1
|
Macori G, Al-Qahtani AA, Koolman L, Althawadi S, Mutabaqani M, Bashtawi R, Aljumaa S, Almaghrabi RS, Fanning S. Stenotrophomonas riyadhensis sp. nov., isolated from a hospital floor swab. Int J Syst Evol Microbiol 2024; 74. [PMID: 38393318 DOI: 10.1099/ijsem.0.006250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
During the analysis of a collection of Pseudomonas strains linked to an outbreak in an intensive care unit at King Faisal Specialist Hospital and Research Center in 2019, one isolate (CFS3442T) was identified phenotypically as Pseudomonas aeruginosa. However, whole-genome sequencing revealed its true identity as a member of the genus Stenotrophomonas, distinct from both P. aeruginosa and Stenotrophomonas maltophilia. The isolate demonstrated: (i) a significant phylogenetic distance from P. aeruginosa; (ii) considerable genomic differences from several S. maltophilia reference strains and other Stenotrophomonas species; and (iii) unique phenotypic characteristics. Based on the combined geno- and phenotypic data, we propose that this isolate represents a novel species within the genus Stenotrophomonas, for which the name Stenotrophomonas riyadhensis sp. nov. is proposed. The type strain is CFS3442T (=NCTC 14921T=LMG 33162T).
Collapse
Affiliation(s)
- Guerrino Macori
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Present address: School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Ahmed Ali Al-Qahtani
- Department of infection control and hospital epidemiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Leonard Koolman
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Ireland
| | - Sahar Althawadi
- Department of Pathology and Laboratory medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maysoon Mutabaqani
- Department of Pathology and Laboratory medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rustom Bashtawi
- Department of infection control and hospital epidemiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sulaiman Aljumaa
- Department of infection control and hospital epidemiology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Reem Saad Almaghrabi
- Organ transplant center of excellence, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Ireland
| |
Collapse
|
2
|
Arnold KE, Laing G, McMahon BJ, Fanning S, Stekel DJ, Pahl O, Coyne L, Latham SM, McIntyre KM. The need for One Health systems-thinking approaches to understand multiscale dissemination of antimicrobial resistance. Lancet Planet Health 2024; 8:e124-e133. [PMID: 38331529 DOI: 10.1016/s2542-5196(23)00278-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/29/2023] [Accepted: 12/15/2023] [Indexed: 02/10/2024]
Abstract
Although the effects of antimicrobial resistance (AMR) are most obvious at clinical treatment failure, AMR evolution, transmission, and dispersal happen largely in environmental settings, for example within farms, waterways, livestock, and wildlife. We argue that systems-thinking, One Health approaches are crucial for tackling AMR, by understanding and predicting how anthropogenic activities interact within environmental subsystems, to drive AMR emergence and transmission. Innovative computational methods integrating big data streams (eg, from clinical, agricultural, and environmental monitoring) will accelerate our understanding of AMR, supporting decision making. There are challenges to accessing, integrating, synthesising, and interpreting such complex, multidimensional, heterogeneous datasets, including the lack of specific metrics to quantify anthropogenic AMR. Moreover, data confidentiality, geopolitical and cultural variation, surveillance gaps, and science funding cause biases, uncertainty, and gaps in AMR data and metadata. Combining systems-thinking with modelling will allow exploration, scaling-up, and extrapolation of existing data. This combination will provide vital understanding of the dynamic movement and transmission of AMR within and among environmental subsystems, and its effects across the greater system. Consequently, strategies for slowing down AMR dissemination can be modelled and compared for efficacy and cost-effectiveness.
Collapse
Affiliation(s)
- Kathryn E Arnold
- Department of Environment and Geography, University of York, York, UK.
| | | | - Barry J McMahon
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, Dublin, Ireland
| | - Dov J Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK; Department of Mathematics and Applied Mathematics, University of Johannesburg, Johannesburg, South Africa
| | - Ole Pahl
- Department of Civil Engineering and Environmental Management, School of Computing, Engineering and Built Environment, Glasgow Caledonian University, Glasgow, UK
| | - Lucy Coyne
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; National Office of Animal Health, Stevenage, UK
| | - Sophia M Latham
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - K Marie McIntyre
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Modelling, Evidence and Policy group, School of Natural and Environmental Sciences, Newcastle University, Newcastle, UK
| |
Collapse
|
3
|
Almaghrabi RS, Macori G, Sheridan F, McCarthy SC, Floss-Jones A, Fanning S, Althawadi S, Mutabagani M, Binsaslloum A, Alrasheed M, Almohaizeie A, Allehyani B, Alghofaili A, Bohol MF, Al-Qahtani AA. Whole genome sequencing of resistance and virulence genes in multi-drug resistant Pseudomonas aeruginosa. J Infect Public Health 2024; 17:299-307. [PMID: 38154433 DOI: 10.1016/j.jiph.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 10/19/2023] [Accepted: 12/14/2023] [Indexed: 12/30/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is an opportunistic bacterium that causes serious hospital-acquired infections. To assess the risk of clinically isolated P. aeruginosa to human health, we analyzed the resistance and virulence mechanisms of a collection of clinical isolates. METHODS This was a retrospective study in which P. aeruginosa isolates collected from January 1, 2018 to August 31, 2019 were analyzed using phenotypic and whole-genome sequencing (WGS) methods. The analysis included 48 clinical samples. Median patient age was 54.0 (29.5) years, and 58.3% of patients were women. Data from the microbiology laboratory database were reviewed to identify P. aeruginosa isolates. All unique isolates available for further testing were included, and related clinical data were collected. Infections were defined as hospital acquired if the index culture was obtained at least 48 h after hospitalization. RESULTS High-risk P. aeruginosa clones, including sequence types (STs) ST235 and ST111, were identified, in addition to 12 new STs. The isolates showed varying degrees of biofilm formation ability when evaluated at room temperature, along with reduced metabolic activity, as measured by metabolic staining, suggesting their ability to evade antimicrobial therapy. Most isolates (77.1%) were multidrug resistant (MDR), with the highest resistance and susceptibility rates to beta-lactams and colistimethate sodium, respectively. CONCLUSIONS The MDR phenotypes of the examined isolates can be explained by the high prevalence of efflux-mediated resistance- and hydrolytic enzyme-encoding genes. These isolates had high cytotoxic potential, as indicated by the detection of toxin production-related genes.
Collapse
Affiliation(s)
- Reem S Almaghrabi
- Section of Transplant Infectious Diseases, Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | | | | | | | | | - Sahar Althawadi
- Section of Microbiology Laboratory, Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Maysoon Mutabagani
- Section of Microbiology Laboratory, Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdulaziz Binsaslloum
- Section of Microbiology Laboratory, Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mai Alrasheed
- Section of Microbiology Laboratory, Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdullah Almohaizeie
- Pharmaceutical Care Division, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Batol Allehyani
- Pharmaceutical Care Division, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Alnajla Alghofaili
- Pharmaceutical Care Division, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Marie F Bohol
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed A Al-Qahtani
- Department of Infection and Immunity, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia; Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| |
Collapse
|
4
|
Bennett C, Coughlan S, Hunt K, Butler F, Fanning S, Ryan E, De Gascun C, O'Gorman J. Detection of hepatitis E RNA in pork products at point of retail in Ireland - Are consumers at risk? Int J Food Microbiol 2024; 410:110492. [PMID: 37988969 DOI: 10.1016/j.ijfoodmicro.2023.110492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/23/2023]
Abstract
Hepatitis E (HEV), a zoonotic virus, is the leading cause of acute viral hepatitis in Europe. The presence of HEV in domestic pigs can result in infections in humans through consumption of pork products which are undercooked or where processing methods are insufficient to inactivate the virus. In Ireland, pork accounts for 34 % of all meat consumption (CSO, 2022) and the prevalence of HEV in products at point of retail has not previously been characterised. A sampling strategy was designed in which high pork content sausages, fresh pork liver and raw fermented sausages were systematically purchased from three types of retailers between May 2018 and March 2019. In total, 200 pork products were tested using a lysing agent to release the HEV from the product for detection. RT-PCR for HEV was performed on samples with an extraction efficiency >1 % (n = 188/200) (94 %). Low level HEV RNA was detected in 9/188 (4.8 %) pork products tested. The highest incidence of HEV RNA was in pork liver where 6/25 (24 %) samples were positive. The concentration of HEV ranged from 0.02 - to 9.4 genome copies/g of pork. Based on these data an exposure assessment was performed which found that if consumers followed advice from the Food Safety Authority of Ireland to achieve core temperatures of 70 °C or higher when cooking, the risk was likely to be negligible.
Collapse
Affiliation(s)
- Charlene Bennett
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Suzie Coughlan
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kevin Hunt
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francis Butler
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Belfield, Dublin 4, Ireland
| | - Eoin Ryan
- Central Veterinary Research Laboratory, Department Agriculture Food and the Marine (DAFM), Backweston, Kildare, Ireland
| | - Cillian De Gascun
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Joanne O'Gorman
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
5
|
McCarthy SC, Macori G, Burgess CM, Duffy G, Fanning S. Hybrid genome assemblies of four Shiga toxin-producing Escherichia coli strains containing a complete locus of enterocyte effacement and an O-Island 122. Microbiol Resour Announc 2023; 12:e0004623. [PMID: 37905991 PMCID: PMC10652964 DOI: 10.1128/mra.00046-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023] Open
Abstract
This study describes the hybrid genome assemblies of four Shiga toxin-producing Escherichia coli strains isolated from the recto-anal junction of slaughter-age Irish sheep. In silico serotyping and genome analysis determined that each of the strains harbored a Shiga-toxin subtype, a complete locus of enterocyte effacement, and a rare O-island 122.
Collapse
Affiliation(s)
- Siobhán C. McCarthy
- UCD-Center for Food Safety, School of Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
- Food Safety Department, Teagasc Food Research Center, Ashtown, Dublin, Ireland
| | - Guerrino Macori
- UCD-Center for Food Safety, School of Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | | | - Geraldine Duffy
- Food Safety Department, Teagasc Food Research Center, Ashtown, Dublin, Ireland
| | - Séamus Fanning
- UCD-Center for Food Safety, School of Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland
| |
Collapse
|
6
|
Mousavi ZE, Koolman L, Macori G, Fanning S, Butler F. Comprehensive Genomic Characterization of Cronobacter sakazakii Isolates from Infant Formula Processing Facilities Using Whole-Genome Sequencing. Microorganisms 2023; 11:2749. [PMID: 38004760 PMCID: PMC10673598 DOI: 10.3390/microorganisms11112749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Cronobacter sakazakii is an opportunistic pathogen linked to outbreaks in powdered infant formula (PIF), primarily causing meningitis and necrotizing enterocolitis. Whole-genome sequencing (WGS) was used to characterize 18 C. sakazakii strains isolated from PIF (powdered infant formula) manufacturing plants (2011-2015). Sequence Type (ST) 1 was identified as the dominant sequence type, and all isolates carried virulence genes for chemotaxis, flagellar motion, and heat shock proteins. Multiple antibiotic resistance genes were detected, with all isolates exhibiting resistance to Cephalosporins and Tetracycline. A significant correlation existed between genotypic and phenotypic antibiotic resistance. The plasmid Col(pHAD28) was identified in the isolates recovered from the same PIF environment. All isolates harbored at least one intact phage. All the study isolates were compared with a collection of 96 publicly available C. sakazakii genomes to place these isolates within a global context. This comprehensive study, integrating phylogenetic, genomic, and epidemiological data, contributes to a deeper understanding of Cronobacter outbreaks. It provides valuable insights to enhance surveillance, prevention, and control strategies in food processing and public health contexts.
Collapse
Affiliation(s)
- Zeinab Ebrahimzadeh Mousavi
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
- School of Biosystems and Food Engineering, University College Dublin, D04 V1W8 Dublin, Ireland;
- Department of Food Science and Engineering, Faculties of Agriculture and Natural Resources, University of Tehran, Karaj 6719418314, Iran
| | - Leonard Koolman
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
| | - Guerrino Macori
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland; (L.K.); (G.M.); (S.F.)
| | - Francis Butler
- School of Biosystems and Food Engineering, University College Dublin, D04 V1W8 Dublin, Ireland;
| |
Collapse
|
7
|
Pakhomov NV, Kostyunina DS, Macori G, Dillon E, Brady T, Sundaramoorthy G, Connolly C, Blanco A, Fanning S, Brennan L, McLoughlin P, Baugh JA. High-Soluble-Fiber Diet Attenuates Hypoxia-Induced Vascular Remodeling and the Development of Hypoxic Pulmonary Hypertension. Hypertension 2023; 80:2372-2385. [PMID: 37851762 DOI: 10.1161/hypertensionaha.123.20914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 08/10/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Hypoxic pulmonary hypertension is a difficult disease to manage that is characterized by sustained elevation of pulmonary vascular resistance and pulmonary artery pressure due to vasoconstriction, perivascular inflammation, and vascular remodeling. Consumption of soluble-fiber is associated with lower systemic blood pressure, but little is known about its ability to affect the pulmonary circulation. METHODS Mice were fed either a low- or high-soluble-fiber diet (0% or 16.9% inulin) and then exposed to hypoxia (FiO2, 0.10) for 21 days to induce pulmonary hypertension. The impact of diet on right ventricular systolic pressure and pulmonary vascular resistance was determined in vivo or in ex vivo isolated lungs, respectively, and correlated with alterations in the composition of the gut microbiome, plasma metabolome, pulmonary inflammatory cell phenotype, and lung proteome. RESULTS High-soluble-fiber diet increased the abundance of short-chain fatty acid-producing bacteria, with parallel increases in plasma propionate levels, and reduced the abundance of disease-related bacterial genera such as Staphylococcus, Clostridioides, and Streptococcus in hypoxic mice with parallel decreases in plasma levels of p-cresol sulfate. High-soluble-fiber diet decreased hypoxia-induced elevations of right ventricular systolic pressure and pulmonary vascular resistance. These changes were associated with reduced proportions of interstitial macrophages, dendritic cells, and nonclassical monocytes. Whole-lung proteomics revealed proteins and molecular pathways that may explain the effect of soluble-fiber supplementation. CONCLUSIONS This study demonstrates for the first time that a high-soluble-fiber diet attenuates hypoxia-induced pulmonary vascular remodeling and the development of pulmonary hypertension in a mouse model of hypoxic pulmonary hypertension and highlights diet-derived metabolites that may have an immuno-modulatory role in the lung.
Collapse
Affiliation(s)
- Nikolai V Pakhomov
- School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (N.V.P., D.S.K., T.B., P.M., J.A.B.)
| | - Daria S Kostyunina
- School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (N.V.P., D.S.K., T.B., P.M., J.A.B.)
| | - Guerrino Macori
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Ireland (G.M., S.F.)
| | - Eugene Dillon
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (E.D., A.B.)
| | - Tara Brady
- School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (N.V.P., D.S.K., T.B., P.M., J.A.B.)
| | - Geetha Sundaramoorthy
- School of Agriculture and Food Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (G.S., C.C., L.B.)
| | - Claire Connolly
- School of Agriculture and Food Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (G.S., C.C., L.B.)
| | - Alfonso Blanco
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (E.D., A.B.)
| | - Séamus Fanning
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Ireland (G.M., S.F.)
| | - Lorraine Brennan
- School of Agriculture and Food Science, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (G.S., C.C., L.B.)
| | - Paul McLoughlin
- School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (N.V.P., D.S.K., T.B., P.M., J.A.B.)
| | - John A Baugh
- School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Ireland (N.V.P., D.S.K., T.B., P.M., J.A.B.)
| |
Collapse
|
8
|
Gao Y, Du P, Zhang P, Wang J, Liu Z, Fanning S, Wang Z, Li R, Bai L. Dynamic evolution and transmission of a bla NDM-1-bearing fusion plasmid in a clinical Escherichia coli. Microbiol Res 2023; 275:127450. [PMID: 37454426 DOI: 10.1016/j.micres.2023.127450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
Plasmids are the main driving forces for the rapid dissemination of blaNDM-1. In recent years, blaNDM-1-carrying fusion plasmids have been frequently reported. However, the evolutionary patterns of blaNDM-1-carrying fusion plasmids remain largely unknown. Herein, we reported a blaNDM-1-bearing fusion plasmid pZX35-269k possessing IncFII and IncA/C2 replicons from clinical ST349 E. coli 13ZX35. The backbone of pZX35-269k was structurally unstable, which was manifested in different types of structural dissociation during conjugation and passage, thereby forming various daughter plasmids. Moreover, the same events were observed in the clinical setting as well. We found that pZX35-269k exhibited highly identical to two plasmids (pZX30-70k and pZX30-192k) in 13ZX30, both of which were isolated from the same hospital. Sequence analysis highlighted that two plasmids in 13ZX30 evolved from pZX35-269k through homologous recombination of a 4856-bp fragment. Collectively, this study confirmed the transmission and structural evolution of a blaNDM-1-bearing fusion plasmid in both laboratory and clinical settings, and provided clear evidence of plasmid spread and evolution in clinical settings. Such versatile plasmids may represent a potential risk for the public health.
Collapse
Affiliation(s)
- Yanyun Gao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, People's Republic of China
| | - Pei Zhang
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, 22, Yangling 712100 Shaanxi, People's Republic of China
| | - Ziyi Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Séamus Fanning
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China; UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People's Republic of China.
| | - Li Bai
- National Health Commission Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| |
Collapse
|
9
|
Andrews N, McCabe E, Wall P, Buckley JF, Fanning S. Validating the Utility of Multilocus Variable Number Tandem-repeat Analysis (MLVA) as a Subtyping Strategy to Monitor Listeria monocytogenes In-built Food Processing Environments. J Food Prot 2023; 86:100147. [PMID: 37619693 DOI: 10.1016/j.jfp.2023.100147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Listeria monocytogenes is a serious human pathogen and an enduring challenge to control for the ready-to-eat food processing industry. Cost-effective tools that can be deployed by commercial or in-house laboratories to rapidly investigate and resolve contamination events in the built food processing environment are of value to the food industry. Multilocus variable number tandem-repeat analysis (MLVA) is a molecular subtyping method, which along with other same-generation methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) is being superseded in disease tracking and outbreak investigations by whole-genome sequencing (WGS). In this paper, it is demonstrated that MLVA can continue to play a valuable role as a valid, fast, simple, and cost-effective method to identify and track Listeria monocytogenes subtypes in factory environments, with the method being highly congruent with MLST. Although MLVA does not have the discriminatory power of WGS to identify truly persistent clones, with careful interpretation of results alongside isolate metadata, it remains a powerful tool in situations and locations where WGS may not be readily available to food business operators.
Collapse
Affiliation(s)
- Nicholas Andrews
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Patrick Wall
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - James F Buckley
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; Institute for Global Food Security, Queen's University Belfast, 19 Chlorine Gardens, Belfast BT5 6AG, United Kingdom.
| |
Collapse
|
10
|
Bharathan G, Mundra S, Darwich DM, Saeed MM, Al Hafri ASA, Alsalmi MMSM, Maqsood S, Mudgil P, Fanning S, Srikumar S. Regulation of iron metabolism is critical for the survival of Salmonella Typhimurium in pasteurized milk. Food Microbiol 2023; 115:104326. [PMID: 37567619 DOI: 10.1016/j.fm.2023.104326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/13/2023]
Abstract
Salmonella is known to survive in raw/pasteurized milk and cause foodborne outbreaks. Lactoferrin, present in milk from all animal sources, is an iron-binding glycoprotein that limits the availability of iron to pathogenic bacteria. Despite the presence of lactoferrins, Salmonella can grow in milk obtained from different animal sources. However, the mechanism by which Salmonella overcomes iron scarcity induced by lactoferrin in milk is not evaluated yet. Salmonella employs the DNA binding transcriptional regulator Fur (ferric update regulator) to mediate iron uptake during survival in iron deplete conditions. To understand the importance of Fur in Salmonella milk growth, we profiled the growth of Salmonella Typhimurium Δfur (ST4/74Δfur) in both bovine and camel milk. ST4/74Δfur was highly inhibited in milk compared to wild-type ST4/74, confirming the importance of Fur mediated regulation of iron metabolism in Salmonella milk growth. We further studied the biology of ST4/74Δfur to understand the importance of iron metabolism in Salmonella milk survival. Using increasing concentrations of FeCl3, and the antibiotic streptonigrin we show that iron accumulates in the cytoplasm of ST4/74Δfur. We hypothesized that the accumulated iron could activate oxidative stress via Fenton's reaction leading to growth inhibition. However, the inhibition of ST4/74Δfur in milk was not due to Fenton's reaction, but due to the 'iron scarce' conditions of milk and microaerophilic incubation conditions which made the presence of the fur gene indispensable for Salmonella milk growth. Subsequently, survival studies of 14 other transcriptional mutants of ST4/74 in milk confirmed that RpoE-mediated response to extracytoplasmic stress is also important for the survival of Salmonella in milk. Though we have data only for fur and rpoE, many other Salmonella transcriptional factors could play important roles in the growth of Salmonella in milk, a theme for future research on Salmonella milk biology. Nevertheless, our data provide early insights into the biology of milk-associated Salmonella.
Collapse
Affiliation(s)
- Greeshma Bharathan
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Sunil Mundra
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Dania Mustafa Darwich
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Maitha Mohammad Saeed
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Ahad Saeed Ali Al Hafri
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | | | - Sajid Maqsood
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Priti Mudgil
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, D04 N2E5, Ireland
| | - Shabarinath Srikumar
- Department of Food Science, College of Agriculture and Veterinary Medicine, UAE University, Al Ain, 15551, United Arab Emirates.
| |
Collapse
|
11
|
Marshall A, McGrath JW, Mitchell M, Fanning S, McMullan G. One size does not fit all - Trehalose metabolism by Clostridioides difficile is variable across the five phylogenetic lineages. Microb Genom 2023; 9:001110. [PMID: 37768179 PMCID: PMC10569727 DOI: 10.1099/mgen.0.001110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile, the leading cause of antibiotic-associated diarrhoea worldwide, is a genetically diverse species which can metabolise a number of nutrient sources upon colonising a dysbiotic gut environment. Trehalose, a disaccharide sugar consisting of two glucose molecules bonded by an α 1,1-glycosidic bond, has been hypothesised to be involved in the emergence of C. difficile hypervirulence due to its increased utilisation by the RT027 and RT078 strains. Here, growth in trehalose as the sole carbon source was shown to be non-uniform across representative C. difficile strains, even though the genes for its metabolism were induced. Growth in trehalose reduced the expression of genes associated with toxin production and sporulation in the C. difficile R20291 (RT027) and M120 (RT078) strains in vitro, suggesting an inhibitory effect on virulence factors. Interestingly, the R20291 TreR transcriptional regulatory protein appeared to possess an activator function as its DNA-binding ability was increased in the presence of its effector, trehalose-6-phosphate. Using RNA-sequencing analysis, we report the identification of a putative trehalose metabolism pathway which is induced during growth in trehalose: this has not been previously described within the C. difficile species. These data demonstrate the metabolic diversity exhibited by C. difficile which warrants further investigation to elucidate the molecular basis of trehalose metabolism within this important gut pathogen.
Collapse
Affiliation(s)
- Andrew Marshall
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - John W. McGrath
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| | - Molly Mitchell
- University College Dublin-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- University College Dublin-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Geoff McMullan
- School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, BT9 5DL, UK
| |
Collapse
|
12
|
Bennett C, Hunt K, Butler F, Keaveney S, Fanning S, De Gascun C, Coughlan S, O'Gorman J. Detection of Hepatitis A RNA, Hepatitis E RNA, Human Adenovirus F DNA, and Norovirus RNA in Fresh and Frozen Berry Products at Point of Retail in Ireland. Food Environ Virol 2023; 15:246-254. [PMID: 37528267 PMCID: PMC10499670 DOI: 10.1007/s12560-023-09561-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/22/2023] [Indexed: 08/03/2023]
Abstract
Soft fruits are at particular risk of contamination with enteric viruses such as Hepatitis A virus (HAV), Hepatitis E Virus (HEV), Norovirus (NoV), Human Adenovirus (HAdV) and Sapovirus (SaV). The aim of this study was to investigate, for the first time, the presence of these biological agents in ready to eat (RTE) berries at point of retail in Ireland. A sampling strategy was designed in which RTE fresh and frozen strawberries and raspberries were purchased from five retailers between May and October 2018. Reverse Transcriptase Polymerase Chain Reaction (RT-qPCR) assays for HEV RNA, Nov RNA, SaV RNA, and human Adenovirus species F DNA (HAdV-F) were performed on 239 samples (25g portions). Viral nucleic acid was present in 6.7% (n = 16) of samples tested as follows: HAV RNA (n = 5), HAdV-F DNA (n = 5), HEV RNA (n = 3) and NoV GII RNA (n = 3). Sapovirus RNA was not detected in any product. No significant differences were found between berry type, fresh/frozen status, or supermarket source. This study suggests a risk that exists across all retail outlets however only low levels of nucleic acid ranging from 0 to 16 genome copies/g were present. Although these findings may reflect non-viable/non-infectious virus the continued provision of risk mitigation advice to consumers is warranted and further work is required to ensure control measures to reduce contamination are implemented and enforced.
Collapse
Affiliation(s)
- Charlene Bennett
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland.
| | - Kevin Hunt
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Francis Butler
- UCD-School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin, 4, Ireland
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Belfield, Dublin, 4, Ireland
| | - Cillian De Gascun
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Suzie Coughlan
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Joanne O'Gorman
- UCD-National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| |
Collapse
|
13
|
Mousavi ZE, Hunt K, Koolman L, Butler F, Fanning S. Cronobacter Species in the Built Food Production Environment: A Review on Persistence, Pathogenicity, Regulation and Detection Methods. Microorganisms 2023; 11:1379. [PMID: 37374881 DOI: 10.3390/microorganisms11061379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
The powdered formula market is large and growing, with sales and manufacturing increasing by 120% between 2012 and 2021. With this growing market, there must come an increasing emphasis on maintaining a high standard of hygiene to ensure a safe product. In particular, Cronobacter species pose a risk to public health through their potential to cause severe illness in susceptible infants who consume contaminated powdered infant formula (PIF). Assessment of this risk is dependent on determining prevalence in PIF-producing factories, which can be challenging to measure with the heterogeneity observed in the design of built process facilities. There is also a potential risk of bacterial growth occurring during rehydration, given the observed persistence of Cronobacter in desiccated conditions. In addition, novel detection methods are emerging to effectively track and monitor Cronobacter species across the food chain. This review will explore the different vehicles that lead to Cronobacter species' environmental persistence in the food production environment, as well as their pathogenicity, detection methods and the regulatory framework surrounding PIF manufacturing that ensures a safe product for the global consumer.
Collapse
Affiliation(s)
- Zeinab Ebrahimzadeh Mousavi
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
- Department of Food Science and Engineering, Faculties of Agriculture and Natural Resources, University of Tehran, Karaj 6719418314, Iran
| | - Kevin Hunt
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
| | - Leonard Koolman
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Francis Butler
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
| |
Collapse
|
14
|
Harding-Crooks R, Smith D, Fanning S, Fox EM. Dissemination of carbapenemase-producing Enterobacteriaceae and associated resistance determinants through global food systems. Compr Rev Food Sci Food Saf 2023. [PMID: 37083194 DOI: 10.1111/1541-4337.13159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 03/27/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
Antimicrobial agents are a critical component of modern healthcare systems, fulfilling a core function in patient care and improving individual patient outcomes and consequently overall public health. However, the efficacy of antimicrobial interventions is being consistently eroded by the emergence and dissemination of various antimicrobial resistance (AMR) mechanisms. One highly valued class of antimicrobial compounds is carbapenems, which retain efficacy in treating most multidrug-resistant infections and are considered "last line" agents. Therefore, recent trends in proliferation of carbapenem resistance (CR) via dissemination of carbapenemase-encoding genes among members of the Enterobacteriaceae family pose a significant threat to public health. While much of the focus relating to this has been on nosocomial environments, community-acquired carbapenemase-producing Enterobacteriaceae (CPE) infections and their associated transmission routes are less well studied. Among these community-associated vectors, the role of food chains and contaminated foods is important, since Enterobacteriaceae occupy niches within these settings. This review examines foodborne CPE transmission by exploring how interactions within and between food, the food chain, and agriculture not only promote and disseminate CPE, but also create reservoirs of mobile genetic elements that may lead to further carbapenemase gene proliferation both within and between microbial communities. Additionally, recent developments regarding the global occurrence and molecular epidemiology of CPEs in food chains will be reviewed.
Collapse
Affiliation(s)
| | - Darren Smith
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
- Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Edward M Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| |
Collapse
|
15
|
Li Y, Zhang P, Du P, Mu Y, Cui S, Fanning S, Wang Z, Li R, Bai L. Insertion sequences mediate clinical ST34 monophasic Salmonella enterica serovar Typhimurium plasmid polymorphism. Microbiol Res 2023; 272:127387. [PMID: 37084538 DOI: 10.1016/j.micres.2023.127387] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/04/2023] [Accepted: 04/15/2023] [Indexed: 04/23/2023]
Abstract
Hybrid plasmids can combine the genetic elements of multiple plasmids, with the potential to carry a variety of antibiotic resistance genes and virulence genes, causing a great public health concern. Hybrid plasmids formed by fusion events may further exacerbate the spread of antibiotic resistance genes as well as plasmid evolution. Salmonella enterica serovar 4,[5],12:i:- is a monophasic variant of S. Typhimurium, which is one of the major causes of foodborne disease outbreaks worldwide. To assess the risk of transmission due to plasmid structure changes, we investigated the structural diversity of plasmids in two S. 4,[5],12:i:- isolates. Nanopore long-read sequencing was performed for plasmid comparison between original plasmids (donor isolates) and reorganized plasmids. We found that the IncHI2-IncHI2A multidrug resistance (MDR) plasmids in S. 4,[5],12:i:- possessed high plasticity, and could undergo recombination with other plasmids to form fusion plasmids of different sizes. Plasmid structural polymorphisms were mainly mediated by insertion sequences such as IS26 and ISPa40, and led to the rearrangement of the plasmid internal structures. To the best of our knowledge, this is the first report of the fusion of the IncHI2-IncHI2A and IncB/O/K/Z plasmids in S. 4,[5],12:i:- mediated by IS26. In addition, we also found that the mcr-1 gene was able to generate duplication during conjugation. Polymorphic changes in MDR plasmids during conjugation may further reduce the choice of clinical therapeutic agents. Therefore, continuous monitoring regarding plasmid polymorphic changes during transmission in both in vitro and in vivo is urgently needed to decipher the MDR plasmid evolution.
Collapse
Affiliation(s)
- Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Pei Zhang
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, China; Henan Center for Disease Control and Prevention, Henan, China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, China
| | - Yujiao Mu
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shenghui Cui
- Department of Food Science, National Institutes for Food and Drug Control, Beijing, China
| | - Séamus Fanning
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, China; UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Li Bai
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, China.
| |
Collapse
|
16
|
Becker AAMJ, Munden S, McCabe E, Hurley D, Fanning S, Chapwanya A, Butaye P. The Endometrial Microbiota—16S rRNA Gene Sequence Signatures in Healthy, Pregnant and Endometritis Dairy Cows. Vet Sci 2023; 10:vetsci10030215. [PMID: 36977254 PMCID: PMC10058826 DOI: 10.3390/vetsci10030215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/18/2023] Open
Abstract
Endometritis is one of the most important causes of infertility in dairy cows, resulting in high economic losses in the dairy industry. Though the presence of a commensal uterine microbiota is now well established, the complex role of these bacteria in genital health, fertility, and susceptibility to uterine diseases remains unclear. In this study, we explore the endometrial microbiota through 16S rRNA gene profiling from cytobrush samples taken ex vivo from healthy, pregnant, and endometritis cows. There were no significant differences between healthy and pregnant cows, whose uterine microbiota were dominated by Streptococcus, Pseudomonas, Fusobacterium, Lactococcus and Bacteroides. Compared to pregnant and clinically healthy cows, the uterine bacterial community of endometritis cows was significantly decreased in species diversity (p < 0.05), reflecting uneven community composition in different patterns with either dominance of Escherichia-Shigella, Histophilus, Bacteroides and Porphyromonas or Actinobacteria.
Collapse
Affiliation(s)
- Anne A. M. J. Becker
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Stacie Munden
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Evonne McCabe
- Science Center South, School of Public Health, Physiotherapy & Sports Science, University College Dublin Belfield, D04 N2E5 Dublin, Ireland
| | - Daniel Hurley
- Science Center South, School of Public Health, Physiotherapy & Sports Science, University College Dublin Belfield, D04 N2E5 Dublin, Ireland
| | - Séamus Fanning
- Science Center South, School of Public Health, Physiotherapy & Sports Science, University College Dublin Belfield, D04 N2E5 Dublin, Ireland
| | - Aspinas Chapwanya
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Patrick Butaye
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
- Correspondence:
| |
Collapse
|
17
|
Mitchell M, Nguyen SV, Connor M, Fairley DJ, Donoghue O, Marshall H, Koolman L, McMullan G, Schaffer KE, McGrath JW, Fanning S. Terrisporobacter hibernicus sp. nov., isolated from bovine faeces in Northern Ireland. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748477 DOI: 10.1099/ijsem.0.005667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
A new species of Terrisporobacter, a Gram-positive, spore-forming anaerobic group, proposed name Terrisporobacter hibernicus sp. nov., was isolated in Northern Ireland from bovine faeces collected in 2016. Designated as MCA3T, cells of T. hibernicus sp. nov. are rod shaped and motile. Cells tolerate NaCl from 0.5 to 5.5 % (w/v), with a pH tolerance between pH 6 and 9. The optimal temperature for growth is 35-40 °C, and temperatures from 20 to 30 °C are tolerated. The polar lipid profile displays diphosphatidylglycerol, phosphatidylglycerol, two aminoglycolipids, one glycophospholipid, one aminolipid, three glycolipids, five phospholipids and one lipid. No respiratory quinones are detected. The predominant fatty acid profile includes C16 : 0 at 22.8 %. Strain MCA3T is positive for glucose and maltose acidification, as well as glycerol and sorbitol. The biochemical results from a VITEK2 assay of strain MCA3T, Terrisporobacter petrolearius LAM0A37T and Terrisporobacter mayombei DSM 6539T are also included for the first time. The closed and complete genome of strain MCA3T from a hybrid Oxford Nanopore Technology MinION/Illumina assembly reveals no evidence for known virulence genes. Draft genome sequencing of T. mayombei DSM 6539T and T. petrolearius LAM0A37T, as performed by Illumina MiSeq, provides reference genomes for these respective species of Terrisporobacter for the first time. DNA-DNA hybridization values (d4) of MCA3T to Terrisporobacter glycolicus ATCC 14880T, T. petrolearius LAM0A37T and T. mayombei DSM 6539T are 48.8, 67.4 and 46.3 %, with cutoff value at 70 %. The type strain for T. hibernicus sp. nov. is MCA3T (=NCTC 14625T=LMG 32430T).
Collapse
Affiliation(s)
- Molly Mitchell
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Scott V Nguyen
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland.,District of Columbia Department of Forensic Sciences, Public Health Laboratory, Washington, DC, USA.,Present address: Sequencing and Bioinformatics Center, American Type Culture Collection (ATCC), Manassas, VA, USA
| | - Mairead Connor
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK.,Department of Microbiology, Belfast Health & Social Care Trust, Belfast, Ireland
| | - Derek J Fairley
- Department of Microbiology, Belfast Health & Social Care Trust, Belfast, Ireland
| | - Orla Donoghue
- Department of Microbiology, St. Vincent's University Hospital, 196 Merrion Road, Elm Park, Dublin, Ireland
| | - Helina Marshall
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Leonard Koolman
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland
| | - Geoff McMullan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Kirsten E Schaffer
- Department of Microbiology, St. Vincent's University Hospital, 196 Merrion Road, Elm Park, Dublin, Ireland
| | - John W McGrath
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Séamus Fanning
- UCD-Centre for Food Safety University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, UK
| |
Collapse
|
18
|
Mitchell M, Nguyen SV, Macori G, Bolton D, McMullan G, Drudy D, Fanning S. Clostridioides difficile as a Potential Pathogen of Importance to One Health: A Review. Foodborne Pathog Dis 2022; 19:806-816. [PMID: 36516404 DOI: 10.1089/fpd.2022.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile (basonym Clostridium) is a bacterial enteropathogen associated with cases of C. difficile infection that can result in pseudomembranous colitis, rapid fluid loss, and death. For decades following its isolation, C. difficile was thought to be a solely nosocomial pathogen, being isolated from individuals undergoing antimicrobial therapy and largely affecting elderly populations. More recently, C. difficile spores have been identified in the broader environment, including in food-producing animals, soil, and food matrices, in both ready-to-eat foods and meat products. Furthermore, evidence has emerged of hypervirulent ribotypes (RTs), such as RT078, similar to those cultured in asymptomatic carriers, also being identified in these environments. This finding may reflect on adaptations arising in these bacteria following selection pressures encountered in these niches, and which occurs due to an increase in antimicrobial usage in both clinical and veterinary settings. As C. difficile continues to adapt to new ecological niches, the taxonomy of this genus has also been evolving. To help understand the transmission and virulence potential of these bacteria of importance to veterinary public health, strategies applying multi-omics-based technologies may prove useful. These approaches may extend our current understanding of this recognized nosocomial pathogen, perhaps redefining it as a zoonotic bacterium. In this review, a brief background on the epidemiological presentation of C. difficile will be highlighted, followed by a review of C. difficile in food-producing animals and food products. The current state of C. difficile taxonomy will provide evidence of Clade 5 (ST11/RT078) delineation, as well as background on the genomic elements linked to C. difficile virulence and ongoing speciation. Recent studies applying second- and third-generation sequencing technologies will be highlighted, and which will further strengthen the argument made by many throughout the world regarding this pathogen and its consideration within a One Health dimension.
Collapse
Affiliation(s)
- Molly Mitchell
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Scott V Nguyen
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland.,District of Columbia Department of Forensic Sciences, Public Health Laboratory, Washington, District of Columbia, USA
| | - Guerrino Macori
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland
| | | | - Geoff McMullan
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| |
Collapse
|
19
|
Hu Y, He Y, Nguyen SV, Liu C, Liu C, Gan X, Wang W, Dong Y, Xu J, Li F, Fanning S. Antimicrobial resistance of Salmonella Indiana from retail chickens in China and emergence of an mcr-1-harboring isolate with concurrent resistance to ciprofloxacin, cefotaxime, and colistin. Front Microbiol 2022; 13:955827. [PMID: 36160190 PMCID: PMC9493365 DOI: 10.3389/fmicb.2022.955827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Salmonella enterica serotype Indiana (S. Indiana) in Chinese poultry meat has aroused widespread concern because of its high prevalence and strong antimicrobial resistance. In consideration of the relationship in our previous study between S. Indiana and co-resistance to ciprofloxacin and cefotaxime (CIP-CTX), which were the first-line drug which were used in Salmonella infection in clinical, the antimicrobial resistance (AMR) of 224 CIP-CTX co-resistant S. Indiana isolated from retail chicken samples in China were investigated, with the aim of characterizing the AMR profiles and related resistance mechanisms to ciprofloxacin and cefotaxime among these CIP-CTX co-resistant S. Indiana isolates, all of which showed multi-drug-resistant (MDR) phenotypes. GyrA (S83F and D87N/G) with ParC (T57S and S80R) were the dominant amino acid substitution types, with oqxA, oqxB, and aac (6′)-Ib-cr identified as common plasmid-mediated quinolone resistance (PMQR)-encoding genes. Five blaCTX-M gene subtypes were identified with blaCTX-M-65 ranking at the top. Equally important, we obtained one isolate CFSA664 harboring the mcr-1 gene was ESBL producer with co-resistance to nine in ten classes of tested drugs inclduing colistin. A single circular chromosome and 3 circular plasmids were found in its genome. Among the 26 AMR genes identified, 24 were located on plasmid pCFSA664-1, including three ESBL genes, while plasmid pCFSA664-3 owning only the mcr-1 gene and sharing the same backbone structure with plasmids from Enterobacteriaceae. No insertion sequences were found near the mcr-1 gene but a relaxase-encoding gene in the flank, which could transfer into E. coli J53 at a relatively high frequency. S. Indiana in this study exhibited highly drug-resistant phenotypes, contributing to the acceleration of the dissemination and emergence of this pathogen among different sources. Surveillance and a One Health strategy are needed to limit the emergence of S. Indiana along the food chain.
Collapse
Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Yingying He
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Scott V. Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
- Public Health Laboratory, District of Columbia Department of Forensic Sciences, Washington, DC, United States
| | - Chang Liu
- Department of Microbiological Laboratory Technology, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- *Correspondence: Fengqin Li,
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
- Séamus Fanning,
| |
Collapse
|
20
|
Dong Y, Wang W, Jiang T, Xu J, Li M, Yan S, Li F, Fanning S. A Family Outbreak of Type E Botulism Caused by Contaminated Vacuum-Packed Ambient-Stored Chili Chicken Feet in Zhangjiakou, China. Foodborne Pathog Dis 2022; 19:613-621. [PMID: 35900283 DOI: 10.1089/fpd.2022.0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The epidemiological investigation and laboratory-based confirmation were performed on samples from a family botulism outbreak in Zhangjiakou, Hebei province, China. Forty-four samples, including 14 samples (leftover food, and swabs taken of both food packaging bags and dishes, and serum and vomitus of the victims) related to outbreak and 30 causative food products after outbreak, were collected and analyzed. Isolation, bacterial identification, toxin detection, and whole-genome sequencing of Clostridium spp. cultured from the latter samples and animal assays were performed. Mice injected with the cultures of the leftover chili chicken feet, together with the inner layer of its packaging bag, the plate for serving it, and supernatant of two patients' serum that demonstrated the typical signs of botulism. The polyvalent anti-botulinum neurotoxin (BoNT) and the monovalent anti-BoNT/E exhibited protective effects when administered to mice. Three Clostridium botulinum cultures were obtained and verified to be positive for BoNT/E. The whole genome analysis of the isolates revealed that the classic bont/e gene orfX cluster was found to be located on the chromosomes of all three isolates. Single nucleotide polymorphism analysis suggested that these might be from the same source. Our findings indicated that this botulism outbreak occurred following the ingestion of vacuum-packed chili chicken feet contaminated with BoNT/E produced by C. botulinum.
Collapse
Affiliation(s)
- Yinping Dong
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Wei Wang
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tao Jiang
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Jin Xu
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Menghan Li
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- Microbiology Laboratory, NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
21
|
Jang H, Eshwar A, Lehner A, Gangiredla J, Patel IR, Beaubrun JJG, Chase HR, Negrete F, Finkelstein S, Weinstein LM, Ko K, Addy N, Ewing L, Woo J, Lee Y, Seo K, Jaradat Z, Srikumar S, Fanning S, Stephan R, Tall BD, Gopinath GR. Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. Microorganisms 2022; 10:microorganisms10071396. [PMID: 35889115 PMCID: PMC9319161 DOI: 10.3390/microorganisms10071396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.
Collapse
Affiliation(s)
- Hyein Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Athmanya Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Isha R. Patel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Junia Jean-Gilles Beaubrun
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Hannah R. Chase
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Flavia Negrete
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Samantha Finkelstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Leah M. Weinstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Katie Ko
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Nicole Addy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Laura Ewing
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Jungha Woo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Youyoung Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Kunho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Ziad Jaradat
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Shabarinath Srikumar
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
| | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
| |
Collapse
|
22
|
Cao Y, Macori G, Naithani A, Tall BD, Gangiredla J, Srikumar S, Fanning S. A 16S rRNA Sequencing Study Describing the Environmental Microbiota of Two Powdered Infant Formula Built Facilities. Foodborne Pathog Dis 2022; 19:473-484. [PMID: 35766923 DOI: 10.1089/fpd.2021.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microbial safety is critically important for powdered infant formula (PIF) fed to neonates, with under-developed immune systems. The quality and safety of food products are dictated by those microorganisms found in both raw materials and the built production environment. In this study, a 2-year monitoring program of a production environment was carried out in two PIF factories located in the Republic of Ireland, and the environmental microbiome in different care areas of these sites was studied by using a 16S ribosomal RNA (rRNA)-based sequencing technique. Results highlighted a core microbiome associated with the PIF factory environment containing 24 bacterial genera representing five phyla, with Acinetobacter and Pseudomonas as the predominant genera. In different care areas of the PIF factory, as hygiene standards increased, deciphered changes in microbial community compositions became smaller over time and approached stability, and bacteria dominating the care area became less influenced by the external environment and more by human interactions and raw materials. These observations indicated that the microbial composition can be altered in response to environmental interventions. Genera Cronobacter and Salmonella were observed in trace amounts in the PIF factory environment, and bacterial genera known to be persistent in a stressed environment, such as Acinetobacter, Bacillus, Streptococcus, and Clostridium, were likely to have higher abundances in dry environment-based care areas. To our knowledge, this is the first study to characterize the PIF production environment microbiome using 16S rRNA-based sequencing. This study described the composition and changing trends of the environmental microbial communities in different care areas of the PIF manufacturing facility, and it provided valuable information to support the safer production of PIF in the future.
Collapse
Affiliation(s)
- Yu Cao
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
| | - Guerrino Macori
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
| | - Ankita Naithani
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
| | - Ben D Tall
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Jayanthi Gangiredla
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Shabarinath Srikumar
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland.,Department of Food, Nutrition and Health, College of Food and Agriculture, UAE University Al Ain Campus, Al Ain, United Arab Emirates
| | - Séamus Fanning
- UCD-Centre for Food Safety, Science Centre South, University College Dublin, Dublin, Ireland
| |
Collapse
|
23
|
Rubiola S, Macori G, Civera T, Fanning S, Mitchell M, Chiesa F. Comparison Between Full-Length 16S rRNA Metabarcoding and Whole Metagenome Sequencing Suggests the Use of Either Is Suitable for Large-Scale Microbiome Studies. Foodborne Pathog Dis 2022; 19:495-504. [PMID: 35819265 DOI: 10.1089/fpd.2022.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Since the number of studies of the microbial communities related to food and food-associated matrices almost completely reliant on next-generation sequencing techniques is rising, evaluations of these high-throughput methods are critical. Currently, the two most used sequencing methods to profile the microbiota of complex samples, including food and food-related matrices, are the 16S ribosomal RNA (rRNA) metabarcoding and the whole metagenome sequencing (WMS), both of which are powerful tools for the monitoring of foodborne pathogens and the investigation of the microbiome. Herein, the microbial profiles of 20 bulk tank milk filters from different dairy farms were investigated using both the full-length 16S (FL-16S) rRNA metabarcoding, a third-generation sequencing method whose application in food and food-related matrices is yet in its infancy, and the WMS, to evaluate the correlation and the reliability of these two methods to explore the microbiome of food-related matrices. Metabarcoding and metagenomic data were generated on a MinION platform (Oxford Nanopore Technologies) and on a Illumina NovaSeq 6000 platform, respectively. Our findings support the greater resolution of WMS in terms of both increased detection of bacterial taxa and enhanced detection of diversity; in contrast, FL-16S rRNA metabarcoding has proven to be a promising, less expensive, and more practical tool to profile most abundant taxa. The significant correlation of the two technologies both in terms of taxa diversity and richness, together with the similar profiles defined for both highly abundant taxa and core microbiomes, including Acinetobacter, Bacillus, and Escherichia genera, highlights the possible application of both methods for different purposes. This study allowed the first comparison of FL-16S rRNA sequencing and WMS to investigate the microbial composition of a food-related matrix, pointing out the advantageous use of FL-16S rRNA to identify dominant microorganisms and the superior power of WMS for the taxonomic detection of low abundant microorganisms and to perform functional analysis of the microbial communities.
Collapse
Affiliation(s)
- Selene Rubiola
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Guerrino Macori
- University College Dublin-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Dublin, Ireland
| | - Tiziana Civera
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Séamus Fanning
- University College Dublin-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Dublin, Ireland
| | - Molly Mitchell
- University College Dublin-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Dublin, Ireland
| | - Francesco Chiesa
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| |
Collapse
|
24
|
Lamba S, Mundanda Muthappa D, Fanning S, Scannell AGM. Sporulation and Biofilms as Survival Mechanisms of Bacillus Species in Low-Moisture Food Production Environments. Foodborne Pathog Dis 2022; 19:448-462. [PMID: 35819266 DOI: 10.1089/fpd.2022.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Low-moisture foods (LMF) have clear advantages with respect to limiting the growth of foodborne pathogens. However, the incidences of Bacillus species in LMF reported in recent years raise concerns about food quality and safety, particularly when these foods are used as ingredients in more complex higher moisture products. This literature review describes the interlinked pathways of sporulation and biofilm formation by Bacillus species and their underlying molecular mechanisms that contribute to the bacteriums' persistence in LMF production environments. The long-standing challenges of food safety and quality in the LMF industry are also discussed with a focus on the bakery industry.
Collapse
Affiliation(s)
- Sakshi Lamba
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Dechamma Mundanda Muthappa
- UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Amalia G M Scannell
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
25
|
Muthappa DM, Lamba S, Sivasankaran SK, Naithani A, Rogers N, Srikumar S, Macori G, Scannell AGM, Fanning S. 16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments. Foodborne Pathog Dis 2022; 19:485-494. [PMID: 35759425 DOI: 10.1089/fpd.2022.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.
Collapse
Affiliation(s)
- Dechamma Mundanda Muthappa
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Sakshi Lamba
- Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | | | - Ankita Naithani
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | | | - Shabarinath Srikumar
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,Department of Food, Nutrition, and Health, College of Food and Agriculture, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Guerrino Macori
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Amalia G M Scannell
- Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
| |
Collapse
|
26
|
Macori G, Fanning S. Detecting and Tracking Zoonotic Bacteria Using Nonculture-Based Methods. Foodborne Pathog Dis 2022; 19:423-424. [PMID: 35731135 DOI: 10.1089/fpd.2022.29017.int] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guerrino Macori
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Dublin, Ireland
| |
Collapse
|
27
|
Negrete FJ, Ko K, Jang H, Hoffmann M, Lehner A, Stephan R, Fanning S, Tall BD, Gopinath GR. Complete genome sequences and genomic characterization of five plasmids harbored by environmentally persistent Cronobacter sakazakii strains ST83 H322 and ST64 GK1025B obtained from powdered infant formula manufacturing facilities. Gut Pathog 2022; 14:23. [PMID: 35668537 PMCID: PMC9169379 DOI: 10.1186/s13099-022-00500-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/16/2022] [Indexed: 11/21/2022] Open
Abstract
Background Cronobacter sakazakii is a foodborne pathogen that causes septicemia, meningitis, and necrotizing enterocolitis in neonates and infants. The current research details the full genome sequences of two extremely persistent C. sakazakii strains (H322 and GK1025B) isolated from powdered infant formula (PIF) manufacturing settings. In addition, the genetic attributes associated with five plasmids, pH322_1, pH322_2, pGK1025B_1, pGK1025B_2, and pGK1025B_3 are described. Materials and Methods Using PacBio single-molecule real-time (SMRT®) sequencing technology, whole genome sequence (WGS) assemblies of C. sakazakii H322 [Sequence type (ST)83, clonal complex [CC] 83) and GK1025B (ST64, CC64) were generated. Plasmids, also sequenced, were aligned with phylogenetically related episomes to determine, and identify conserved and missing genomic regions. Results A truncated ~ 13 Kbp type 6 secretion system (T6SS) gene cluster harbored on virulence plasmids pH322_2 and pGK1025B_2, and a second large deletion (~ 6 Kbp) on pH322_2, which included genes for a tyrosine-type recombinase/integrase, a hypothetical protein, and a phospholipase D was identified. Within the T6SS of pH322_2 and pGK1025B_2, an arsenic resistance operon was identified which is in common with that of plasmids pSP291_1 and pESA3. In addition, PHASTER analysis identified an intact 96.9 Kbp Salmonella SSU5 prophage gene cluster in pH322_1 and pGK1025B_1 and showed that these two plasmids were phylogenetically related to C. sakazakii plasmids: pCS1, pCsa767a, pCsaC757b, pCsaC105731a. Plasmid pGK1025B_3 was identified as a novel conjugative Cronobacter plasmid. Furthermore, WGS analysis identified a ~ 16.4 Kbp type 4 secretion system gene cluster harbored on pGK1025B_3, which contained a phospholipase D gene, a key virulence factor in several host–pathogen diseases. Conclusion These data provide high resolution information on C. sakazakii genomes and emphasizes the need for furthering surveillance studies to link genotype to phenotype of strains from previous investigations. These results provide baseline data necessary for future in-depth investigations of C. sakazakii that colonize PIF manufacturing facility settings and genomic analyses of these two C. sakazakii strains and five associated plasmids will contribute to a better understanding of this pathogen's survival and persistence within various “built environments” like PIF manufacturing facilities. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-022-00500-5.
Collapse
|
28
|
Macori G, Russell T, Barry G, McCarthy SC, Koolman L, Wall P, Sammin D, Mulcahy G, Fanning S. Inactivation and Recovery of High Quality RNA From Positive SARS-CoV-2 Rapid Antigen Tests Suitable for Whole Virus Genome Sequencing. Front Public Health 2022; 10:863862. [PMID: 35592078 PMCID: PMC9113430 DOI: 10.3389/fpubh.2022.863862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 12/23/2022] Open
Abstract
The diagnostic protocol currently used globally to identify Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is RT-qPCR. The spread of these infections and the epidemiological imperative to describe variation across the virus genome have highlighted the importance of sequencing. SARS-CoV-2 rapid antigen diagnostic tests (RADTs) are designed to detect viral nucleocapsid protein with positive results suggestive of the presence of replicating virus and potential infectivity. In this study, we developed a protocol for recovering SARS-CoV-2 RNA from “spent” RADT devices of sufficient quality that can be used directly for whole virus genome sequencing. The experimental protocol included the spiking of RADTs at different concentrations with viable SARS-CoV-2 variant Alpha (lineage B.1.1.7), lysis for direct use or storage. The lysed suspensions were used for RNA extraction and RT-qPCR. In parallel, we also tested the stability of the viral RNA in the RADTs and the RNA extracted from the RADTs was used as a template for tiling-PCR and whole virus genome sequencing. RNA recovered from RADTs spiked with SARS-CoV-2 was detected through RT-qPCR with Ct values suitable for sequencing and the recovery from RADTs was confirmed after 7 days of storage at both 4 and 20°C. The genomic sequences obtained at each time-point aligned to the strain used for the spiking, demonstrating that sufficient SARS-CoV-2 viral genome can be readily recovered from positive-RADT devices in which the virus has been safely inactivated and genomically conserved. This protocol was applied to obtain whole virus genome sequence from RADTs ran in the field where the omicron variant was detected. The study demonstrated that viral particles of SARS-CoV-2 suitable for whole virus genome sequencing can be recovered from positive spent RADTs, extending their diagnostic utility, as a risk management tool and for epidemiology studies. In large deployment of the RADTs, positive devices could be safely stored and used as a template for sequencing allowing the rapid identification of circulating variants and to trace the source and spread of outbreaks within communities and guaranteeing public health.
Collapse
Affiliation(s)
- Guerrino Macori
- Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Tristan Russell
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Gerald Barry
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Siobhán C McCarthy
- Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Leonard Koolman
- Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Patrick Wall
- Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Donal Sammin
- Department of Agriculture, Food and the Marine Laboratories, Celbridge, Ireland
| | - Grace Mulcahy
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland.,Conway Institute, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
29
|
Pareek V, Gupta R, Devineau S, Sivasankaran SK, Bhargava A, Khan MA, Srikumar S, Fanning S, Panwar J. Does Silver in Different Forms Affect Bacterial Susceptibility and Resistance? A Mechanistic Perspective. ACS Appl Bio Mater 2022; 5:801-817. [PMID: 35073697 DOI: 10.1021/acsabm.1c01179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The exceptional increase in antibiotic resistance in past decades motivated the scientific community to use silver as a potential antibacterial agent. However, due to its unknown antibacterial mechanism and the pattern of bacterial resistance to silver species, it has not been revolutionized in the health sector. This study deciphers mechanistic aspects of silver species, i.e., ions and lysozyme-coated silver nanoparticles (L-Ag NPs), against E. coli K12 through RNA sequencing analysis. The obtained results support the reservoir nature of nanoparticles for the controlled release of silver ions into bacteria. This study differentiates between the antibacterial mechanism of silver species by discussing the pathway of their entry in bacteria, sequence of events inside cells, and response of bacteria to overcome silver stress. Controlled release of ions from L-Ag NPs not only reduces bacterial growth but also reduces the likelihood of resistance development. Conversely, direct exposure of silver ions, leads to rapid activation of the bacterial defense system leading to development of resistance against silver ions, like the well-known antibiotic resistance problem. These findings provide valuable insight on the mechanism of silver resistance and antibacterial strategies deployed by E. coli K12, which could be a potential target for the generation of aim-based and effective nanoantibiotics.
Collapse
Affiliation(s)
- Vikram Pareek
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India.,School of Public Health, Physiotherapy and Sports Science, Centre for Food Safety, Science Centre South, University College Dublin, Dublin 4, Ireland
| | - Rinki Gupta
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | | | | | - Arpit Bhargava
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | - Mohd Azeem Khan
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| | - Shabrinath Srikumar
- Department of Food, Nutrition and Health, College of Food and Agriculture, UAE University, Al Ain 15551, UAE
| | - Séamus Fanning
- School of Public Health, Physiotherapy and Sports Science, Centre for Food Safety, Science Centre South, University College Dublin, Dublin 4, Ireland.,Institute for Global Food Security, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jitendra Panwar
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani 333031, India
| |
Collapse
|
30
|
Wang W, Hu Y, Baker M, Dottorini T, Li H, Dong Y, Bai Y, Fanning S, Li F. Novel SCCmec type XV (7A) and two pseudo-SCCmec variants in foodborne MRSA in China. J Antimicrob Chemother 2022; 77:903-909. [PMID: 35040979 DOI: 10.1093/jac/dkab500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/17/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Staphylococcal cassette chromosome mec (SCCmec) elements are highly diverse and have been classified into 14 types. Novel SCCmec variants have been frequently detected from humans and animals but rarely from food. OBJECTIVES To characterize a novel SCCmec type and two SCCmec variants identified from food-associated MRSA in China. METHODS Three MRSA (NV_1, NT_611 and NT_8) collected from retail foods in China were subjected to WGS and the SCCmec elements were determined. RESULTS The novel SCCmecXV identified in NV_1 carried the mec gene complex class A (mecI-mecR1-mecA-IS431) and the ccr gene complex 7 (ccrA1B6), and a Tn558-mediated phenicol exporter gene fexA was detected in this SCCmecXV cassette. The pseudo-SCCmec elements ΨSCCmecNT_611 and ΨSCCmecNT_8 showed a truncated SCCmec pattern, carrying the class C2 mec gene complex but missing the ccr genes. The ΨSCCmecNT_611 element shared more similarities with those of Staphylococcus haemolyticus (AB478934.1) and carried a heavy metal resistance gene cluster cadD-cadX-arsC-arsB-arsR-copA. The ΨSCCmecNT_8 MRSA exhibited a highly resistant phenotype, showing the absence of a 19.3 kb segment compared with the reference SCCmecXII element (CP019945.1). Notably, a 46 kb region containing multiple transposons encoding antimicrobial or metal resistance genes flanked by IS431 or IS256 was identified ∼30 kb downstream from the mec gene complex in ΨSCCmecNT_8, which might explain such high resistance in MRSA NT_8. CONCLUSIONS Our finding of novel and pseudo-SCCmec elements reflected the ongoing intra/interspecies genetic rearrangements in staphylococci. Further study will be needed to investigate the biological significance and prevalence of those SCCmec variants along the food chain.
Collapse
Affiliation(s)
- Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, UK
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, College Road, Sutton Bonington, Leicestershire, UK
| | - Hui Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yao Bai
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Stranmillis Road, Belfast, Northern Ireland
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| |
Collapse
|
31
|
Sutton U, Lynch J, Fitzgerald N, Macori G, Fanning S, Fennell J. 30. SARS-CoV2 Reinfections in a University Teaching Hospital. Open Forum Infect Dis 2021. [PMCID: PMC8644504 DOI: 10.1093/ofid/ofab466.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The consequences of SARS-CoV2 reinfections for patients, healthcare workers and society are unclear. We reviewed the clinical, laboratory, and epidemiological characteristics of patients re-infected with genetically distinct strains of SARS-CoV2 identified by Whole Virus Genome Sequencing (WvGS).
Methods
Cases were selected based on a positive SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) test, clinical resolution, a negative interim test and a subsequent positive nasopharyngeal swab. Positive samples were prepared for sequencing by cDNA synthesis, tiled-PCR following the ARTIC protocol and amplicon sequencing using Illumina MiSeq platform. Raw reads were mapped to the reference sequence using bowtie and Samtools was used for variants calling and to generate the consensus sequences. Comparative sequence analysis was conducted by phylogenetic inference maximum likelihood method with RAxML using the multiple sequence aligned by MAFFT. Clades and variants were assigned respectively using Nextstrain and Pangolin COVID-19 lineage assigner (Figure 1). The clinical, radiological and laboratory data were collected from patient medical notes and laboratory information system.
Results
Two cases of SARS-CoV-2 reinfection were detected by RT-PCR (patient 1 and 2). CT values and strain variants are presented in Table 1. The time between detection of the first and second infection was 67 and 270 days respectively. WvGS confirmed that the second episodes were due to a genetically distinct strain of SARS CoV2. These reflected the dominant contemporaneous variants in circulation.
Both patients were immunocompromised from co-morbidities and medications. First and subsequent infections were minimally symptomatic. Both cases were associated with known hospital outbreaks. They passed away within 2 weeks of the second infection of unrelated causes.
Conclusion
Two patients in this study were diagnosed with a SARS-CoV-2 reinfection confirmed by WvGS. A common factor in these cases was immunocompromise. Where a previously infected patient test shows a new positive or an unexpected reduction in CT value is observed, we recommend individual risk assessment to determine the timing of discontinuation of isolation and infection control precautions.
Disclosures
Jérôme Fennell, MB BCh BAO MSc PhD FRCPath FRCPI, Roche Diagnostics (Advisor or Review Panel member)
Collapse
Affiliation(s)
- Una Sutton
- Tallaght University Hospital, Dublin, Dublin, Ireland
| | - Judi Lynch
- Tallaght University Hospital, Dublin, Dublin, Ireland
| | | | - Guerrino Macori
- UCD School of Public Health, Physiotherapy & Sports Science, Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD School of Public Health, Physiotherapy & Sports Science, Dublin, Dublin, Ireland
| | | |
Collapse
|
32
|
Hickey C, Nguyen S, Anes J, Hurley D, Donoghue O, Fanning S, Schaffer K. Differences in antimicrobial susceptibility testing complicating management of IMP carbapenemase-producing Enterobacterales infection. J Glob Antimicrob Resist 2021; 27:284-288. [PMID: 34775131 DOI: 10.1016/j.jgar.2021.09.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 09/02/2021] [Accepted: 09/29/2021] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES IMP-type carbapenemases are rarely detected in Europe and limited information is available to guide the treatment of infections caused by carbapenemase-producing Enterobacterales (CPE) producing these carbapenemases. Accurate antimicrobial susceptibility testing (AST) results are essential for optimal antibiotic management. Here we report discrepancies in AST of IMP-producing Enterobacterales (IMP-CPE) complicating the management of severe sepsis. METHODS Antimicrobial susceptibilities were analysed by in-house VITEK® 2, Etest and broth microdilution (BMD). Carbapenemase-encoding genes were detected by PCR. Whole-genome sequencing (WGS) was performed using an Illumina MiSeq platform. RESULTS Minimum inhibitory concentrations (MICs) determined by VITEK® 2 for Enterobacter hormaechei and Klebsiella oxytoca blood culture isolates were ≥16 mg/L for meropenem and ≤0.5 mg/L for ertapenem. In contrast, Etest analysis and BMD returned MICs of 2 mg/L and 1 mg/L, respectively. Both isolates tested positive for IMP carbapenemase-encoding genes by PCR. WGS revealed that both isolates carried the same blaIMP-4 gene. Based on VITEK® 2 susceptibilities, initial treatment was with tigecycline and amikacin. After subsequent deterioration, the patient was successfully treated with ertapenem and amikacin. CONCLUSION This case highlights that automated AST by VITEK® 2 can over-report meropenem resistance for IMP carbapenemase-producers compared with Etest and BMD. Clinicians need to be cautious deciding against carbapenem treatment based on VITEK® 2 susceptibility testing results for IMP-positive Enterobacterales. Tigecycline was inferior to carbapenem treatment for pyelonephritis caused by isolates expressing IMP carbapenemases, however specific evidence guiding the treatment of these infections is lacking.
Collapse
Affiliation(s)
- C Hickey
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Department of Clinical Microbiology, St Vincent's University Hospital, Elm Park, Dublin D04 T6F4, Ireland
| | - S Nguyen
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - J Anes
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - D Hurley
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - O Donoghue
- Department of Clinical Microbiology, St Vincent's University Hospital, Elm Park, Dublin D04 T6F4, Ireland
| | - S Fanning
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - K Schaffer
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Department of Clinical Microbiology, St Vincent's University Hospital, Elm Park, Dublin D04 T6F4, Ireland.
| |
Collapse
|
33
|
Zhao J, Cheng T, Xu W, Han X, Zhang J, Zhang H, Wang C, Fanning S, Li F. Natural co-occurrence of multi-mycotoxins in unprocessed wheat grains from China. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
34
|
Bourdichon F, Betts R, Dufour C, Fanning S, Farber J, McClure P, Stavropoulou DA, Wemmenhove E, Zwietering MH, Winkler A. Processing environment monitoring in low moisture food production facilities: Are we looking for the right microorganisms? Int J Food Microbiol 2021; 356:109351. [PMID: 34500287 DOI: 10.1016/j.ijfoodmicro.2021.109351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/16/2021] [Accepted: 07/28/2021] [Indexed: 11/27/2022]
Abstract
Processing environment monitoring is gaining increasing importance in the context of food safety management plans/HACCP programs, since past outbreaks have shown the relevance of the environment as contamination pathway, therefore requiring to ensure the safety of products. However, there are still many open questions and a lack of clarity on how to set up a meaningful program, which would provide early warnings of potential product contamination. Therefore, the current paper aims to summarize and evaluate existing scientific information on outbreaks, relevant pathogens in low moisture foods, and knowledge on indicators, including their contribution to a "clean" environment capable of limiting the spread of pathogens in dry production environments. This paper also outlines the essential elements of a processing environment monitoring program thereby supporting the design and implementation of better programs focusing on the relevant microorganisms. This guidance document is intended to help industry and regulators focus and set up targeted processing environment monitoring programs depending on their purpose, and therefore provide the essential elements needed to improve food safety.
Collapse
Affiliation(s)
- François Bourdichon
- Food Safety, Microbiology, Hygiene, 16 Rue Gaston de Caillavet, 75015 Paris, France; Facoltà di Scienze Agrarie, Alimentarie Ambientali, Università Cattolica del Sacro Cuore, Piacenza-Cremona, Italy.
| | - Roy Betts
- Campden BRI, Chipping Campden, Gloucestershire, United Kingdom
| | - Christophe Dufour
- Mérieux NutriSciences, 25 Boulevard de la Paix, 95891 Cergy Pontoise, France
| | - Séamus Fanning
- UCD - Centre for Food Safety, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Jeffrey Farber
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Peter McClure
- Mondelēz International, Bournville Lane, Birmingham B30 2LU, United Kingdom
| | | | | | - Marcel H Zwietering
- Food Microbiology, Wageningen University, PO Box 17, 6700AA, Wageningen, The Netherlands
| | - Anett Winkler
- Cargill Germany GmbH, Cerestar str. 2, D-47809 Krefeld, Germany
| |
Collapse
|
35
|
Unrath N, McCabe E, Macori G, Fanning S. Application of Whole Genome Sequencing to Aid in Deciphering the Persistence Potential of Listeria monocytogenes in Food Production Environments. Microorganisms 2021; 9:1856. [PMID: 34576750 PMCID: PMC8464834 DOI: 10.3390/microorganisms9091856] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 01/26/2023] Open
Abstract
Listeria monocytogenes is the etiological agent of listeriosis, a foodborne illness associated with high hospitalizations and mortality rates. This bacterium can persist in food associated environments for years with isolates being increasingly linked to outbreaks. This review presents a discussion of genomes of Listeria monocytogenes which are commonly regarded as persisters within food production environments, as well as genes which are involved in mechanisms aiding this phenotype. Although criteria for the detection of persistence remain undefined, the advent of whole genome sequencing (WGS) and the development of bioinformatic tools have revolutionized the ability to find closely related strains. These advancements will facilitate the identification of mechanisms responsible for persistence among indistinguishable genomes. In turn, this will lead to improved assessments of the importance of biofilm formation, adaptation to stressful conditions and tolerance to sterilizers in relation to the persistence of this bacterium, all of which have been previously associated with this phenotype. Despite much research being published around the topic of persistence, more insights are required to further elucidate the nature of true persistence and its implications for public health.
Collapse
Affiliation(s)
- Natalia Unrath
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
| | - Evonne McCabe
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
- Department of Microbiology, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland
| | - Guerrino Macori
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, University College Dublin, D04 N2E5 Dublin, Ireland; (N.U.); (E.M.); (G.M.)
| |
Collapse
|
36
|
Fanning S, Macori G. Call for Special Issue Papers: Special Issue on Detecting and Tracking Zoonotic Bacteria Using Non-Culture-Based Methods. Foodborne Pathog Dis 2021; 18:507. [PMID: 34403270 DOI: 10.1089/fpd.2020.29014.cfp5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
37
|
Li M, Yan S, Fanning S, Li F, Xu J. Whole Genome Analysis of Three Multi-Drug Resistant Listeria innocua and Genomic Insights Into Their Relatedness With Resistant Listeria monocytogenes. Front Microbiol 2021; 12:694361. [PMID: 34367093 PMCID: PMC8343405 DOI: 10.3389/fmicb.2021.694361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/21/2021] [Indexed: 11/27/2022] Open
Abstract
Listeria innocua are Gram-positive rod-shaped bacteria, which are not generally infectious as opposed to Listeria monocytogenes. However, the comparatively high genomic similarity between both along with on occasion, their coexistence in similar ecological niches may present the opportunity for resistance or virulence gene transfer. In this study, three multi-drug resistant L. innocua originally cultured from food were put forward for long-read genome sequencing. Chromosome and plasmid genomes were assembled and annotated. Analysis demonstrated that the resistant phenotypes correlated well with genotypes. Three plasmids pLI42, pLI203, and pLI47-1 were identified which harbor resistance islands. Sequence alignments suggested that plasmids pLI42 and pLI203 were highly similar to a previously sequenced L. monocytogenes plasmid pLR1. Similarly, another three types of resistance gene islands were observed on chromosome, including tet(M) gene islands (transposon Tn916 orthologs), dfrG gene islands and optrA-erm(A) gene islands. All three L. innocua isolates possessed listeria pathogenicity island-4 (LIPI-4) which is linked to cases of mengitis. Further genome environment and phylogenic analysis of regions flanking LIPI-4 of L. innocua and L. monocytogenes showed that these may have common origins and with the potential to transmit from the former. Our findings raise the possible need to include both L. monocytogenes and L. innocua in food surveillance programs so as to further understand of the origins of antimicrobial resistance and virulence markers of public health importance in L. monocytogenes.
Collapse
Affiliation(s)
- Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, China
| |
Collapse
|
38
|
Hu Y, Fanning S, Nguyen SV, Wang W, Liu C, Cui X, Dong Y, Gan X, Xu J, Li F. Emergence of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, carrying a novel mcr-1.19 variant cultured from egg in China. J Antimicrob Chemother 2021; 76:1776-1785. [PMID: 33822965 DOI: 10.1093/jac/dkab090] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/26/2021] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES This study aimed to characterize the genomic features of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, which carried a novel mcr-1 variant, designated as mcr-1.19, mapped to an ESBL-encoding IncHI2 plasmid. METHODS Antimicrobial susceptibility assays as well as WGS were carried out on isolate CFSA629. The complete closed genome was obtained and then explored to obtain genomic features. Plasmid sequence comparison was performed for pCFSA629 with similar plasmids and the mcr-1 genetic environment was analysed. RESULTS S. Typhimurium ST34 CFSA629 expressed an MDR phenotype to six classes of compound and consisted of a single circular chromosome and one plasmid. It possessed 11 resistance genes including 2 ESBL genes that mapped to the chromosome and the plasmid; an IS26-flanked composite-like transposon was identified. A novel mcr-1 variant (mcr-1.19) was identified, which had a unique SNP (G1534A) that gave rise to a novel MCR-1 protein containing a Val512Ile amino acid substitution. Plasmid pCFSA629 possessed a conjugative plasmid transfer gene cluster as well as an antimicrobial resistance-encoding gene cluster-containing region that contained two IS26 composite-like transposonal modules, but was devoid of any plasmid-mediated quinolone resistance genes. The background of mcr-1.19 consisted of an ISApl1-mcr-1-PAP2-ter module. CONCLUSIONS We report on an MDR S. Typhimurium ST34 CFSA629 isolate cultured from egg in China, harbouring an mcr-1.19 variant mapped to an IncHI2 plasmid. This highlights the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella. Improved surveillance is important for tackling the dissemination of mcr genes among foodborne Salmonella around the world.
Collapse
Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Chlorine Gardens, Belfast, UK
| | - Scott V Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xinnan Cui
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China.,China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| |
Collapse
|
39
|
Fanning S, Macori G. Call for Special Issue Papers: Special Issue on Detecting and Tracking Zoonotic Bacteria Using Non-Culture-Based Methods. Foodborne Pathog Dis 2021; 18:437. [PMID: 34251906 DOI: 10.1089/fpd.2020.29014.cfp4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
40
|
Lynch M, Macori G, Fanning S, O’Regan E, Hunt E, O’Callaghan D, McCullagh B, Jennings C, Fortune A. Genomic Evolution of SARS-CoV-2 Virus in Immunocompromised Patient, Ireland. Emerg Infect Dis 2021; 27:2499-2501. [PMID: 34161223 PMCID: PMC8386806 DOI: 10.3201/eid2709.211159] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We examined virus genomic evolution in an immunocompromised patient with prolonged severe acute respiratory syndrome coronavirus 2 infection. Genomic sequencing revealed genetic variation during infection: 3 intrahost mutations and possible superinfection with a second strain of the virus. Prolonged infection in immunocompromised patients may lead to emergence of new virus variants.
Collapse
|
41
|
Hu Y, Fanning S, Nguyen SV, Wang W, Liu C, Cui X, Dong Y, Gan X, Xu J, Li F. Emergence of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, carrying a novel mcr-1.19 variant cultured from egg in China. J Antimicrob Chemother 2021. [PMID: 33822965 DOI: 10.1093/jac/dkab09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
OBJECTIVES This study aimed to characterize the genomic features of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, which carried a novel mcr-1 variant, designated as mcr-1.19, mapped to an ESBL-encoding IncHI2 plasmid. METHODS Antimicrobial susceptibility assays as well as WGS were carried out on isolate CFSA629. The complete closed genome was obtained and then explored to obtain genomic features. Plasmid sequence comparison was performed for pCFSA629 with similar plasmids and the mcr-1 genetic environment was analysed. RESULTS S. Typhimurium ST34 CFSA629 expressed an MDR phenotype to six classes of compound and consisted of a single circular chromosome and one plasmid. It possessed 11 resistance genes including 2 ESBL genes that mapped to the chromosome and the plasmid; an IS26-flanked composite-like transposon was identified. A novel mcr-1 variant (mcr-1.19) was identified, which had a unique SNP (G1534A) that gave rise to a novel MCR-1 protein containing a Val512Ile amino acid substitution. Plasmid pCFSA629 possessed a conjugative plasmid transfer gene cluster as well as an antimicrobial resistance-encoding gene cluster-containing region that contained two IS26 composite-like transposonal modules, but was devoid of any plasmid-mediated quinolone resistance genes. The background of mcr-1.19 consisted of an ISApl1-mcr-1-PAP2-ter module. CONCLUSIONS We report on an MDR S. Typhimurium ST34 CFSA629 isolate cultured from egg in China, harbouring an mcr-1.19 variant mapped to an IncHI2 plasmid. This highlights the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella. Improved surveillance is important for tackling the dissemination of mcr genes among foodborne Salmonella around the world.
Collapse
Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Chlorine Gardens, Belfast, UK
| | - Scott V Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xinnan Cui
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
- China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| |
Collapse
|
42
|
Hu Y, Nguyen SV, Wang W, Gan X, Dong Y, Liu C, Cui X, Xu J, Li F, Fanning S. Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016. Front Microbiol 2021; 12:636284. [PMID: 34211439 PMCID: PMC8239406 DOI: 10.3389/fmicb.2021.636284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The mcr-1 gene mediating mobile colistin resistance in Escherichia coli was first reported in China in 2016 followed by reports among different species worldwide, especially in E. coli and Klebsiella. However, data on its transmission in Salmonella are still lacking. This study analyzed the antimicrobial resistance (AMR) profiles and the mcr-1 gene presence in 755 foodborne Salmonella from 26 provinces of mainland, China in 2016. Genomic features of two mcr-1-carrying isolates, genome sequencing, serotypes and further resistance profiles were studied. Among the 755 Salmonella tested, 72.6% were found to be resistant to at least one antimicrobial agent and 10% were defined as multi-drug resistant (MDR). Salmonella Derby CFSA231 and Salmonella Typhimurium CFSA629 were mcr-1-harboring isolates. Both expressed an MDR phenotype and included a single circular chromosome and one plasmid. Among the 22 AMR genes identified in S. Derby CFSA231, only the mcr-1 gene was localized on the IncX4 type plasmid pCFSA231 while 20 chromosomal AMR genes, including four plasmid-mediated quinolone resistance (PMQR) genes, were mapped within a 64 kb Salmonella genomic island (SGI) like region. S. Typhimurium CFSA629 possessed 11 resistance genes including an mcr-1.19 variant and two ESBL genes. Two IS26-flanked composite-like transposons were identified. Additionally, 153 and 152 virulence factors were separately identified in these two isolates with secretion system and fimbrial adherence determinants as the dominant virulence classes. Our study extends our concern on mcr-1-carrying Salmonella in regards to antimicrobial resistance and virulence factors, and highlight the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella.
Collapse
Affiliation(s)
- Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Scott V Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland.,Public Health Laboratory, District of Columbia Department of Forensic Sciences, Washington, DC, United States
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Xin Gan
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland
| | - Chang Liu
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China
| | - Xinnan Cui
- Food Science and Engineering College, Beijing University of Agriculture, Beijing, China.,China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing, China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Population Science, University College Dublin, Dublin, Ireland.,Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| |
Collapse
|
43
|
Breheny J, Kingston C, Doran R, Anes J, Martins M, Fanning S, Guiry PJ. Investigation of the Anti-Methicillin-Resistant Staphylococcus aureus Activity of (+)-Tanikolide- and (+)-Malyngolide-Based Analogues Prepared by Asymmetric Synthesis. Int J Mol Sci 2021; 22:ijms22126400. [PMID: 34203787 PMCID: PMC8232695 DOI: 10.3390/ijms22126400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
Herein, we report antibacterial and antifungal evaluation of a series of previously prepared (+)-tanikolide analogues. One analogue, (4S,6S)-4-methyltanikolide, displayed promising anti-methicillin-resistant Staphylococcus aureus activity with a MIC of 12.5 µg/mL. Based on the antimicrobial properties of the structurally related (-)-malyngolide, two further analogues (4S,6S)-4-methylmalyngolide and (4R,6S)-4-methylmalyngolide bearing a shortened n-nonyl alkyl side chain were prepared in the present study using a ZrCl4-catalysed deprotection/cyclisation as the key step in their asymmetric synthesis. When these were tested for activity against anti-methicillin-resistant Staphylococcus aureus, the MIC increased to 50 µg/mL.
Collapse
Affiliation(s)
- Joseph Breheny
- Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; (J.B.); (R.D.)
| | - Cian Kingston
- Synthesis and Solid State Pharmaceutical Centre, School of Chemistry, University College Dublin, Belfield, Dublin D04 N2E5, Ireland;
| | - Robert Doran
- Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; (J.B.); (R.D.)
| | - Joao Anes
- UCD-Centre for Food Safety, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; (J.A.); (M.M.); (S.F.)
| | - Marta Martins
- UCD-Centre for Food Safety, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; (J.A.); (M.M.); (S.F.)
| | - Séamus Fanning
- UCD-Centre for Food Safety, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; (J.A.); (M.M.); (S.F.)
| | - Patrick J. Guiry
- Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Belfield, Dublin D04 N2E5, Ireland; (J.B.); (R.D.)
- Synthesis and Solid State Pharmaceutical Centre, School of Chemistry, University College Dublin, Belfield, Dublin D04 N2E5, Ireland;
- Correspondence: ; Tel.: +353-1-716-2309
| |
Collapse
|
44
|
Gray J, Chandry PS, Kaur M, Kocharunchitt C, Fanning S, Bowman JP, Fox EM. Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments. Sci Rep 2021; 11:12195. [PMID: 34108547 PMCID: PMC8190317 DOI: 10.1038/s41598-021-91503-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Listeria monocytogenes is a ubiquitous bacterium capable of colonising and persisting within food production environments (FPEs) for many years, even decades. This ability to colonise, survive and persist within the FPEs can result in food product cross-contamination, including vulnerable products such as ready to eat food items. Various environmental and genetic elements are purported to be involved, with the ability to form biofilms being an important factor. In this study we examined various mechanisms which can influence colonisation in FPEs. The ability of isolates (n = 52) to attach and grow in biofilm was assessed, distinguishing slower biofilm formers from isolates forming biofilm more rapidly. These isolates were further assessed to determine if growth rate, exopolymeric substance production and/or the agr signalling propeptide influenced these dynamics and could promote persistence in conditions reflective of FPE. Despite no strong association with the above factors to a rapid colonisation phenotype, the global transcriptome suggested transport, energy production and metabolism genes were widely upregulated during the initial colonisation stages under nutrient limited conditions. However, the upregulation of the metabolism systems varied between isolates supporting the idea that L. monocytogenes ability to colonise the FPEs is strain-specific.
Collapse
Affiliation(s)
- Jessica Gray
- CSIRO Agriculture and Food, Werribee, VIC, Australia. .,Food Safety Centre, Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Hobart, TAS, Australia.
| | | | - Mandeep Kaur
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Chawalit Kocharunchitt
- Food Safety Centre, Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, D04 N2E5, Ireland.,Institute for Global Food Security, Queen's University Belfast, Chlorine Gardens, Belfast, BT5 6AG, UK
| | - John P Bowman
- Food Safety Centre, Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Hobart, TAS, Australia
| | - Edward M Fox
- CSIRO Agriculture and Food, Werribee, VIC, Australia. .,Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.
| |
Collapse
|
45
|
Lucey M, Macori G, Mullane N, Sutton-Fitzpatrick U, Gonzalez G, Coughlan S, Purcell A, Fenelon L, Fanning S, Schaffer K. Whole-genome Sequencing to Track Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Transmission in Nosocomial Outbreaks. Clin Infect Dis 2021; 72:e727-e735. [PMID: 32954414 PMCID: PMC7543366 DOI: 10.1093/cid/ciaa1433] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
Background During the first wave of the coronavirus disease 2019 (COVID-19) pandemic, outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in healthcare institutions posed a significant problem. Due to limited evidence, guidance on appropriate infection prevention and control (IPC) measures such as the wearing of face masks varied. Here, we applied whole virus genome sequencing (WvGS) to analyse transmission routes of SARS-CoV-2 in hospital-acquired (HA) COVID-19. Methods An investigation was undertaken for all HA cases of COVID-19 from March to April 2020. Fifty SARS-CoV-2 samples were analysed by WvGS and their phylogenetic relationship established. Results WvGS identified transmission events previously undetected by epidemiological analysis and provided evidence for SARS-CoV-2 transmission between healthcare workers (HCW) and patients and among HCW themselves. The majority of HA COVID-19 cases occurred in patients highly dependent on nursing care, suggesting the likely route of transmission was by close contact or droplet, rather than aerosol, transmission. Mortality among HA COVID-19 infections was recorded as 33%. Conclusions This study provides evidence that SARS-CoV-2 transmission occurs from symptomatic and asymptomatic HCWs to patients. Interventions including comprehensive screening of HCWs for COVID-19 symptoms, PCR testing of asymptomatic HCWs upon identification of HA cases and implementation of universal use of surgical masks for all clinical care is indicated to prevent viral transmission. Our study highlights the importance of close collaboration between guidance bodies and frontline IPC experts for developing control measures in an emergency pandemic situation caused by a virus with undefined transmission modus.
Collapse
Affiliation(s)
- Mary Lucey
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Guerrino Macori
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Niamh Mullane
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Una Sutton-Fitzpatrick
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Gabriel Gonzalez
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Suzie Coughlan
- National Virus Reference Laboratory, University College Dublin, Belfield, Dublin, Ireland
| | - Aisling Purcell
- Department of Occupational Health, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Lynda Fenelon
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- School of Public Health, Physiotherapy & Sports Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kirsten Schaffer
- Department of Microbiology, St. Vincent's University Hospital, School of Medicine, University College Dublin, Dublin, Ireland
| |
Collapse
|
46
|
Godwin JE, Mattar B, Maris M, Bachier C, Stevens DA, Hoda D, Varela JC, Cherry M, Fanning S, Essell J, Yimer H, Courtright J, Sharman J, Trede NS, Youssef M, Lymp J, Shaughnessy P. OUTREACH: PRELIMINARY SAFETY & EFFICACY RESULTS FROM A PHASE 2 STUDY OF LISOCABTAGENE MARALEUCEL (LISO‐CEL) IN THE NONUNIVERSITY SETTING. Hematol Oncol 2021. [DOI: 10.1002/hon.185_2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- J. E. Godwin
- Providence Cancer Center Earle A. Chiles Research Institute Oncology Hematology Clinic Portland Oregon USA
| | - B. Mattar
- Cancer Center of Kansas Internal Medicine Wichita Kansas USA
| | - M. Maris
- Colorado Blood and Cancer Institute and Sarah Cannon Research Institute Hematology/Oncology Denver Colorado USA
| | - C. Bachier
- Sarah Cannon Center for Blood Cancer Hematology Nashville Tennessee USA
| | - D. A. Stevens
- Norton Healthcare Medical Oncology Louisville Kentucky USA
| | - D. Hoda
- Intermountain Healthcare Loveland Clinic for Blood Cancer Therapy Salt Lake City Utah USA
| | - J. C. Varela
- Advent Health Blood and Marrow Transplant Program Orlando Florida USA
| | - M. Cherry
- Atlantic Health System Carol Simon Cancer Center Morristown New Jersey USA
| | - S. Fanning
- Prisma Health Hematology Greenville South Carolina USA
| | - J. Essell
- Oncology Hematology Care Medical Oncology, Hematology, Blood and Marrow Transplantation Cincinnati Ohio USA
| | - H. Yimer
- Texas Oncology‐Tyler Hematology Medical Oncology Tyler Texas USA
| | | | - J. Sharman
- Willamette Valley Cancer Institute Blood Cancers General Oncology Eugene Oregon USA
| | - N. S. Trede
- Bristol Myers Squibb Clinical Development Seattle Washington USA
| | - M. Youssef
- Bristol Myers Squibb Global Drug Development Princeton New Jersey USA
| | - J. Lymp
- Bristol Myers Squibb Cell Therapy Biostatistics Seattle Washington USA
| | - P. Shaughnessy
- Sarah Cannon Transplant and Cellular Therapy Program Methodist Hospital San Antonio Texas USA
| |
Collapse
|
47
|
Fanning S. Call for Special Issue Papers: Special Issue on Detecting and Tracking Zoonotic Bacteria Using Non-Culture-Based Methods. Foodborne Pathog Dis 2021; 18:367. [PMID: 34097499 DOI: 10.1089/fpd.2020.29014.cfp3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Séamus Fanning
- University College Dublin (UCD)-Centre for Food Safety and Guerrino Macori, BSc, PhD, University College Dublin (UCD)-Centre for Food Safety
| |
Collapse
|
48
|
Peng Z, Dottorini T, Hu Y, Li M, Yan S, Fanning S, Baker M, Xu J, Li F. Comparative Genomic Analysis of the Foodborne Pathogen Burkholderia gladioli pv. cocovenenans Harboring a Bongkrekic Acid Biosynthesis Gene Cluster. Front Microbiol 2021; 12:628538. [PMID: 34079526 PMCID: PMC8166232 DOI: 10.3389/fmicb.2021.628538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
The environmental bacterium Burkholderia gladioli pv. cocovenenans (B. cocovenenans) has been linked to fatal food poisoning cases in Asia and Africa. Bongkrekic acid (BA), a mitochondrial toxin produced by B. cocovenenans, is thought to be responsible for these outbreaks. While there are over 80 species in the Burkholderia genus, B. cocovenenans is the only pathovar capable of producing BA and causing human death. However, the genomic features of B. gladioli and the evolution of the BA biosynthesis gene cluster, bon, in B. cocovenenans remain elusive. In this study, 239 whole genome sequences (WGSs) of B. gladioli, isolated from 12 countries collected over 100 years, were used to analyze the intra-species genomic diversity and phylogenetic relationships of B. gladioli and to explore the origin and evolution of the bon gene cluster. Our results showed that the genome-wide average nucleotide identity (ANI) values were above 97.29% for pairs of B. gladioli genomes. Thirty-six of the 239 (15.06%) B. gladioli genomes, isolated from corn, rice, fruits, soil, and patients from Asia, Europe, North America, and South America, contained the bon gene cluster and formed three clades within the phylogenetic tree. Pan- and core-genome analysis suggested that the BA biosynthesis genes were recently acquired. Comparative genome analysis of the bon gene cluster showed that complex recombination events contributed to this toxin biosynthesis gene cluster's evolution and formation. This study suggests that a better understanding of the genomic diversity and evolution of this lethal foodborne pathovar will potentially contribute to B. cocovenenans food poisoning outbreak prevention.
Collapse
Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| |
Collapse
|
49
|
Fanning S, Palmer H, Sturrock B, Hussain A, Carney C, Jaunoo S. 546 Patient Opinions on Care Received in Virtual Clinics Compared to A Face-To-Face Clinic Appointments in General Surgery During The COVID-19 Pandemic. A Retrospective Patient Feedback Study. Br J Surg 2021. [PMCID: PMC8135990 DOI: 10.1093/bjs/znab134.450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Introduction Virtual clinics were implemented during COVID-19 to reduce patient contact. We identified the need to seek feedback from patients relating to their perceptions on care received at a virtual clinic compared to a face-to-face clinics. Method Patients who attended a virtual clinic in General Surgery were selected at random from a database of 627 patients. They were called and asked to complete a google survey which was sent via email. A shorter survey was also conducted over the phone for patients who did not have an email address. Results 79.6% (n = 43) of patients felt their care did not suffer because of non-face-to-face contact. 63% (n = 34) reported that their symptoms were fully assessed during the virtual clinic. 77.8% (n = 42) did not feel rushed by the virtual clinic, 92.6% (n = 50) answered that they had the opportunity to ask questions. 68.5% (n = 35) answered their care did not suffer by not being examined. 72.2% (n = 39) felt that the outcome of the clinic was not changed because of non face-to-face contact. Conclusions Patient feedback on the care received in the virtual clinic was positive. This may suggest that virtual clinics could be utilised in outpatients care with good reception from patients.
Collapse
Affiliation(s)
- S Fanning
- St Richard's Hospital, Chichester, United Kingdom
| | - H Palmer
- Worthing Hospital, Worthing, United Kingdom
| | - B Sturrock
- Royal Sussex County Hospital, Brighton, United Kingdom
| | - A Hussain
- Royal Sussex County Hospital, Brighton, United Kingdom
| | - C Carney
- Swansea Medical School, Swansea, United Kingdom
| | - S Jaunoo
- Royal Sussex County Hospital, Brighton, United Kingdom
| |
Collapse
|
50
|
Fanning S, Macori G. Call for Special Issue Papers: Special Issue on Detecting and Tracking Zoonotic Bacteria Using Non-Culture-Based Methods. Foodborne Pathog Dis 2021; 18:297. [PMID: 33970696 DOI: 10.1089/fpd.2020.29014.cfp2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|