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Chen Z, Moreno-Switt AI, Reyes-Jara A, Delgado Suarez E, Adell AD, Oliveira CJB, Bonelli RR, Huang X, Brown E, Allard M, Grim C, Bell R, Meng J, Toro M. A multicenter genomic epidemiological investigation in Brazil, Chile, and Mexico reveals the diversity and persistence of Salmonella populations in surface waters. mBio 2024; 15:e0077724. [PMID: 38920393 PMCID: PMC11253603 DOI: 10.1128/mbio.00777-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
This study examined the diversity and persistence of Salmonella in the surface waters of agricultural regions of Brazil, Chile, and Mexico. Research groups (three in 2019-2020 and five in 2021-2022) conducted a long-term survey of surface water across 5-8 months annually (n = 30 monthly). On-site, each team filtered 10-L water samples with modified Moore Swabs to capture Salmonella, which were then isolated and identified using conventional microbiological techniques. Salmonella isolates were sequenced on Illumina platforms. Salmonella was present in 1,493/3,291 water samples (45.8%), with varying isolation rates across countries and years. Newport, Infantis, and Typhimurium were the most frequent among the 128 different serovars. Notably, 22 serovars were found in all three countries, representing almost half of the 1,911 different isolates collected. The resistome comprised 72 antimicrobial resistance (AMR) genes and six point mutations in three genes. At least one AMR determinant was observed in 33.8% (646/1,911) of the isolates, of which 47.4% (306/646) were potentially multidrug resistant. Phylogeny based on core genome multilocus sequence typing (cgMLST) showed that most isolates clustered according to sequence type and country of origin. Only 14 cgMLST multi-country clusters were detected among the 275 clusters. However, further analysis confirmed that close genetic relatedness occurred mostly among isolates from the same country, with three exceptions. Interestingly, isolates closely related phylogenetically were recovered over multiple years within the same country, indicating the persistence of certain Salmonella in those areas. In conclusion, surface waters in these regions are consistently contaminated with diverse Salmonella, including strains that persist over time.IMPORTANCESalmonella is a leading foodborne pathogen responsible for millions of illnesses, hospitalizations, and deaths annually. Although Salmonella-contaminated water has now been recognized as an important contamination source in the agrifood chain, there is a lack of knowledge on the global occurrence and diversity of Salmonella in surface water. Moreover, there has been insufficient research on Salmonella in surface waters from Latin American countries that are major producers and exporters of agricultural products. Incorporating genetic profiling of Salmonella isolates from underrepresented regions, such as Latin America, enhances our understanding of the pathogen's ecology, evolution, antimicrobial resistance, and pathogenicity. Moreover, leveraging genomic data derived from pathogens isolated from diverse geographical areas is critical for assessing the potential public health risk posed by the pathogen and expediting investigations of foodborne outbreaks. Ultimately, global efforts contribute significantly to reducing the incidence of foodborne infections.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
- Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Andrea I. Moreno-Switt
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Angelica Reyes-Jara
- Institute of Nutrition and Food Technology, University of Chile, Santiago, Chile
| | - Enrique Delgado Suarez
- Faculty of Veterinary Medicine and Zootechnics, National Autonomous University of Mexico, Mexico City, Mexico
| | - Aiko D. Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | | | - Raquel Regina Bonelli
- Medical Microbiology Research Laboratory, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xinyang Huang
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
- Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Eric Brown
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Christopher Grim
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
- Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
| | - Magaly Toro
- Joint Institute for Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, USA
- Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Institute of Nutrition and Food Technology, University of Chile, Santiago, Chile
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2
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Mather AE, Gilmour MW, Reid SWJ, French NP. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nat Rev Microbiol 2024:10.1038/s41579-024-01051-z. [PMID: 38789668 DOI: 10.1038/s41579-024-01051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2024] [Indexed: 05/26/2024]
Abstract
Foodborne illnesses pose a substantial health and economic burden, presenting challenges in prevention due to the diverse microbial hazards that can enter and spread within food systems. Various factors, including natural, political and commercial drivers, influence food production and distribution. The risks of foodborne illness will continue to evolve in step with these drivers and with changes to food systems. For example, climate impacts on water availability for agriculture, changes in food sustainability targets and evolving customer preferences can all have an impact on the ecology of foodborne pathogens and the agrifood niches that can carry microorganisms. Whole-genome and metagenome sequencing, combined with microbial surveillance schemes and insights from the food system, can provide authorities and businesses with transformative information to address risks and implement new food safety interventions across the food chain. In this Review, we describe how genome-based approaches have advanced our understanding of the evolution and spread of enduring bacterial foodborne hazards as well as their role in identifying emerging foodborne hazards. Furthermore, foodborne hazards exist in complex microbial communities across the entire food chain, and consideration of these co-existing organisms is essential to understanding the entire ecology supporting pathogen persistence and transmission in an evolving food system.
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Affiliation(s)
- Alison E Mather
- Quadram Institute Bioscience, Norwich, UK.
- University of East Anglia, Norwich, UK.
| | - Matthew W Gilmour
- Quadram Institute Bioscience, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Nigel P French
- Tāuwharau Ora, School of Veterinary Science, Te Kunenga Ki Pūrehuroa, Massey University, Papaioea, Palmerston North, Aotearoa New Zealand
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3
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Vaz CSL, da Fonseca FN, Voss-Rech D, Morés MAZ, Coldebella A, Cantão ME. Wild-type lytic bacteriophages against Salmonella Heidelberg: Further characterization and effect of prophylactic therapy in broiler chickens. Res Vet Sci 2024; 171:105247. [PMID: 38554611 DOI: 10.1016/j.rvsc.2024.105247] [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: 07/18/2023] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
To characterize wild-type bacteriophages and their effect on Salmonella Heidelberg intestinal colonization in broilers, phages combined in a cocktail were continuously delivered via drinking water since the first day after hatching. After challenge with a field strain, broilers were evaluated at regular intervals for S. Heidelberg and bacteriophages in tissues and cecum, and gross and microscopic lesions in organs. Phages were highly virulent against S. Heidelberg by efficiency of plating. One-step growth curves exhibited eclipse period from 20 to 25 min, whereas the lowest latent period and higher burst size found were 45 min and 54 PFU/cell, respectively. Bacteriophage whole genomic sequencing analyses revealed a lack of genes related to lysogeny, antimicrobial resistance, and virulence factors. Relevant gross or microscopic lesions were absent in tissues analyzed from treated broilers. Although numerically stable bacteriophage concentrations were detected in the cecal contents of treated broilers, no significant difference was found for the S. Heidelberg cecal load in comparison to the untreated group and for the prevalence of positive tissues throughout the evaluated period. The phages produced turbid plaques against some S. Heidelberg re-isolated from treated broilers, suggesting the evolving of a resistant subpopulation. Overall, the results provide new evidence of the safety and in vitro replication of such phages in S. Heidelberg. Nevertheless, continuous administration of the phage suspension most likely induced the development of bacteriophage-resistant mutants, which might have affected the in vivo effect. Therefore, a putative administration protocol should be based on other strategies, such as short-term therapy at pre-harvest age.
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Affiliation(s)
| | | | - Daiane Voss-Rech
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
| | | | - Arlei Coldebella
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
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4
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Aggarwal R, Mahajan P, Pandiya S, Bajaj A, Verma SK, Yadav P, Kharat AS, Khan AU, Dua M, Johri AK. Antibiotic resistance: a global crisis, problems and solutions. Crit Rev Microbiol 2024:1-26. [PMID: 38381581 DOI: 10.1080/1040841x.2024.2313024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/28/2024] [Indexed: 02/23/2024]
Abstract
Healthy state is priority in today's world which can be achieved using effective medicines. But due to overuse and misuse of antibiotics, a menace of resistance has increased in pathogenic microbes. World Health Organization (WHO) has announced ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) as the top priority pathogens as these have developed resistance against certain antibiotics. To combat such a global issue, it is utmost important to identify novel therapeutic strategies/agents as an alternate to such antibiotics. To name certain antibiotic adjuvants including: inhibitors of beta-lactamase, efflux pumps and permeabilizers for outer membrane can potentially solve the antibiotic resistance problems. In this regard, inhibitors of lytic domain of lytic transglycosylases provide a novel way to not only act as an alternate to antibiotics but also capable of restoring the efficiency of previously resistant antibiotics. Further, use of bacteriophages is another promising strategy to deal with antibiotic resistant pathogens. Taking in consideration the alternatives of antibiotics, a green synthesis nanoparticle-based therapy exemplifies a good option to combat microbial resistance. As horizontal gene transfer (HGT) in bacteria facilitates the evolution of new resistance strains, therefore identifying the mechanism of resistance and development of inhibitors against it can be a novel approach to combat such problems. In our perspective, host-directed therapy (HDT) represents another promising strategy in combating antimicrobial resistance (AMR). This approach involves targeting specific factors within host cells that pathogens rely on for their survival, either through replication or persistence. As many new drugs are under clinical trials it is advisable that more clinical data and antimicrobial stewardship programs should be conducted to fully assess the clinical efficacy and safety of new therapeutic agents.
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Affiliation(s)
- Rupesh Aggarwal
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Pooja Mahajan
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sameeksha Pandiya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aayushi Bajaj
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shailendra Kumar Verma
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Puja Yadav
- Department of Microbiology, Central University of Haryana, Mahendergarh, India
| | - Arun S Kharat
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Asad Ullah Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Meenakshi Dua
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Atul Kumar Johri
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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5
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Sanderson H, White AP. Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella. Methods Mol Biol 2024; 2813:19-37. [PMID: 38888768 DOI: 10.1007/978-1-0716-3890-3_2] [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] [Indexed: 06/20/2024]
Abstract
Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.
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Affiliation(s)
- Haley Sanderson
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
- Biological Informatics Center of Excellence, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
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6
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Aguilera M, Tobar-Calfucoy E, Rojas-Martínez V, Norambuena R, Serrano MJ, Cifuentes O, Zamudio MS, San Martín D, Lara P, Sabag A, Zabner M, Tichy D, Camejo P, León L, Pino M, Ulloa S, Rojas F, Pieringer C, Muster C, Castillo D, Ferreira N, Avendaño C, Canaval M, Pieringer H, Cifuentes P, Cifuentes Muñoz N. Development and characterization of a bacteriophage cocktail with high lytic efficacy against field-isolated Salmonella enterica. Poult Sci 2023; 102:103125. [PMID: 37879168 PMCID: PMC10618821 DOI: 10.1016/j.psj.2023.103125] [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: 08/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 10/27/2023] Open
Abstract
Salmonella spp. is a prevalent pathogen that causes great public health concern worldwide. Bacteriophage-based cocktails have arisen as an alternative to antibiotics to inhibit the growth of Salmonella. However, the bactericidal effect of bacteriophage cocktails in vivo largely differs from their observed effect in vitro. This is partly because in vitro developments of cocktails do not always consider the bacterial diversity nor the environmental conditions where bacteriophages will have to replicate. Here, we isolated and sequenced 47 bacteriophages that showed variable degrees of lytic activity against 258 Salmonella isolates from a commercial broiler company in Brazil. Three of these bacteriophages were characterized and selected to assemble a cocktail. In vitro quantitative assays determined the cocktail to be highly effective against multiple serovars of Salmonella, including Minnesota and Heidelberg. Remarkably, the in vitro lytic activity of the cocktail was retained or improved in conditions that more closely resembled the chicken gut, such as anaerobiosis, 42°C, and Salmonella mono-strain biofilms. Analysis of bacterial cross-resistance between the 3 bacteriophages composing the cocktail revealed limited or no generation of cross-resistance. Our results highlight the relevance of an optimized flux of work to develop bacteriophage cocktails against Salmonella with high lytic efficacy and strong potential to be applied in vivo in commercial broiler farms.
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Affiliation(s)
- Matías Aguilera
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Eduardo Tobar-Calfucoy
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Victoria Rojas-Martínez
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Rodrigo Norambuena
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - María Jesús Serrano
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Onix Cifuentes
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - María Sofía Zamudio
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Daniel San Martín
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Pabla Lara
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Andrea Sabag
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Marcela Zabner
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Daniel Tichy
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Pamela Camejo
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Luis León
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Michael Pino
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Soledad Ulloa
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Felipe Rojas
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Christian Pieringer
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Cecilia Muster
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Daniel Castillo
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Nicolás Ferreira
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Camilo Avendaño
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Mauro Canaval
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Hans Pieringer
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Pablo Cifuentes
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile
| | - Nicolás Cifuentes Muñoz
- PhageLab Chile SpA, Vicuña Mackenna 4860, Centro de Innovación Anacleto Angelini 5th floor, Santiago, Chile..
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7
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Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [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: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
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Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
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da Silva EC, de Oliveira CD, Ribeiro LFM, Casas MRT, Pereira JG, Possebon FS, Junior JPA. Salmonella detection with LAMP and qPCR and identification of serovars of interest by multiplex qPCR in poultry carcasses. Braz J Microbiol 2023; 54:2173-2182. [PMID: 37582950 PMCID: PMC10484893 DOI: 10.1007/s42770-023-01095-y] [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: 02/10/2023] [Accepted: 08/03/2023] [Indexed: 08/17/2023] Open
Abstract
Salmonella is present in the poultry production chain and is a major challenge in terms of food safety and animal health. The early Salmonella detection is one of the main tools to control and prevent the transmission of this pathogen. Microbiological isolation and serotyping to identify and differentiate Salmonella serovars are laborious processes, time-consuming, and expensive. Therefore, molecular diagnostic methods can be rapid and efficient alternatives to the detection of this pathogen. Thus, the aim herein was to standardize and evaluate the use of loop-mediated isothermal amplification (LAMP) in comparison with real-time PCR (qPCR) for detection of Salmonella associated with a multiplex qPCR for simultaneous identification and differentiation of S. Enteritidis, S. Typhimurium, S. Pullorum, and S. Gallinarum. The LAMP, qPCR, and multiplex qPCR assays were comparable in specificity. The three techniques were evaluated for specificity for 16 different serovars of Salmonella and for 37 strains of the serovars of interest. The limit of detection and the efficiency of the LAMP, qPCR, and multiplex qPCR reactions were determined. The techniques were applied to 33 samples of chicken carcasses and compared to the results of conventional microbiology for validation. As results, LAMP was specific in the detection of different Salmonella serovars but presented lower limit of detection ranging from 101 to 104 CFU/reaction. In comparison, qPCR could detect less cells (100 to 102 CFU/reaction), reaching equal specificity and better repeatability in the assays. The qPCR multiplexing for identification of the different serovars also showed good specificity, with the detection threshold between entre 101 and 102 CFU/reaction. The results obtained in the analyses on poultry carcasses suggested a correspondence between the results obtained in molecular methods and in conventional microbiology. Thus, the proposed assays are promising for the diagnosis of Salmonella in poultry carcasses, already proved to be faster and more efficient than conventional diagnostics techniques, being of great interest for poultry production, animal, and public health.
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Affiliation(s)
- Evelyn Cristine da Silva
- Institute for Biotechnology, São Paulo State University (UNESP), Tecomarias Avenue, Botucatu, SP, 18607-440, Brazil.
| | - Catarina Demarchi de Oliveira
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - Lucas Franco Miranda Ribeiro
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - Monique Ribeiro Tiba Casas
- Bacteriology Division, Adolfo Lutz Institute (IAL), Doutor Arnaldo Avenue, São Paulo, SP, 01246-000, Brazil
| | - Juliano Gonçalves Pereira
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - Fábio Sossai Possebon
- Institute for Biotechnology, São Paulo State University (UNESP), Tecomarias Avenue, Botucatu, SP, 18607-440, Brazil
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Prof. Walter Maurício Correa St., SP, 18618-681, Botucatu, Brazil
| | - João Pessoa Araújo Junior
- Institute for Biotechnology, São Paulo State University (UNESP), Tecomarias Avenue, Botucatu, SP, 18607-440, Brazil
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Aboah J, Ngom B, Emes E, Fall AG, Seydi M, Faye A, Dione M. Mapping the effect of antimicrobial resistance in poultry production in Senegal: an integrated system dynamics and network analysis approach. Front Vet Sci 2023; 10:1189109. [PMID: 37519996 PMCID: PMC10374361 DOI: 10.3389/fvets.2023.1189109] [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: 03/18/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
The impact of antimicrobial resistance (AMR) extends beyond the farm-level to other stakeholders warranting the need for a collaborative approach to combat AMR while optimising production objectives and safeguarding human health. This study maps out the effect of AMR originating from poultry production in Senegal and highlights the entry points for interventions from stakeholders' perspectives. A causal loop diagram (CLD) was developed following a group model building procedure with 20 stakeholders and integrated with network analysis by translating the CLD into an unweighted directed network. Results indicate that with an eigenvector centrality of 1, 0.85, and 0.74, the production cost, on-farm profit, and on-farm productivity, respectively are the most ranked influential variables driving the complexity of AMR in the poultry production system. Two reinforcing feedback loops highlight the dual benefits of improving on-farm productivity and increasing on-farm profit. However, one balancing feedback loop that revolves around the causal link between producers' investment in qualified human resource personnel to ensure good farm management practices underline the financial implication of producers' investment decisions. The findings provide precursory groundings for the development of a quantitative SD model, the formulation of intervention scenarios and ex-ante impact assessment of the cost-effectiveness of the interventions.
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Affiliation(s)
- Joshua Aboah
- International Livestock Research Institute (Senegal), Saint-Louis, Senegal
- Commonwealth Scientific and Industrial Research Organisation, St Lucia, QLD, Australia
| | - Babacar Ngom
- Directorate of Veterinary Services, Ministry of Livestock and Animal Productions, Dakar, Senegal
| | - Eves Emes
- Vaccine Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Awa Gueye Fall
- Directorate of Veterinary Services, Ministry of Livestock and Animal Productions, Dakar, Senegal
| | - Moutar Seydi
- Directorate of Veterinary Services, Ministry of Livestock and Animal Productions, Dakar, Senegal
| | - Ardiouma Faye
- Université Cheikh Anta Diop de Dakar, Département de Sociologie, Dakar, Senegal
| | - Michel Dione
- International Livestock Research Institute (Senegal), Saint-Louis, Senegal
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Bloomfield SJ, Janecko N, Palau R, Alikhan NF, Mather AE. Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK. Microb Genom 2023; 9:mgen001075. [PMID: 37523225 PMCID: PMC10438825 DOI: 10.1099/mgen.0.001075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is a major cause of bacterial gastroenteritis. Although many countries have implemented whole genome sequencing (WGS) of NTS, there is limited knowledge on NTS diversity on food and its contribution to human disease. In this study, the aim was to characterise the NTS genomes from retail foods in a particular region of the UK and assess the contribution to human NTS infections. Raw food samples were collected at retail in a repeated cross-sectional design in Norfolk, UK, including chicken (n=311), leafy green (n=311), pork (n=311), prawn (n=279) and salmon (n=157) samples. Up to eight presumptive NTS isolates per positive sample underwent WGS and were compared to publicly available NTS genomes from UK human cases. NTS was isolated from chicken (9.6 %), prawn (2.9 %) and pork (1.3 %) samples and included 14 serovars, of which Salmonella Infantis and Salmonella Enteritidis were the most common. The S. Enteritidis isolates were only isolated from imported chicken. No antimicrobial resistance determinants were found in prawn isolates, whilst 5.1 % of chicken and 0.64 % of pork samples contained multi-drug resistant NTS. The maximum number of pairwise core non-recombinant single nucleotide polymorphisms (SNPs) amongst isolates from the same sample was used to measure diversity and most samples had a median of two SNPs (range: 0-251). NTS isolates that were within five SNPs to clinical UK isolates belonged to specific serovars: S. Enteritidis and S. Infantis (chicken), and S. I 4,[5],12:i- (pork and chicken). Most NTS isolates that were closely related to human-derived isolates were obtained from imported chicken, but further epidemiological data are required to assess definitively the probable source of the human cases. Continued WGS surveillance of Salmonella on retail food involving multiple isolates from each sample is necessary to capture the diversity of Salmonella and determine the relative importance of different sources of human disease.
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Affiliation(s)
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Raphaёlle Palau
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
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11
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Jenkins C, Griffith P, Hoban A, Brown C, Garner J, Bardsley M, Willis C, Jorgensen F, Bird M, Greig DR, Edmunds M, Beck C, Larkins L. Foodborne outbreak of extended spectrum beta lactamase producing Shigella sonnei associated with contaminated spring onions in the United Kingdom. J Food Prot 2023; 86:100074. [PMID: 37030629 DOI: 10.1016/j.jfp.2023.100074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 04/10/2023]
Abstract
Globalization of the food supply chain has created conditions favourable for emergence and spread of multidrug resistant (MDR) foodborne pathogens. In November 2021, the UK Health Security Agency detected an outbreak of 17 cases infected with the same strain of MDR extended spectrum beta-lactamase (ESBL)-producing Shigella sonnei. Phylogenetic analysis of whole genome sequencing data revealed the outbreak was closely related to strains of S. sonnei isolated from travellers returning to the UK from Egypt. None of the outbreak cases reported travel and all 17 cases reported eating food from a restaurant/food outlet in the week prior to symptom onset, of which 11/17 (64.7%) ate at branches of the same national restaurant franchise. All 17 cases were adults and 14/17 (82.4%) were female. Ingredient-level analyses of the meals consumed by the cases identified spring onions as the common ingredient. Food chain investigations revealed that the spring onions served at the implicated restaurants could be traced back to a single Egyptian producer. The foodborne transmission of ESBL-producing bacteria is an emerging global health concern, and concerted action from all stakeholders is required to ensure an effective response to mitigate the risks to public health.
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Affiliation(s)
- Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, NW9 5AT.
| | | | - Anne Hoban
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, NW9 5AT
| | - Claire Brown
- Field Service South West, UK Health Security Agency
| | | | | | - Caroline Willis
- Food Water and Environmental Microbiology Laboratory Porton, UK Health Security Agency, Salisbury SP4 0JG, UK
| | - Frieda Jorgensen
- Food Water and Environmental Microbiology Laboratory Porton, UK Health Security Agency, Salisbury SP4 0JG, UK
| | - Matthew Bird
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, NW9 5AT
| | - David R Greig
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, NW9 5AT
| | - Matt Edmunds
- Field Service South West, UK Health Security Agency
| | - Charles Beck
- Field Service South West, UK Health Security Agency
| | - Lesley Larkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency, London, NW9 5AT
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12
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Saidenberg ABS, Franco LS, Reple JN, Hounmanou YMG, Casas MRT, Cardoso B, Esposito F, Lincopan N, Dalsgaard A, Stegger M, Knöbl T. Salmonella Heidelberg and Salmonella Minnesota in Brazilian broilers: Genomic characterization of third-generation cephalosporin and fluoroquinolone-resistant strains. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:119-128. [PMID: 36629129 PMCID: PMC10103857 DOI: 10.1111/1758-2229.13132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/12/2022] [Indexed: 05/20/2023]
Abstract
Salmonella serovars Heidelberg and Minnesota encoding antimicrobial resistance to third-generation cephalosporins and fluoroquinolones are often detected in poultry/poultry meat. We analysed the genomes of 10 Salmonella Heidelberg (SH) and 4 Salmonella Minnesota (SM) from faecal isolates of Brazilian poultry. These featured virulent and multidrug-resistant characteristics, with AmpC beta-lactamase (blaCMY-2 ) predominance (9/14), for all SM (4/4) and some SH (3/10) located on IncC plasmid replicons. IncC carrying blaCTX-M-2 was only detected among SH (3/10). Mutation in the gyrA/parC genes was present in all SH, whereas SM harboured parC mutation plus qnrB19 on ColRNAI plasmids (3/4). In silico resistance overall corroborated with phenotypic results. Core genome phylogenies showed close clustering and high similarities between the Brazilian and poultry meat/food isolates from Europe, and to human isolates from European countries with documented import of Brazilian poultry meat. Conjugation assays with SM successfully transferred blaCMY-2 , and qnrB19 to an Escherichia coli recipient. The findings reinforce the ongoing antimicrobial resistance acquisition of SH and Minnesota and the risks for disseminating resistant strains and/or mobile elements which may increasingly affect importing countries and the need for controlling AMR in major poultry-exporting countries like Brazil.
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Affiliation(s)
- Andre Becker Simoes Saidenberg
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
- Department of Bacteria, Parasites and FungiStatens Serum InstitutCopenhagenDenmark
| | - Leticia Soares Franco
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
| | - Jessica Nacarato Reple
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
| | | | - Brenda Cardoso
- Department of MicrobiologyInstitute of Biomedical Science, University of São PauloSão PauloBrazil
| | - Fernanda Esposito
- Department of Clinical AnalysisSchool of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Nilton Lincopan
- Department of MicrobiologyInstitute of Biomedical Science, University of São PauloSão PauloBrazil
- Department of Clinical AnalysisSchool of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Section for Food Safety and ZoonosesInstitute for Veterinary and Companion Animal Science, Københavns UniversitetCopenhagenDenmark
| | - Marc Stegger
- Department of Bacteria, Parasites and FungiStatens Serum InstitutCopenhagenDenmark
| | - Terezinha Knöbl
- Department of Veterinary PathologySchool of Veterinary Medicine and Animal ScienceSão PauloBrazil
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13
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Shen X, Yin L, Zhang A, Zhao R, Yin D, Wang J, Dai Y, Hou H, Pan X, Hu X, Zhang D, Liu Y. Prevalence and Characterization of Salmonella Isolated from Chickens in Anhui, China. Pathogens 2023; 12:pathogens12030465. [PMID: 36986387 PMCID: PMC10054756 DOI: 10.3390/pathogens12030465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Salmonella is one of the most important zoonotic pathogens that can cause both acute and chronic illnesses in poultry flocks, and can also be transmitted to humans from infected poultry. The purpose of this study was to investigate the prevalence, antimicrobial resistance, and molecular characteristics of Salmonella isolated from diseased and clinically healthy chickens in Anhui, China. In total, 108 Salmonella isolates (5.66%) were successfully recovered from chicken samples (n = 1908), including pathological tissue (57/408, 13.97%) and cloacal swabs (51/1500, 3.40%), and S. Enteritidis (43.52%), S. Typhimurium (23.15%), and S. Pullorum (10.19%) were the three most prevalent isolates. Salmonella isolates showed high rates of resistance to penicillin (61.11%), tetracyclines (47.22% to tetracycline and 45.37% to doxycycline), and sulfonamides (48.89%), and all isolates were susceptible to imipenem and polymyxin B. In total, 43.52% isolates were multidrug-resistant and had complex antimicrobial resistance patterns. The majority of isolates harbored cat1 (77.78%), blaTEM (61.11%), and blaCMY-2 (63.89%) genes, and the antimicrobial resistance genes in the isolates were significantly positively correlated with their corresponding resistance phenotype. Salmonella isolates carry high rates of virulence genes, with some of these reaching 100% (invA, mgtC, and stn). Fifty-seven isolates (52.78%) were biofilm-producing. The 108 isolates were classified into 12 sequence types (STs), whereby ST11 (43.51%) was the most prevalent, followed by ST19 (20.37%) and ST92 (13.89%). In conclusion, Salmonella infection in chicken flocks is still serious in Anhui Province, and not only causes disease in chickens but might also pose a threat to public health security.
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Affiliation(s)
- Xuehuai Shen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Lei Yin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Anyun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Ruihong Zhao
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Dongdong Yin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Jieru Wang
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Yin Dai
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Hongyan Hou
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Xiaocheng Pan
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
- Correspondence: (X.P.); (Y.L.)
| | - Xiaomiao Hu
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Danjun Zhang
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Yongjie Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (X.P.); (Y.L.)
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14
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Alzahrani KO, AL-Reshoodi FM, Alshdokhi EA, Alhamed AS, Al Hadlaq MA, Mujallad MI, Mukhtar LE, Alsufyani AT, Alajlan AA, Al Rashidy MS, Al Dawsari MJ, Al-Akeel SI, AL-Harthi MH, Al Manee AM, Alghoribi MF, Alajel SM. Antimicrobial resistance and genomic characterization of Salmonella enterica isolates from chicken meat. Front Microbiol 2023; 14:1104164. [PMID: 37065154 PMCID: PMC10100587 DOI: 10.3389/fmicb.2023.1104164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/15/2023] [Indexed: 04/18/2023] Open
Abstract
This study investigated genotypic and phenotypic antimicrobial resistance profiles, phylogenic relatedness, plasmid and virulence composition of 39 Salmonella enterica strains isolated from chicken meat samples using whole genome sequencing (WGS) technology. Four distinct serotypes were identified; Salmonella Minnesota (16/39, 41%), Salmonella Infantis (13/39, 33.3%), Salmonella Enteritidis (9/39, 23.1%), and one isolate was detected for Salmonella Kentucky (1/39, 2.6%), with sequence types (STs) as followed: ST548, ST32, ST11, and ST198, respectively. Phenotypic resistance to tetracycline (91.2%), ampicillin (82.4%), sulfisoxazole (64.7%), and nalidixic acid (61.6%) was the most observed. Resistome analysis revealed the presence of resistance genes to aminoglycosides, β-lactamase, sulfonamides, trimethoprim, phenicol, lincosamide, macrolides, and tetracyclines. Plasmidome showed the presence of eight incompatibility groups, including IncA/C2, IncFIB(K)_1_Kpn3, Col440I_1, IncR, IncX1, IncI1_1_Alpha, IncFIB(S)/IncFII(S), IncHI2/IncHI2A, IncX2 and ColpVC plasmids across the 39 genomes. Three resistance genes, sul2, tetA and blaCMY-2, were predicted to be located on IncA/C2 plasmid in S. Minnesota isolates, whereas all S. Infantis isolates were positive to IncFIB(K)_1_Kpn3 plasmid that carries bla CTX-M-65 gene. Eleven Salmonella pathogenicity islands and up to 131 stress and/or virulence genes were identified in the evaluated genomes. Phylogenetic analysis showed four phylogroups that were consistent with the identified ST profiles with a high level of inter-diversity between isolates. This is the first genomic characterization of Salmonella isolates from retail chicken meat in Saudi Arabia using WGS technology. The availability of Salmonella genomes from multiple geographic locations, including Saudi Arabia, would be highly beneficial in future source-tracking, especially during epidemiological surveillance and outbreak investigations.
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Affiliation(s)
- Khaloud O. Alzahrani
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Fahad M. AL-Reshoodi
- Antimicrobial Resistance Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Elaf A. Alshdokhi
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Ashwaq S. Alhamed
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Meshari A. Al Hadlaq
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Mohammed I. Mujallad
- Molecular Biology Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Lenah E. Mukhtar
- Antimicrobial Resistance Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Amani T. Alsufyani
- Antimicrobial Resistance Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Abdullah A. Alajlan
- Microbial Identification Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Malfi S. Al Rashidy
- Microbial Identification Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Mashan J. Al Dawsari
- Microbial Identification Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Saleh I. Al-Akeel
- Microbial Identification Division, Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Meshari H. AL-Harthi
- Microbiology Section, Food Laboratory, Laboratories Executive Department, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
| | - Abdulaziz M. Al Manee
- Microbial Hazards Division, Risk Assessment Department, Executive Department of Monitoring and Risk Assessment, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
- Biology Department, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majed F. Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences (KSAU), Riyadh, Saudi Arabia
| | - Suliman M. Alajel
- Reference Laboratory for Microbiology, Executive Department of Reference Laboratories, Research and Laboratories Sector, Saudi Food and Drug Authority (SFDA), Riyadh, Saudi Arabia
- *Correspondence: Suliman M. Alajel,
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Davies N, Jørgensen F, Willis C, McLauchlin J, Chattaway MA. Whole genome sequencing reveals antimicrobial resistance determinants (AMR genes) of Salmonella enterica recovered from raw chicken and ready-to-eat leaves imported into England between 2014 and 2019. J Appl Microbiol 2022; 133:2569-2582. [PMID: 35880358 PMCID: PMC9804530 DOI: 10.1111/jam.15728] [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: 05/04/2022] [Revised: 07/08/2022] [Accepted: 07/19/2022] [Indexed: 01/05/2023]
Abstract
AIMS To compare the antimicrobial resistance (AMR) genes in a genetically diverse group of Salmonella enterica recovered from foods imported into England between 2014 and 2018. METHODS AND RESULTS Whole genome sequence was used to detect AMR genes or chromosomal mutations associated with AMR in Salmonella recovered from edible leaves imported from Asia (n = 115) as compared to Salmonella (n = 231) isolated from raw chicken, 74% originated from South America. Among isolates from edible leaves, three (3%) showed resistance to at least one antimicrobial agent, two (2%) of which were multidrug resistant (MDR, resistance to three or more antimicrobial classes). Resistance to at least one antimicrobial agent was detected in 214 (93%) in the chicken isolates, with 164 (71%) showing MDR. Genetic diversity and AMR profiles were highly heterogeneous across the different serovars. CONCLUSIONS Resistance was rare among the Salmonella isolates from edible leaves but common (including MDR) among those from raw chicken. SIGNIFICANCE AND IMPACT OF THE STUDY Surveillance of AMR in imported foods is essential for monitoring the risk of transmission of resistance from the food chain to humans and provides added public health value to pre-existing controls of the food chain.
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Affiliation(s)
- Nicola Davies
- Gastrointestinal Bacteria Reference Unit (GBRU)UK Health Security AgencyLondonUK,Division of Infection and ImmunityUniversity College LondonLondonUK
| | - Frieda Jørgensen
- Food Water and Environmental Microbiology Laboratory PortonUK Health Security AgencySalisburyUK
| | - Caroline Willis
- Food Water and Environmental Microbiology Laboratory PortonUK Health Security AgencySalisburyUK
| | - Jim McLauchlin
- Food Water and Environmental Microbiology ServicesUK Health Security AgencyLondonUK
| | - Marie Anne Chattaway
- Gastrointestinal Bacteria Reference Unit (GBRU)UK Health Security AgencyLondonUK
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