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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a One Health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 PMCID: PMC11180571 DOI: 10.1016/j.anaerobe.2024.102839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; National Center for Biotechnology Information, NIH, Bethesda, MD, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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Abo Elyazeed H, Elhariri M, Eldeen NE, Aziz DA, Elhelw R. Genetic diversity and phylogenetic relationships of Clostridium perfringens strains isolated from mastitis and enteritis in Egyptian dairy farms. BMC Microbiol 2024; 24:157. [PMID: 38710998 DOI: 10.1186/s12866-024-03260-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/14/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Clostridium perfringens, a common environmental bacterium, is responsible for a variety of serious illnesses including food poisoning, digestive disorders, and soft tissue infections. Mastitis in lactating cattle and sudden death losses in baby calves are major problems for producers raising calves on dairy farms. The pathogenicity of this bacterium is largely mediated by its production of various toxins. RESULTS The study revealed that Among the examined lactating animals with a history of mastitis, diarrheal baby calves, and acute sudden death cases in calves, C. perfringens was isolated in 23.5% (93/395) of the total tested samples. Eighteen isolates were obtained from mastitic milk, 59 from rectal swabs, and 16 from the intestinal contents of dead calves. Most of the recovered C. perfringens isolates (95.6%) were identified as type A by molecular toxinotyping, except for four isolates from sudden death cases (type C). Notably, C. perfringens was recovered in 100% of sudden death cases compared with 32.9% of rectal swabs and 9% of milk samples. This study analyzed the phylogeny of C. perfringens using the plc region and identified the plc region in five Egyptian bovine isolates (milk and fecal origins). Importantly, this finding expands the known data on C. perfringens phospholipase C beyond reference strains in GenBank from various animal and environmental sources. CONCLUSION Phylogenetic analyses of nucleotide sequence data differentiated between strains of different origins. The plc sequences of Egyptian C. perfringens strains acquired in the present study differed from those reported globally and constituted a distinct genetic ancestor.
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Affiliation(s)
- Heidy Abo Elyazeed
- Microbiology and Immunology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mahmoud Elhariri
- Microbiology and Immunology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt.
| | - Nashwa Ezz Eldeen
- Microbiology and Immunology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
- Biology Department, Faculty of Science - Taif University, Taif, Saudi Arabia
| | - Dalal Ahmed Aziz
- Microbiology and Immunology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Rehab Elhelw
- Microbiology and Immunology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
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Tree M, Lam TJGM, Townsend K, McDougall S, Beggs DS, Barnes AL, Robertson ID, Aleri JW. A scoping review of antimicrobial resistance in the Australian dairy cattle industry. Prev Vet Med 2024; 226:106161. [PMID: 38460345 DOI: 10.1016/j.prevetmed.2024.106161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 02/09/2024] [Accepted: 02/19/2024] [Indexed: 03/11/2024]
Abstract
INTRODUCTION Quantification of antimicrobial resistance (AMR) is beneficial to inform policies and direct prudent antimicrobial use. AIM This study aimed to assess the current published evidence of AMR from passive and active ad hoc surveillance activities within the Australian dairy cattle industry. METHODS Following a scoping review framework 373 articles published before January 2023 were retrieved using the keyword search function from two online databases (PubMed® and Web of Science™ Core Collection). The duplicate articles were removed and the title, abstract, and full text of the remaining articles were reviewed following the study objectives and inclusion criteria (location, subject/theme, and data). Data from the remaining articles were extracted, summarised, interpreted and the study quality assessed using the Grades of Recommendations, Assessment, Development, and Evaluation guidelines. RESULTS A total of 29 articles dating from the 1960 s until 2022 were identified to meet the study criteria (passive: n = 15; active: n = 14). Study characteristics such as sampling type, sampling method, and AMR assessment were all common characteristics from both passive and active surveillance articles, being milk samples, individual sampling, and phenotypic assessment respectively. Passive surveillance articles had a wider range in both the type of bacteria and the number of antimicrobials investigated, while active surveillance articles included a higher number of bacterial isolates and sampling from healthy populations. There was an overall low level of clinical AMR across all articles. Higher prevalence of non-wildtype Escherichia coli, Salmonella spp., and Staphylococcus spp., although limited in data, was suggested for commonly used Australian veterinary antimicrobials for these bacteria. The prevalence of phenotypic AMR varied due to the health and age status of the sampled animals. The articles reviewed in this study suggest the prevalence of AMR genes was higher for commonly used antimicrobials, although genes were not always related to the phenotypic AMR profile. CONCLUSIONS Published evidence of AMR in the Australian dairy cattle industry is limited as demonstrated by only 29 articles included in this review following selection criteria screening. However, collectively these articles provide insight on industry AMR prevalence. For example, the suggestion of non-wildtype bacteria within the Australian dairy cattle indicating a risk of emerging or increasing industry AMR. Therefore, further surveillance is required to monitor the development of future AMR risk within the industry. Additionally, evidence suggesting that animals varying in health and age differ in prevalence of AMR imply a requirement for further research into animal population demographics to reduce potential bias in data collated in both national and global surveillance activities.
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Affiliation(s)
- Michele Tree
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.
| | - Theo J G M Lam
- GD Animal Health, Deventer, and Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, the Netherlands
| | - Kristy Townsend
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Scott McDougall
- Cognosco, Anexa Veterinary Services, PO Box 21, Morrinsville 3340, New Zealand; School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - David S Beggs
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, 250 Princes Highway, Werribee, VIC 3030, Australia
| | - Anne L Barnes
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Ian D Robertson
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Josh W Aleri
- School of Veterinary Medicine, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia; Centre for Animal Production and Health, Future Foods Institute, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.
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McDonald AG, Lisacek F. Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens. Sci Rep 2024; 14:1649. [PMID: 38238389 PMCID: PMC10796942 DOI: 10.1038/s41598-023-51012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/29/2023] [Indexed: 01/22/2024] Open
Abstract
The development of a stable human gut microbiota occurs within the first year of life. Many open questions remain about how microfloral species are influenced by the composition of milk, in particular its content of human milk oligosaccharides (HMOs). The objective is to investigate the effect of the human HMO glycome on bacterial symbiosis and competition, based on the glycoside hydrolase (GH) enzyme activities known to be present in microbial species. We extracted from UniProt a list of all bacterial species catalysing glycoside hydrolase activities (EC 3.2.1.-), cross-referencing with the BRENDA database, and obtained a set of taxonomic lineages and CAZy family data. A set of 13 documented enzyme activities was selected and modelled within an enzyme simulator according to a method described previously in the context of biosynthesis. A diverse population of experimentally observed HMOs was fed to the simulator, and the enzymes matching specific bacterial species were recorded, based on their appearance of individual enzymes in the UniProt dataset. Pairs of bacterial species were identified that possessed complementary enzyme profiles enabling the digestion of the HMO glycome, from which potential symbioses could be inferred. Conversely, bacterial species having similar GH enzyme profiles were considered likely to be in competition for the same set of dietary HMOs within the gut of the newborn. We generated a set of putative biodegradative networks from the simulator output, which provides a visualisation of the ability of organisms to digest HMO and mucin-type O-glycans. B. bifidum, B. longum and C. perfringens species were predicted to have the most diverse GH activity and therefore to excel in their ability to digest these substrates. The expected cooperative role of Bifidobacteriales contrasts with the surprising capacities of the pathogen. These findings indicate that potential pathogens may associate in human gut based on their shared glycoside hydrolase digestive apparatus, and which, in the event of colonisation, might result in dysbiosis. The methods described can readily be adapted to other enzyme categories and species as well as being easily fine-tuneable if new degrading enzymes are identified and require inclusion in the model.
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Affiliation(s)
- Andrew G McDonald
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland.
- Computer Science Department, University of Geneva, Geneva, Switzerland.
- Section of Biology, University of Geneva, Geneva, Switzerland.
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Wu K, Li Z, Fang M, Yuan Y, Fox EM, Liu Y, Li R, Bai L, Zhang W, Zhang WM, Yang Q, Chang L, Li P, Wang X, Wang J, Yang Z. Genome characteristics of the optrA-positive Clostridium perfringens strain QHY-2 carrying a novel plasmid type. mSystems 2023; 8:e0053523. [PMID: 37458450 PMCID: PMC10469678 DOI: 10.1128/msystems.00535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/04/2023] [Indexed: 09/01/2023] Open
Abstract
Clostridium perfringens is a bacterial species of importance to both public and animal health. The gene optrA is the first gene that confers resistance to the tedizolid, a last-resort antimicrobial agent in human medicine. Herein, we whole-genome sequenced and analyzed one optrA-positive C. perfringens strain QHY-2 from Tibetan sheep in Qinghai province and identified one optrA plasmid pQHY-2. The plasmid shared similar structure with the optrA-positive plasmids p2C45 and p21-D-5b previously identified in C. perfringens, demonstrating the potential horizontal transmission of the optrA plasmids among C. perfringens strains. Annotation of the optrA-positive plasmids showed optrA and erm(A) located on a segment flanked by IS element IS1216E, and fexA, optrA, and erm(A) located on a segment flanked by IS element ISVlu1, which revealed the possible dissemination mechanism. Additionally, a Tn6218-like transposon carrying aac(6')-aph(2″) and erm(B) was also detected on pQHY-2, demonstrating the transposition of Tn6218 and spread of antibiotic resistance among Clostridium bacteria. Molecular analysis indicated the optrA-positive plasmids belonged to a plasmid type distinct from the pCW3-like plasmids, pCP13-like plasmids, or pIP404-like plasmids. Further structure analysis showed they might be formed by inserting segments into plasmid pCPCPI53k-r1_1, which coexist with two pCW3-like plasmids and one pCP13-like plasmid in C. perfringens strain CPI 53k-r1 isolated from a healthy human in Finland. IMPORTANCE Antimicrobial resistance is now a global concern posing threats to food safety and public health. The pCW3-like plasmids can encode several main toxin genes and three antibiotic resistance genes (ARGs), including tetA(P), tetB(P), and erm(B), which used to be considered as the main carrier of ARGs in Clostridium perfringens. In this study, we found the optrA plasmids, which belonged to a novel plasmid type, could also harbor many other ARGs, indicating this type of plasmid might be the potential repository of ARGs in C. perfringens. Additionally, this type of plasmid could coexist with the pCW3-like plasmids and pCP13-like plasmids that encoded toxin genes associated with gastrointestinal diseases, which showed the potential threat to public health.
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Affiliation(s)
- Ke Wu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Zhe Li
- Bureau of Agriculture and Rural Affairs, Junan, China
| | - Mingjin Fang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Yuan Yuan
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Edward M. Fox
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Yingqiu Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Ruichao Li
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Li Bai
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing, China
| | - Wen Zhang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan, Ningxia, China
| | - Wei-Min Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qi Yang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan, Ningxia, China
| | - Lingling Chang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Pu Li
- Department of Critical Care Medicine, the Second Affiliated Hospital of Air Force Medical University, Shaanxi, China
| | - Xinglong Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
| | - Juan Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
- Research Unit of Food Safety, Chinese Academy of Medical Sciences (No. 2019RU014); NHC Key Lab of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment (CFSA), Beijing, China
| | - Zengqi Yang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory for Prevention and Control of Major Ruminant Diseases, Ministry of Agriculture and Rural Affairs, Yangling, China
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