duodu
- Biochemistry Cell and Molecular Biology Department, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
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Habib I, Khan M, Mohamed MYI, Ghazawi A, Abdalla A, Lakshmi G, Elbediwi M, Al Marzooqi HM, Afifi HS, Shehata MG, Al-Rifai R. Assessing the Prevalence and Potential Risks of Salmonella Infection Associated with Fresh Salad Vegetable Consumption in the United Arab Emirates. Foods 2023; 12:3060. [PMID: 37628060 PMCID: PMC10453016 DOI: 10.3390/foods12163060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
This study aimed to investigate the occurrence and characteristics of Salmonella isolates in salad vegetables in the United Arab Emirates (UAE). Out of 400 samples tested from retail, only 1.25% (95% confidence interval, 0.41-2.89) were found to be positive for Salmonella, all of which were from conventional local produce, presented at ambient temperature, and featured as loose items. The five Salmonella-positive samples were arugula (n = 3), dill (n = 1), and spinach (n = 1). The Salmonella isolates from the five samples were found to be pan-susceptible to a panel of 12 antimicrobials tested using a disc diffusion assay. Based on whole-genome sequencing (WGS) analysis, only two antimicrobial resistance genes were detected-one conferring resistance to aminoglycosides (aac(6')-Iaa) and the other to fosfomycin (fosA7). WGS enabled the analysis of virulence determinants of the recovered Salmonella isolates from salad vegetables, revealing a range from 152 to 165 genes, collectively grouped under five categories, including secretion system, fimbrial adherence determinants, macrophage-inducible genes, magnesium uptake, and non-fimbrial adherence determinants. All isolates were found to possess genes associated with the type III secretion system (TTSS), encoded by Salmonella pathogenicity island-1 (SPI-1), but various genes associated with the second type III secretion system (TTSS-2), encoded by SPI-2, were absent in all isolates. Combining the mean prevalence of Salmonella with information regarding consumption in the UAE, an exposure of 0.0131 salmonellae consumed per person per day through transmission via salad vegetables was calculated. This exposure was used as an input in a beta-Poisson dose-response model, which estimated that there would be 10,584 cases of the Salmonella infection annually for the entire UAE population. In conclusion, salad vegetables sold in the UAE are generally safe for consumption regarding Salmonella occurrence, but occasional contamination is possible. The results of this study may be used for the future development of risk-based food safety surveillance systems in the UAE and to elaborate on the importance for producers, retailers, and consumers to follow good hygiene practices, particularly for raw food items such as leafy salad greens.
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Affiliation(s)
- Ihab Habib
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates; (M.-Y.I.M.); (A.A.); (G.L.)
- Environmental Health Department, High Institute of Public Health, Alexandria University, Alexandria 21531, Egypt
| | - Mushtaq Khan
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates; (M.K.); (A.G.)
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
| | - Mohamed-Yousif Ibrahim Mohamed
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates; (M.-Y.I.M.); (A.A.); (G.L.)
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates; (M.K.); (A.G.)
| | - Afra Abdalla
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates; (M.-Y.I.M.); (A.A.); (G.L.)
| | - Glindya Lakshmi
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates; (M.-Y.I.M.); (A.A.); (G.L.)
| | - Mohammed Elbediwi
- Evolutionary Biology, Institute for Biology, Freie Universität Berlin, 14163 Berlin, Germany;
- Animal Health Research Institute, Agriculture Research Centre, Cairo 12618, Egypt
| | - Hassan Mohamed Al Marzooqi
- Food Research Section, Research and Development Division, Abu Dhabi Agriculture and Food Safety Authority (ADAFSA), Abu Dhabi P.O. Box 52150, United Arab Emirates; (H.M.A.M.); (H.S.A.); (M.G.S.)
| | - Hanan Sobhy Afifi
- Food Research Section, Research and Development Division, Abu Dhabi Agriculture and Food Safety Authority (ADAFSA), Abu Dhabi P.O. Box 52150, United Arab Emirates; (H.M.A.M.); (H.S.A.); (M.G.S.)
| | - Mohamed Gamal Shehata
- Food Research Section, Research and Development Division, Abu Dhabi Agriculture and Food Safety Authority (ADAFSA), Abu Dhabi P.O. Box 52150, United Arab Emirates; (H.M.A.M.); (H.S.A.); (M.G.S.)
- Food Technology Department, Arid Lands Cultivation Research Institute (ALCRI), City of Scientific Research and Technological Applications (SRTACITY), New Borg El-Arab City 21934, Egypt
| | - Rami Al-Rifai
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates;
- Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates
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Vázquez X, García-Fierro R, Fernández J, Bances M, Herrero-Fresno A, Olsen JE, Rodicio R, Ladero V, García V, Rodicio MR. Incidence and Genomic Background of Antibiotic Resistance in Food-Borne and Clinical Isolates of Salmonella enterica Serovar Derby from Spain. Antibiotics (Basel) 2023; 12:1204. [PMID: 37508300 PMCID: PMC10376468 DOI: 10.3390/antibiotics12071204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Salmonella enterica serovar Derby (S. Derby) ranks fifth among nontyphoidal Salmonella serovars causing human infections in the European Union. S. Derby isolates (36) collected between 2006 and 2018 in a Spanish region (Asturias) from human clinical samples (20) as well as from pig carcasses, pork- or pork and beef-derived products, or wild boar (16) were phenotypically characterized with regard to resistance, and 22 (12 derived from humans and 10 from food-related samples) were also subjected to whole genome sequence analysis. The sequenced isolates belonged to ST40, a common S. Derby sequence type, and were positive for SPI-23, a Salmonella pathogenicity island involved in adherence and invasion of the porcine jejune enterocytes. Isolates were either susceptible (30.6%), or resistant to one or more of the 19 antibiotics tested for (69.4%). Resistances to tetracycline [tet(A), tet(B) and tet(C)], streptomycin (aadA2), sulfonamides (sul1), nalidixic acid [gyrA (Asp87 to Asn)] and ampicillin (blaTEM-1-like) were detected, with frequencies ranging from 8.3% to 66.7%, and were higher in clinical than in food-borne isolates. The fosA7.3 gene was present in all sequenced isolates. The most common phenotype was that conferred by the tet(A), aadA2 and sul1 genes, located within identical or closely related variants of Salmonella Genomic Island 1 (SGI1), where mercury resistance genes were also present. Diverse IncI1-I(α) plasmids belonging to distinct STs provided antibiotic [blaTEM-1, tet(A) and/or tet(B)] and heavy metal resistance genes (copper and silver), while small pSC101-like plasmids carried tet(C). Regardless of their location, most resistance genes were associated with genetic elements involved in DNA mobility, including a class one integron, multiple insertion sequences and several intact or truncated transposons. By phylogenetic analysis, the isolates were distributed into two distinct clades, both including food-borne and clinical isolates. One of these clades included all SGI1-like positive isolates, which were found in both kinds of samples throughout the entire period of study. Although the frequency of S. Derby in Asturias was very low (0.5% and 3.1% of the total clinical and food isolates of S. enterica recovered along the period of study), it still represents a burden to human health linked to transmission across the food chain. The information generated in the present study can support further epidemiological surveillance aimed to control this zoonotic pathogen.
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Affiliation(s)
- Xenia Vázquez
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain
| | - Raquel García-Fierro
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain
- Centro de Investigación Biomédica en Red-Enfermedades Respiratorias, 30627 Madrid, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, 33001 Oviedo, Spain
| | - Margarita Bances
- Laboratorio de Salud Pública, Dirección General de Salud Pública, Consejería de Salud del Principado de Asturias, 33011 Oviedo, Spain
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo (UO), 33006 Oviedo, Spain
| | - Víctor Ladero
- Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), 33300 Villaviciosa, Spain
- Grupo de Microbiología Molecular, Instituto de Investigación Sanitaria del Principado de Asturias (IAPA), 33011 Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Campus Terra, Universidade de Santiago de Compostela, 27002 Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - M Rosario Rodicio
- Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo (UO), 33006 Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
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Mattioni Marchetti V, Kraftova L, Finianos M, Sourenian T, Hrabak J, Bitar I. Polyclonal Spread of Fosfomycin Resistance among Carbapenemase-Producing Members of the Enterobacterales in the Czech Republic. Microbiol Spectr 2023; 11:e0009523. [PMID: 37098942 PMCID: PMC10269928 DOI: 10.1128/spectrum.00095-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/31/2023] [Indexed: 04/27/2023] Open
Abstract
Fosfomycin (FOS) has been recently reintroduced into clinical practice, but its effectiveness against multidrug-resistant (MDR) Enterobacterales is reduced due to the emergence of FOS resistance. The copresence of carbapenemases and FOS resistance could drastically limit antibiotic treatment. The aims of this study were (i) to investigate fosfomycin susceptibility profiles among carbapenem-resistant Enterobacterales (CRE) in the Czech Republic, (ii) to characterize the genetic environment of fosA genes among the collection, and (iii) to evaluate the presence of amino acid mutations in proteins involved in FOS resistance mechanisms. During the period from December 2018 to February 2022, 293 CRE isolates were collected from different hospitals in the Czech Republic. FOS MICs were assessed by the agar dilution method (ADM), FosA and FosC2 production was detected by the sodium phosphonoformate (PPF) test, and the presence of fosA-like genes was confirmed by PCR. Whole-genome sequencing was conducted with an Illumina NovaSeq 6000 system on selected strains, and the effect of point mutations in the FOS pathway was predicted using PROVEAN. Of these strains, 29% showed low susceptibility to fosfomycin (MIC, ≥16 μg/mL) by ADM. An NDM-producing Escherichia coli sequence type 648 (ST648) strain harbored a fosA10 gene on an IncK plasmid, while a VIM-producing Citrobacter freundii ST673 strain harbored a new fosA7 variant, designated fosA7.9. Analysis of mutations in the FOS pathway revealed several deleterious mutations occurring in GlpT, UhpT, UhpC, CyaA, and GlpR. Results regarding single substitutions in amino acid sequences highlighted a relationship between ST and specific mutations and an enhanced predisposition for certain STs to develop resistance. This study highlights the occurrence of several FOS resistance mechanisms in different clones spreading in the Czech Republic. IMPORTANCE Antimicrobial resistance (AMR) currently represents a concern for human health, and the reintroduction of antibiotics such as fosfomycin into clinical practice can provide further option in treatment of multidrug-resistant (MDR) bacterial infections. However, there is a global increase of fosfomycin-resistant bacteria, reducing its effectiveness. Considering this increase, it is crucial to monitor the spread of fosfomycin resistance in MDR bacteria in clinical settings and to investigate the resistance mechanism at the molecular level. Our study reports a large variety of fosfomycin resistance mechanisms among carbapenemase-producing Enterobacterales (CRE) in the Czech Republic. Our study summarizes the main achievements of our research on the use of molecular technologies, such as next-generation sequencing (NGS), to describe the heterogeneous mechanisms that reduce fosfomycin effectiveness in CRE. The results suggest that a program for widespread monitoring of fosfomycin resistance and epidemiology fosfomycin-resistant organisms can aide timely implementation of countermeasures to maintain the effectiveness of fosfomycin.
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Affiliation(s)
- V. Mattioni Marchetti
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - L. Kraftova
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - M. Finianos
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - T. Sourenian
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - J. Hrabak
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
| | - I. Bitar
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czech Republic
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Casaux ML, D'Alessandro B, Vignoli R, Fraga M. Phenotypic and genotypic survey of antibiotic resistance in Salmonella enterica isolates from dairy farms in Uruguay. Front Vet Sci 2023; 10:1055432. [PMID: 36968467 PMCID: PMC10033963 DOI: 10.3389/fvets.2023.1055432] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/15/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella enterica is an important zoonotic pathogen that is frequently identified in dairy farming systems. An increase in antibiotic resistance has led to inadequate results of treatments, with impacts on animal and human health. Here, the phenotypic and genotypic susceptibility patterns of Salmonella isolates from dairy cattle and dairy farm environments were evaluated and compared. A collection of 75 S. enterica isolates were evaluated, and their phenotypic susceptibility was determined. For genotypic characterization, the whole genomes of the isolates were sequenced, and geno-serotypes, sequence types (STs) and core-genome-sequence types were determined using the EnteroBase pipeline. To characterize antibiotic resistance genes and gene mutations, tools from the Center for Genomic Epidemiology were used. Salmonella Dublin (SDu), S. Typhimurium (STy), S. Anatum (SAn), S. Newport (SNe), S. Agona (Sag), S. Montevideo (SMo) and IIIb 61:i:z53 were included in the collection. A single sequence type was detected per serovar. Phenotypic non-susceptibility to streptomycin and tetracycline was very frequent in the collection, and high non-susceptibility to ciprofloxacin was also observed. Multidrug resistance (MDR) was observed in 42 isolates (56.0%), with SAn and STy presenting higher MDR than the other serovars, showing non-susceptibility to up to 6 groups of antibiotics. Genomic analysis revealed the presence of 21 genes associated with antimicrobial resistance (AMR) in Salmonella isolates. More than 60% of the isolates carried some gene associated with resistance to aminoglycosides and tetracyclines. Only one gene associated with beta-lactam resistance was found, in seven isolates. Two different mutations were identified, parC_T57S and acrB_R717Q, which confer resistance to quinolones and azithromycin, respectively. The accuracy of predicting antimicrobial resistance phenotypes based on AMR genotypes was 83.7%. The genomic approach does not replace the phenotypic assay but offers valuable information for the survey of circulating antimicrobial resistance. This work represents one of the first studies evaluating phenotypic and genotypic AMR in Salmonella from dairy cattle in South America.
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Affiliation(s)
- María Laura Casaux
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- *Correspondence: María Laura Casaux
| | - Bruno D'Alessandro
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Martín Fraga
- Plataforma de Investigación en Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental INIA La Estanzuela, Colonia, Uruguay
- Martín Fraga
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9
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Gao R, Zhang J, Geng H, Wang Y, Kang X, Geng S, Jiao X, Barrow P. The Loss of focA Gene Increases the Ability of Salmonella Enteritidis to Exit from Macrophages and Boosts Early Extraintestinal Spread for Systemic Infection in a Mouse Model. Microorganisms 2022; 10:microorganisms10081557. [PMID: 36013975 PMCID: PMC9414335 DOI: 10.3390/microorganisms10081557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 11/29/2022] Open
Abstract
Salmonella Enteritidis (SE) can spread from the intestines to cause systemic infection, mainly involving macrophages. Intramacrophage Salmonella exits and reinfects neighboring cells, leading to severe disease. Salmonella genes involved in exiting from macrophages are not well understood or fully identified. A focA::Tn5 mutant was identified by an in vitro assay, with increased ability to exit from macrophages. A defined SEΔfocA mutant and its complemented derivative strain, SEΔfocA::focA, were constructed to confirm this phenotype. Although the lethal ability of focA mutants was similar to that of the parental SE in mice, it was isolated earlier from the liver and spleen than the parental SE. focA mutants induced higher levels of proinflammatory IL-12 and TNF-α compared with the parental SE and SEΔfocA::focA. focA mutants showed higher cytotoxicity and lower formate concentrations than SE and SEΔfocA::focA, whereas there was no change in pyroptosis, apoptosis and flagella formation ability. These current data suggest that the focA gene plays an important role in regulating intramacrophage Salmonella exiting and extraintestinal spread in mice, although the specific mechanism requires further in-depth studies.
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Affiliation(s)
- Ran Gao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (R.G.); (J.Z.); (H.G.); (Y.W.); (X.K.); (X.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Jian Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (R.G.); (J.Z.); (H.G.); (Y.W.); (X.K.); (X.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Haoyu Geng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (R.G.); (J.Z.); (H.G.); (Y.W.); (X.K.); (X.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Yaonan Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (R.G.); (J.Z.); (H.G.); (Y.W.); (X.K.); (X.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Xilong Kang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (R.G.); (J.Z.); (H.G.); (Y.W.); (X.K.); (X.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Shizhong Geng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (R.G.); (J.Z.); (H.G.); (Y.W.); (X.K.); (X.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-(514)-87971136; Fax: +86-(514)-87991747
| | - Xin’an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; (R.G.); (J.Z.); (H.G.); (Y.W.); (X.K.); (X.J.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Paul Barrow
- School of Veterinary Medicine, University of Surrey, Daphne Jackson Road, Guildford GU2 7AL, UK;
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10
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Spread and Molecular Characteristics of
Enterobacteriaceae
Carrying
fosA
-Like Genes from Farms in China. Microbiol Spectr 2022; 10:e0054522. [PMID: 35852324 PMCID: PMC9431306 DOI: 10.1128/spectrum.00545-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the widespread and complex genetic environments of
fosA
-like genes in animal-derived strains in China. The
fosA7.5
gene was identified in this study and was found to confer resistance to fosfomycin.
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