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Rathod S, Dey S, Pawar S, Dhavale R, Choudhari P, Rajakumara E, Mahuli D, Bhagwat D, Tamboli Y, Sankpal P, Mali S, More H. Identification of potential biogenic chalcones against antibiotic resistant efflux pump (AcrB) via computational study. J Biomol Struct Dyn 2024; 42:5178-5196. [PMID: 37340697 DOI: 10.1080/07391102.2023.2225099] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/09/2023] [Indexed: 06/22/2023]
Abstract
The cases of bacterial multidrug resistance are increasing every year and becoming a serious concern for human health. Multidrug efflux pumps are key players in the formation of antibiotic resistance, which transfer out a broad spectrum of drugs from the cell and convey resistance to the host. Efflux pumps have significantly reduced the efficacy of the previously available antibiotic armory, thereby increasing the frequency of therapeutic failures. In gram-negative bacteria, the AcrAB-TolC efflux pump is the principal transporter of the substrate and plays a major role in the formation of antibiotic resistance. In the current work, advanced computer-aided drug discovery approaches were utilized to find hit molecules from the library of biogenic chalcones against the bacterial AcrB efflux pump. The results of the performed computational studies via molecular docking, drug-likeness prediction, pharmacokinetic profiling, pharmacophore mapping, density functional theory, and molecular dynamics simulation study provided ZINC000004695648, ZINC000014762506, ZINC000014762510, ZINC000095099506, and ZINC000085510993 as stable hit molecules against the AcrB efflux pumps. Identified hits could successfully act against AcrB efflux pumps after optimization as lead molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Sreenath Dey
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Swaranjali Pawar
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Rakesh Dhavale
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Eerappa Rajakumara
- Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, Sangareddy, Telangana, India
| | - Deepak Mahuli
- Department of Pharmacology, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Durgacharan Bhagwat
- Department of Pharmaceutics, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
| | - Yasinalli Tamboli
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Poournima Sankpal
- Department of Pharmaceutical Chemistry, Ashokrao Mane College of Pharmacy, Kolhapur, MS, India
| | - Sachin Mali
- Department of Pharmaceutics, Y. D. Mane College of Pharmacy, Kagal, MS, India Kolhapur
| | - Harinath More
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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Boutin S, Lussier E, Laforest-Lapointe I. Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards. Can J Microbiol 2024; 70:238-251. [PMID: 38452350 DOI: 10.1139/cjm-2023-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.
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Affiliation(s)
- Sophie Boutin
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Ema Lussier
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Isabelle Laforest-Lapointe
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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Liu YH, Wang FL, Ren XL, Li CK, Jin LH, Zhou X. Synthesis, Structural Characterization, and Biological Activities of 1,3,4- Thiadiazole Derivatives Containing Sulfonylpiperazine Structures. Chem Biodivers 2024; 21:e202400408. [PMID: 38441384 DOI: 10.1002/cbdv.202400408] [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: 02/16/2024] [Accepted: 03/05/2024] [Indexed: 06/19/2024]
Abstract
To develop novel bacterial biofilm inhibiting agents, a series of 1,3,4-thiadiazole derivatives containing sulfonylpiperazine structures were designed, synthesized, and characterized using 1H nuclear magnetic resonance (1H NMR), 13C nuclear magnetic resonance (13C NMR), and high-resolution mass spectrometry. Meanwhile, their biological activities were evaluated, and the ensuing structure-activity relationships were discussed. The bioassay results showed the substantial antimicrobial efficacy exhibited by most of the compounds. Among them, compound A24 demonstrated a strong efficacy with an EC50 value of 7.8 μg/mL in vitro against the Xanthomonas oryzae pv. oryzicola (Xoc) pathogen, surpassing commercial agents thiodiazole copper (31.8 μg/mL) and bismerthiazol (43.3 μg/mL). Mechanistic investigations into its anti-Xoc properties revealed that compound A24 operates by increasing the permeability of bacterial cell membranes, inhibiting biofilm formation and cell motility, and inducing morphological changes in bacterial cells. Importantly, in vivo tests showed its excellent protective and curative effects on rice bacterial leaf streak. Besides, molecular docking showed that the hydrophobic effect and hydrogen-bond interactions are key factors between the binding of A24 and AvrRxo1-ORF1. Therefore, these results suggest the utilization of 1,3,4-thiadiazole derivatives containing sulfonylpiperazine structures as a bacterial biofilm inhibiting agent, warranting further exploration in the realm of agrochemical development.
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Affiliation(s)
- You-Hua Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Fa-Li Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Xiao-Li Ren
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Chang-Kun Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Lin-Hong Jin
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Xia Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
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Todorov SD, Alves VF, Popov I, Weeks R, Pinto UM, Petrov N, Ivanova IV, Chikindas ML. Antimicrobial Compounds in Wine. Probiotics Antimicrob Proteins 2024; 16:763-783. [PMID: 37855943 DOI: 10.1007/s12602-023-10177-0] [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] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Ipsum vinum est potestas et possession (wine itself is power and possession). Wine is a complex system that triggers multisensory cognitive stimuli. Wine and its consumption are thoroughly intertwined with the development of human society. The beverage was appreciated in many ancient mythologies and plays an essential part in Christianity and rituals to this day. Wine has been said to enlighten and inspire artists and has even been prohibited by law and some religions, but has nevertheless played a role in human civilizations since the beginning. Winemaking is also a prospering and economically important industry and a longtime symbol of status and luxury. In winemaking, the formation of the final product is influenced by several factors that contribute to the chemical and sensory complexity often associated with quality vintages. Factors such as terroir, climatic conditions, variety of the grape, all aspects of the winemaking process to the smallest details, including metabolic processes carried out by yeast and malolactic bacteria, and the conditions for the maturation and storage of the final product, up to, and even beyond the point of deciding to open the bottle and enjoy the wine. In conjunction with the empiric and scientific process of winemaking, different molecules with antibacterial activity can be identified in wine during the production process, and several of them are clearly present in the final product. Some of these antibacterial components are phytochemicals, such as flavonoids and phenolic compounds, that may be delivered to the final product (wine) as a part of the grape, a variety of potential additive compounds, or from the oak barrels or clay amphoras used during the maturation process. Others are produced by yeasts and malolactic bacteria and play a role not only in the moderation of the fermentation process but contributing to the microbiological safety and beneficial properties spectra of the final product. Lactic acid bacteria, responsible for conducting malolactic fermentation, contribute to the final balance of the wine but are also directly involved in the production of different compounds exhibiting antibacterial activity. Some examples of these compounds include bacteriocins (antibacterial peptides), diacetyl, organic acids, reuterin, hydrogen peroxide, and carbon dioxide. Major aspects of these different beneficial metabolites are the subject of discussion in this review with the aim of highlighting their beneficial functions.
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Affiliation(s)
- Svetoslav Dimitrov Todorov
- ProBacLab, Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.
- Food Research Center (FoRC), Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil.
- CISAS- Center for Research and Development in Agrifood Systems and Sustainability, Instituto Politécnico de Viana do Castelo, 4900-347, Viana do Castelo, Portugal.
| | - Virginia Farias Alves
- Faculdade de Farmácia, Universidade Federal de Goiás (UFG), 74605-170, Goiânia, GO, Brazil
| | - Igor Popov
- Center for Agrobiotechnology, Don State Technical University, 344000, Gagarina Sq., 1, Rostov-On-Don, Russia
- Division of Immunobiology and Biomedicine, Center of Genetics and Life Sciences, Sirius University of Science and Technology, Olimpijskij av., 1, 354340, Federal Territory Sirius, Russia
| | - Richard Weeks
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, 08901, New Brunswick, NJ, USA
| | - Uelinton Manoel Pinto
- Food Research Center (FoRC), Laboratório de Microbiologia de Alimentos, Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Nikolay Petrov
- Laboratory of Virology, New Bulgarian University, Montevideo str. 21, 1618, Sofia, Bulgaria
| | - Iskra Vitanova Ivanova
- Department of General and Industrial Microbiology, Faculty of Biology, Sofia University St. Kliment Ohridski, 8, Bul. Dragan Tzankov, 1164, Sofia, Bulgaria
| | - Michael L Chikindas
- Center for Agrobiotechnology, Don State Technical University, 344000, Gagarina Sq., 1, Rostov-On-Don, Russia
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, 65 Dudley Road, 08901, New Brunswick, NJ, USA
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, 119991, Moscow, Russia
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Mohammed YHI, Shamkh IM, Shntaif AH, Sufyan M, Rehman MT, AlAjmi MF, Shahwan M, Alghamdi S, Abd El-Lateef AE, Khidir EB, Abouzied AS, Khalifa NE, A Khojali WM, Huwaimel B, Al Farraj DA, Almutairi SM. Synthesis and evaluation of pyridine-3-carboxamide analogs as effective agents against bacterial wilt in tomatoes. Sci Rep 2024; 14:11118. [PMID: 38750062 PMCID: PMC11096348 DOI: 10.1038/s41598-024-59609-z] [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: 09/07/2023] [Accepted: 04/12/2024] [Indexed: 05/18/2024] Open
Abstract
This study focused on developing novel pyridine-3-carboxamide analogs to treat bacterial wilt in tomatoes caused by Ralstonia solanacearum. The analogs were synthesized through a multistep process and their structures confirmed using spectroscopy. Molecular docking studies identified the most potent analog from the series. A specific analog, compound 4a, was found to significantly enhance disease resistance in tomato plants infected with R. solanacearum. The structure-activity relationship analysis showed the positions and types of substituents on the aromatic rings of compounds 4a-i strongly influenced their biological activity. Compound 4a, with a chloro group at the para position on ring C and hydroxyl group at the ortho position on ring A, was exceptionally effective against R. solanacearum. When used to treat seeds, the analogs displayed remarkable efficacy, especially compound 4a which had specific activity against bacterial wilt pathogens. Compound 4a also promoted vegetative and reproductive growth of tomato plants, increasing seed germination and seedling vigor. In plants mechanically infected with bacteria, compound 4a substantially reduced the percentage of infection, pathogen quantity in young tissue, and disease progression. The analogs were highly potent due to their amide linkage. Molecular docking identified the best compounds with strong binding affinities. Overall, the strategic design and synthesis of these pyridine-3-carboxamide analogs offers an effective approach to targeting and controlling R. solanacearum and bacterial wilt in tomatoes.
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Affiliation(s)
- Yasser Hussein Issa Mohammed
- Department of Biochemistry, Faculty of Applied Science, University of Hajjah, Hajjah, Yemen.
- Department of Pharmacy, Faculty of Medicine and Medical Science, University of Al-Razi, Al-Razi, Yemen.
| | - Israa M Shamkh
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
- Chemo and Bioinformatics Lab, Bio Search Research Institution, BSRI, Giza, Egypt
| | - Ahmed Hassen Shntaif
- Department of Chemistry, College of Science for Women, University of Babylon, Alhilla, 51002, Iraq
| | - Muhammad Sufyan
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Moayad Shahwan
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Saad Alghamdi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | | | - Elshiekh B Khidir
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Amr S Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NODCAR), Giza, 12553, Egypt
| | - Nasrin E Khalifa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, Sudan
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
| | - Dunia A Al Farraj
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, 11451, Riyadh, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. 2455, 11451, Riyadh, Saudi Arabia
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Zalewska M, Błażejewska A, Szadziul M, Ciuchciński K, Popowska M. Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:30819-30835. [PMID: 38616224 PMCID: PMC11096248 DOI: 10.1007/s11356-024-33276-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/06/2024] [Indexed: 04/16/2024]
Abstract
Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.
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Affiliation(s)
- Magdalena Zalewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Aleksandra Błażejewska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Mateusz Szadziul
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Karol Ciuchciński
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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Omar KM, Kitundu GL, Jimoh AO, Namikelwa DN, Lisso FM, Babajide AA, Olufemi SE, Awe OI. Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics. PeerJ 2024; 12:e17181. [PMID: 38666081 PMCID: PMC11044882 DOI: 10.7717/peerj.17181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.
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Affiliation(s)
- Kauthar M. Omar
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - George L. Kitundu
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Adijat O. Jimoh
- Division of Immunology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Genetics, Genomics and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
| | - Dorcus N. Namikelwa
- Department of Data Management, Modelling and Geo-Information Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Felix M. Lisso
- Department of Biochemistry and Biotechnology, School of Pure and Applied Sciences, Pwani University, Kilifi, Kenya
| | - Abiola A. Babajide
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Seun E. Olufemi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Olaitan I. Awe
- African Society for Bioinformatics and Computational Biology, Cape Town, South Africa
- Department of Computer Science, University of Ibadan, Ibadan, Oyo State, Nigeria
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Gupta AK, Mann A, Polla Ravi S, Wang T. Navigating fungal infections and antifungal stewardship: drug resistance, susceptibility testing, therapeutic drug monitoring and future directions. Ital J Dermatol Venerol 2024; 159:105-117. [PMID: 38088126 DOI: 10.23736/s2784-8671.23.07694-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2024]
Abstract
Antifungal stewardship refers to the rational use of antifungal agents. Historically, in some instances, the misuse or overuse of antifungal agents has predisposed patients to an elevated risk of systemic side-effects and treatment resistance, as well as increased healthcare costs. Superficial mycoses, such as onychomycosis, are sometimes treated without any diagnostic testing and is associated with a high likelihood of self-diagnosis and self-treatment, potentially leading to the emergence of resistance against commonly used antifungals like terbinafine. Practitioners need to ensure that a proper clinical diagnosis is backed up by appropriate testing. This may include the traditional light microscopy and culture; additionally, molecular techniques (such as polymerase chain reaction, terbinafine gene mutational analysis) and antifungal susceptibility testing are considerations as appropriate. The choice of antifungal agent should be guided by what is the standard of care in the location where the clinician practices as well as more broadly state and national prescription patterns. Recently, reports of treatment resistance concerning both superficial and deep fungal infections have added another layer of difficulty to clinical practice. This review aims to explore the phenomenon of antifungal drug resistance, and highlights the importance of adopting antifungal stewardship programs. We provide an overview of treatment resistance and mechanisms of resistance reported thus far in dermatophytes. Challenges of performing antifungal susceptibility testing and therapeutic drug monitoring are discussed, as well as principles, recommendations and future directions of antifungal stewardship programs.
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Affiliation(s)
- Aditya K Gupta
- Division of Dermatology, Department of Medicine, University of Toronto, Toronto, ON, Canada -
- Mediprobe Research Inc, London, ON, Canada -
| | | | | | - Tong Wang
- Mediprobe Research Inc, London, ON, Canada
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Scicchitano D, Leuzzi D, Babbi G, Palladino G, Turroni S, Laczny CC, Wilmes P, Correa F, Leekitcharoenphon P, Savojardo C, Luise D, Martelli P, Trevisi P, Aarestrup FM, Candela M, Rampelli S. Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment. Anim Microbiome 2024; 6:17. [PMID: 38555432 PMCID: PMC10981832 DOI: 10.1186/s42523-024-00305-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge on the dispersion of ARGs in pig production system, including the external environment. RESULTS In the present study, we longitudinally followed one swine farm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe. CONCLUSIONS Collectively, our results highlight the urgency to implement more effective countermeasures to limit the dispersion of ARGs in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems.
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Affiliation(s)
- Daniel Scicchitano
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Daniela Leuzzi
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giorgia Palladino
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Paul Wilmes
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Federico Correa
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Diana Luise
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Pierluigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Paolo Trevisi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Marco Candela
- Fano Marine Center, Fano, Italy.
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Simone Rampelli
- Fano Marine Center, Fano, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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10
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Dewi RR, Nuryawan A, Jajere SM, Sihombing JM, Tambunan IJ. Antimicrobial resistance profiles of Escherichia coli derived from an integrated agroforestry-livestock system in Deli Serdang Regency, Indonesia. Vet World 2024; 17:690-699. [PMID: 38680150 PMCID: PMC11045535 DOI: 10.14202/vetworld.2024.690-699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/05/2024] [Indexed: 05/01/2024] Open
Abstract
Background and Aim Antimicrobial resistance (AMR) has become a significant global concern. Epidemiological data do not provide a robust description of the potential risks associated with AMR in the integrated agroforestry-livestock systems in Indonesia. Thus, the present study investigated the phenotypic and multidrug resistance (MDR) profiles of Escherichia coli strains isolated from the feces of livestock raised in the agro-silvopastoral system in Deli Serdang Regency, North Sumatra Province. Materials and Methods A standard microbiological culture procedure was followed to isolate the organism and test antibiotic susceptibility using the Kirby-Bauer disk diffusion protocol. Furthermore, the multiple antibiotic resistance index was determined. Univariate analysis was conducted to identify the risk factors associated with AMR. Results The vast majority (77.5%) of livestock farmers were aged >30 years. All farmers were men and had no higher education (100% of them). The majority of the animal species managed were cattle and goats (37.5% each) and the livestock grazing pasture system (67.5%). In addition, the majority of farmers reported high antimicrobial use on their farms (87.5%). Of the samples (n = 142) analyzed, n = 70 were positive, with an overall prevalence of 44.4%. The species-specific prevalences of E. coli were 32.5%, 47.8%, and 50% in buffalo, goat, and cattle, respectively. Ampicillin and tetracyclines exhibited high resistance levels among the studied animal species. A relatively lower MDR for E. coli was associated with grazing on the pasture. Conclusion The findings from the current study provide baseline epidemiological information for future robust studies aimed at elucidating the drivers and patterns of AMR in agro-silvopastoral systems in the study area or elsewhere.
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Affiliation(s)
- Rita Rosmala Dewi
- Department of Animal Husbandry, Faculty of Science and Technology, Universitas Tjut Nyak Dhien, Medan, Indonesia
| | - Arif Nuryawan
- Department of Forestry, Faculty of Forestry, Universitas Sumatera Utara, Medan, Indonesia
| | - Saleh Mohammed Jajere
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri, Borno State, Nigeria
| | - Juli Mutiara Sihombing
- Department of Animal Husbandry, Faculty of Science and Technology, Universitas Tjut Nyak Dhien, Medan, Indonesia
| | - Ika Julianti Tambunan
- Department of Pharmacy, Faculty of Pharmacy, Universitas Tjut Nyak Dhien, Medan, Indonesia
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11
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Singh S, Sharma P, Pal N, Sarma DK, Kumar M. Antibiotic disposal challenges in India: investigating causes and effects. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:325. [PMID: 38421517 DOI: 10.1007/s10661-024-12425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Antibiotic resistance has become a global problem and India emerges as a key battlefield in the fight against it. While inappropriate use of antibiotics is well known, the review article deliberates a less recognized yet equally perilous facet of the crisis i.e. improper antibiotic disposal. An investigation of the sources of antibiotic pollution in Indian water bodies identifies discharge of pharmaceutical effluents, hospital waste, and agricultural runoff as major contributing factors. Furthermore, it discusses the repercussions of antibiotic pollution including those relating to human health, aquatic ecosystems, and antibiotic resistance. Reviewing the causes and consequences of improper antibiotic disposal practices emphasizes the necessity of rethinking antibiotic waste management practices. The review highlights the need for stringent rules and increased awareness, while also discussing the emerging technologies and strategies to mitigate the risks of antibiotic disposal in India.
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Affiliation(s)
- Samradhi Singh
- ICMR-National Institute for Research in Environmental Health, Bhopal, 462030, Madhya Pradesh, India
| | - Poonam Sharma
- ICMR-National Institute for Research in Environmental Health, Bhopal, 462030, Madhya Pradesh, India
| | - Namrata Pal
- ICMR-National Institute for Research in Environmental Health, Bhopal, 462030, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- ICMR-National Institute for Research in Environmental Health, Bhopal, 462030, Madhya Pradesh, India
| | - Manoj Kumar
- ICMR-National Institute for Research in Environmental Health, Bhopal, 462030, Madhya Pradesh, India.
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12
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Ager EO, Carvalho T, Silva EM, Ricke SC, Hite JL. Global trends in antimicrobial resistance on organic and conventional farms. Sci Rep 2023; 13:22608. [PMID: 38114527 PMCID: PMC10730711 DOI: 10.1038/s41598-023-47862-7] [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: 01/11/2023] [Accepted: 11/19/2023] [Indexed: 12/21/2023] Open
Abstract
The important hypothesis that organic livestock management reduces the prevalence of antimicrobial resistance is either fiercely supported or bitterly contested. Yet, empirical evidence supporting this view remains fragmentary, in part because relationships between antimicrobial use and drug resistance vary dramatically across contexts, hosts, pathogens, and country-specific regulations. Here, we synthesize global policies and definitions of 'organic' and ask if organic farming results in notable reductions in the prevalence of antimicrobial resistance when directly examined alongside conventional analogs. We synthesized the results of 72 studies, spanning 22 countries and five pathogens. Our results highlight substantial variations in country-specific policies on drug use and definitions of 'organic' that hinder broad-scale and generalizable patterns. Overall, conventional farms had slightly higher levels of antimicrobial resistance (28%) relative to organic counterparts (18%), although we found significant context-dependent variation in this pattern. Notably, environmental samples from organic and conventional farms often exhibited high levels of resistance to medically important drugs, underscoring the need for more stringent and consistent policies to control antimicrobial contaminants in the soil (particularly on organic farms, where the application of conventional manure could faciliate the spread antimicrobial resistance). Taken together, these results emphasize the challenges inherent in understanding links between drug use and drug resistance, the critical need for global standards governing organic policies, and greater investment in viable alternatives for managing disease in livestock.
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Affiliation(s)
- Eldon O Ager
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
- The Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Midlothian, UK
| | - Tamilie Carvalho
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Erin M Silva
- Center for Integrated Agricultural Systems, University of Wisconsin, Madison, WI, USA
| | - Steven C Ricke
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, USA
| | - Jessica L Hite
- Department of Pathobiological Sciences, University of Wisconsin, Madison, WI, USA.
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13
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Gangar T, Patra S. Antibiotic persistence and its impact on the environment. 3 Biotech 2023; 13:401. [PMID: 37982084 PMCID: PMC10654327 DOI: 10.1007/s13205-023-03806-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
From boon molecules to molecules contributing to rising concern has been the sojourn of antibiotics. The problem of antibiotic contamination has gotten worse due to antibiotics' pervasive use in every aspect of the environment. One such consequence of pollution is the increase in infections with antibiotic resistance. All known antimicrobials being used for human benefit lead to their repetitive and routine release into the environment. The misuse of antibiotics has aggravated the situation to a level that we are short of antibiotics to treat infections as organisms have developed resistance against them. Overconsumption is not just limited to human health care, but also occurs in other areas such as aquaculture, livestock, and veterinary applications for the purpose of improving feed and meat products. Due to their harmful effects on non-target species, the trace level of antibiotics in the aquatic ecosystem presents a significant problem. Since the introduction of antibiotics into the environment is more than their removal, they have been given the status of persistent pollutants. The buildup of antibiotics in the environment threatens aquatic life and may lead to bacterial strains developing resistance. As newer organisms are becoming resistant, there exists a shortage of antibiotics to treat infections. This has presented a very critical problem for the health-care community. Another rising concern is that the development of newer drug molecules as antibiotics is minimal. This review article critically explains the cause and nature of the pollution and the effects of this emerging trend. Also, in the latter sections, why we need newer antibiotics is questioned and discussed.
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Affiliation(s)
- Tarun Gangar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039 India
| | - Sanjukta Patra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, North Guwahati, Assam 781039 India
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14
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Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
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Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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15
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Mörschbächer AP, Berghahn E, Shibuya FY, Cardoso ML, Ulguim GK, de Freitas Michelon N, Torgeski N, Vivian TP, Wissmann D, de Camargo FCDLS, de Andrade GM, Sturza DAF, Dos Santos HF, Dilkin P, Timmers LFSM, Granada CE. Feeding laying hens with lactobacilli improves internal egg quality and animal health. World J Microbiol Biotechnol 2023; 40:5. [PMID: 37925366 DOI: 10.1007/s11274-023-03820-z] [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: 06/27/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Feeding animals with lactobacilli strains is a biotechnological strategy to improve production, food quality, and animal health. Thus, this study aimed to select new lactic acid bacteria (LAB) able to improve laying hens health and egg production. Forty Bovans White layers (two days old) were randomly divided into four experimental groups that receive an oral gavage with saline solution (control group) or with one of the three lactobacilli selected (KEG3, TBB10, and KMG127) by their antagonistic activity against the foodborne pathogen Bacillus cereus GGD_EGG01. 16 S rRNA sequencing identified KEG3 as Lentilactobacillus sp., and TBB10 and KMG127 as Lactiplantibacillus sp. The data showed that feeding birds with LAB increased weight uniformity and improved the internal quality of the eggs (high yolk index and Haugh unit) compared with the control group (p < 0.05). Beta-diversity analysis showed that LAB supplementation modifies the cecal microbiota of laying hens. The prokaryotic families Bacteroidaceae, Ruminococcaceae, Rikenellaceae, and Lactobacillaceae were most important to the total dissimilarity of the cecal microbial community (calculated by SIMPER test). At end of in vivo experiments, it was possible to conclude that the feed of laying hens with Lentilactobacillus sp. TBB10 and Lentilactobacillus sp. KEG3 can be an important biotechnological tool for improving food quality and animal health.
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Affiliation(s)
- Ana Paula Mörschbächer
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, Brazil
| | - Emílio Berghahn
- Graduate Program in Biotechnology, University of Taquari Valley - Univates, Lajeado, Brazil
| | - Fabio Yuji Shibuya
- Graduate Program in Veterinary Medicine, Federal University of Santa Maria - UFSM, Santa Maria, Brazil
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Mateus Luis Cardoso
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Gustavo Kutscher Ulguim
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Nathalia de Freitas Michelon
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Natália Torgeski
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Tamiris Prussiano Vivian
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Daiani Wissmann
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
- Uniprofessional Residency Program in Veterinary Medicine, Federal University of Santa Maria, Santa Maria, Brazil
| | - Flávia Constância de Los Santos de Camargo
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
- Uniprofessional Residency Program in Veterinary Medicine, Federal University of Santa Maria, Santa Maria, Brazil
| | - Gabriela Monteiro de Andrade
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
- Uniprofessional Residency Program in Veterinary Medicine, Federal University of Santa Maria, Santa Maria, Brazil
| | | | - Helton Fernandes Dos Santos
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
| | - Paulo Dilkin
- Laboratory of Diagnosis of Avian Pathologies, Department of Preventive Veterinary Medicine, Center for Rural Sciences, Federal University of Santa Maria, Santa Maria, Brazil
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16
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Abubakar B, Sárváry A. Knowledge, attitude, and practice on antibiotics use among healthcare workers: A cross-sectional study in Niger state, Nigeria. J Infect Prev 2023; 24:206-215. [PMID: 37736128 PMCID: PMC10510657 DOI: 10.1177/17571774231165407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/01/2023] [Indexed: 09/23/2023] Open
Abstract
Introduction Antibiotic resistance is a public health concern in Nigeria and the world, and healthcare workers contributed to the upsurge of antibiotic resistance in hospital settings. This study focused on the knowledge, attitude, and practice (KAP) of antibiotic use and the frequency of prescriptions of antibiotics from the list of WHO Model Essentials Antibiotics (AWaRe) (in the last 6 months) among healthcare workers and established the determining factors in six hospitals in Niger state, Nigeria. Methodology A KAP survey was conducted in Niger State, Nigeria, from March to June 2022. A structured self-administered, pretested questionnaire was distributed to six hospitals in the state following a stratified random sampling considering the staff capacity, the population of the city, and patients' patronage. Results A total of 350 questionnaires distributed, and 313 (89.4%) completed and returned from the six hospitals. The median scores were knowledge (75%), attitude (69%), practice (62%), and self-reported prescription (70%), and respondents with good scores were knowledge [195 (62.3%)], attitude [185 (59.1%)], practice [201 (64.2%)], and prescription [117 (37.4%)]. In multivariate analysis, older respondents are more likely to have a good prescription (p = 0.006), and prior antimicrobial training improved their knowledge (p < 0.001), attitude (p = 0.007), and prescription pattern (p = 0.009). All the study participants had prescribed one or more of the most prescribed antibiotics; Amoxicillin clavulanate (Access group, 96.5%), Amoxicillin (Access group, 95.9%), and Metronidazole (Access group, 95.7%). Conclusions The study suggests that antibiotic education for healthcare workers and antimicrobial stewardship programs are significant interventions to mitigate antibiotic overuse in the state.
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Affiliation(s)
- Bala Abubakar
- Faculty of Health Sciences, University of Debrecen, Debrecen, Hungary
| | - Attila Sárváry
- Department of Integrative Health Sciences, Faculty of Health Sciences, University of Debrecen, Nyíregyháza, Hungary
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17
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Alvarado-Martinez Z, Julianingsih D, Tabashsum Z, Aditya A, Tung CW, Phung A, Suh G, Hshieh K, Wall M, Kapadia S, Canagarajah C, Maskey S, Sellers G, Scriba A, Biswas D. Assessment of the prevalence, serotype, and antibiotic resistance pattern of Salmonella enterica in integrated farming systems in the Maryland-DC area. Front Microbiol 2023; 14:1240458. [PMID: 37637118 PMCID: PMC10448900 DOI: 10.3389/fmicb.2023.1240458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Implementation of organic/pasture farming practices has been increasing in the USA regardless of official certification. These practices have created an increasingly growing demand for marketing safe products which are produced through these systems. Products from these farming systems have been reported to be at greater risk of transmitting foodborne pathogens because of current trends in their practices. Salmonella enterica (SE) is a ubiquitous foodborne pathogen that remains a public health issue given its prevalence in various food products, but also in the environment and as part of the microbial flora of many domestic animals. Monitoring antibiotic resistance and identifying potential sources contamination are increasingly important given the growing trend of organic/pasture markets. This study aimed to quantify prevalence of SE at the pre- and post-harvest levels of various integrated farms and sites in Maryland-Washington D.C. area, as well as identify the most prevalent serovars and antibiotic resistance patterns. Samples from various elements within the farm environment were collected and screened for SE through culture and molecular techniques, which served to identify and serotype SE, using species and serovar-specific primers, while antibiotic resistance was evaluated using an antibiogram assay. Results showed a prevalence of 7.80% of SE pre-harvest and 1.91% post-harvest. These results also showed the main sources of contamination to be soil (2.17%), grass (1.28%), feces (1.42%) and unprocessed produce (1.48%). The most commonly identified serovar was Typhimurium (11.32%) at the pre-harvest level, while the only identified serovar from post-harvest samples was Montevideo (4.35%). With respect to antibiotic resistance, out of the 13 clinically relevant antibiotics tested, gentamycin and kanamycin were the most effective, demonstrating 78.93 and 76.40% of isolates, respectively, to be susceptible. However, ampicillin, amoxicillin and cephradine had the lowest number of susceptible isolates with them being 10.95, 12.36, and 9.83%, respectively. These results help inform farms striving to implement organic practices on how to produce safer products by recognizing areas that pose greater risks as potential sources of contamination, in addition to identifying serotypes of interest, while also showcasing the current state of antibiotic efficacy and how this can influence antibiotic resistance trends in the future.
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Affiliation(s)
- Zabdiel Alvarado-Martinez
- Biological Sciences Program, Molecular and Cellular Biology, University of Maryland, College Park, College Park, MD, United States
| | - Dita Julianingsih
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Zajeba Tabashsum
- Biological Sciences Program, Molecular and Cellular Biology, University of Maryland, College Park, College Park, MD, United States
| | - Arpita Aditya
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Chuan-Wei Tung
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
| | - Anna Phung
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Grace Suh
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Katherine Hshieh
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Matthew Wall
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Sarika Kapadia
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Christa Canagarajah
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Saloni Maskey
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - George Sellers
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Aaron Scriba
- Department of Biology, University of Maryland, College Park, College Park, MD, United States
| | - Debabrata Biswas
- Biological Sciences Program, Molecular and Cellular Biology, University of Maryland, College Park, College Park, MD, United States
- Department of Animal and Avian Sciences, University of Maryland, College Park, College Park, MD, United States
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18
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Romanò A, Ivanovic I, Segessemann T, Vazquez Rojo L, Widmer J, Egger L, Dreier M, Sesso L, Vaccani M, Schuler M, Frei D, Frey J, Ahrens CH, Steiner A, Graber HU. Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin. Front Microbiol 2023; 14:1183018. [PMID: 37583512 PMCID: PMC10425240 DOI: 10.3389/fmicb.2023.1183018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/17/2023] Open
Abstract
Healthy, untreated cows of nine dairy herds from the Swiss Canton Tessin were analyzed three times within one year to identify the most abundant species of the intramammary bacteriome. Aseptically collected milk samples were cultured and bacteria identified using MALDI-TOF. Of 256 cows analyzed, 96% were bacteriologically positive and 80% of the 1,024 quarters were positive for at least one bacterial species. 84.5% of the quarters were healthy with somatic cell counts (SCC) < 200,000 cells/mL, whereas 15.5% of the quarters showed a subclinical mastitis (SCC ≥ 200,000 cells/mL). We could assign 1,288 isolates to 104 different bacterial species including 23 predominant species. Non-aureus staphylococci and mammaliicocci (NASM) were most prevalent (14 different species; 73.5% quarters). Staphylococcus xylosus and Mammaliicoccus sciuri accounted for 74.7% of all NASM isolates. To describe the intramammary resistome, 350 isolates of the predominant species were selected and subjected to short-read whole genome sequencing (WGS) and phenotypic antibiotic resistance profiling. While complete genomes of eight type strains were available, the remaining 15 were de novo assembled with long reads as a resource for the community. The 23 complete genomes served for reference-based assembly of the Illumina WGS data. Both chromosomes and mobile genetic elements were examined for antibiotic resistance genes (ARGs) using in-house and online software tools. ARGs were then correlated with phenotypic antibiotic resistance data from minimum inhibitory concentration (MIC). Phenotypic and genomic antimicrobial resistance was isolate-specific. Resistance to clindamycin and oxacillin was most frequently observed (65 and 30%) in Staphylococcus xylosus but could not be linked to chromosomal or plasmid-borne ARGs. However, in several cases, the observed antimicrobial resistance could be explained by the presence of mobile genetic elements like tetK carried on small plasmids. This represents a possible mechanism of transfer between non-pathogenic bacteria and pathogens of the mammary gland within and between herds. The-to our knowledge-most extensive bacteriome reported and the first attempt to link it with the resistome promise to profoundly affect veterinary bacteriology in the future and are highly relevant in a One Health context, in particular for mastitis, the treatment of which still heavily relies on antibiotics.
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Affiliation(s)
- Alicia Romanò
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Ivana Ivanovic
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Tina Segessemann
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Laura Vazquez Rojo
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
| | - Jérôme Widmer
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Lotti Egger
- Method Development and Analytics, Group Biochemistry of Milk, Agroscope, Bern, Switzerland
| | - Matthias Dreier
- Food Microbial Systems, Group Cultures, Biodiversity, and Terroir, Agroscope, Bern, Switzerland
| | - Lorenzo Sesso
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Michael Vaccani
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Schuler
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Daniel Frei
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Juerg Frey
- Method Development and Analytics, Group Molecular Diagnostics, Genomics, and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Christian H. Ahrens
- SIB, Swiss Institute of Bioinformatics, Zürich, Switzerland
- Method Development and Analytics, Group Molecular Ecology, Agroscope, Zürich, Switzerland
| | - Adrian Steiner
- Clinic of Ruminants, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Hans Ulrich Graber
- Food Microbial Systems, Group Microbiological Safety of Foods of Animal Origin, Agroscope, Bern, Switzerland
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19
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Gonzales MEM, Ureta JC, Shrestha AMS. Protein embeddings improve phage-host interaction prediction. PLoS One 2023; 18:e0289030. [PMID: 37486915 PMCID: PMC10365317 DOI: 10.1371/journal.pone.0289030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
With the growing interest in using phages to combat antimicrobial resistance, computational methods for predicting phage-host interactions have been explored to help shortlist candidate phages. Most existing models consider entire proteomes and rely on manual feature engineering, which poses difficulty in selecting the most informative sequence properties to serve as input to the model. In this paper, we framed phage-host interaction prediction as a multiclass classification problem that takes as input the embeddings of a phage's receptor-binding proteins, which are known to be the key machinery for host recognition, and predicts the host genus. We explored different protein language models to automatically encode these protein sequences into dense embeddings without the need for additional alignment or structural information. We show that the use of embeddings of receptor-binding proteins presents improvements over handcrafted genomic and protein sequence features. The highest performance was obtained using the transformer-based protein language model ProtT5, resulting in a 3% to 4% increase in weighted F1 and recall scores across different prediction confidence thresholds, compared to using selected handcrafted sequence features.
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Affiliation(s)
- Mark Edward M Gonzales
- Bioinformatics Laboratory, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines
- Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines
| | - Jennifer C Ureta
- Bioinformatics Laboratory, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines
- Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines
| | - Anish M S Shrestha
- Bioinformatics Laboratory, Advanced Research Institute for Informatics, Computing and Networking, De La Salle University, Manila, Philippines
- Systems and Computational Biology Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, Manila, Philippines
- Department of Software Technology, College of Computer Studies, De La Salle University, Manila, Philippines
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Cardoso JMS, Esteves I, Egas C, Braga MEM, de Sousa HC, Abrantes I, Maleita C. Transcriptome analysis reveals the high ribosomal inhibitory action of 1,4-naphthoquinone on Meloidogyne luci infective second-stage juveniles. FRONTIERS IN PLANT SCIENCE 2023; 14:1191923. [PMID: 37342130 PMCID: PMC10277735 DOI: 10.3389/fpls.2023.1191923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/03/2023] [Indexed: 06/22/2023]
Abstract
The root-knot nematode (RKN) Meloidogyne luci presents a threat to the production of several important crops. This nematode species was added to the European Plant Protection Organization Alert list in 2017. The scarce availability of efficient nematicides to control RKN and the phasing out of nematicides from the market have intensified the search for alternatives, such as phytochemicals with bionematicidal properties. The nematicidal activity of 1,4-naphthoquinone (1,4-NTQ) against M. luci has been demonstrated; however, knowledge of the potential mode(s) of action of this compound is still scarce. In this study, the transcriptome profile of M. luci second-stage juveniles (J2), the infective stage, in response to 1,4-NTQ exposure was determined by RNA-seq to identify genes and pathways that might be involved in 1,4-NTQ's mode(s) of action. Control treatments, consisting of nematodes exposed to Tween® 80 (1,4-NTQ solvent) and to water, were included in the analysis. A large set of differentially expressed genes (DEGs) was found among the three tested conditions, and a high number of downregulated genes were found between 1,4-NTQ treatment and water control, reflecting the inhibitory effect of this compound on M. luci, with a great impact on processes related to translation (ribosome pathway). Several other nematode gene networks and metabolic pathways affected by 1,4-NTQ were also identified, clarifying the possible mode of action of this promising bionematicide.
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Affiliation(s)
- Joana M. S. Cardoso
- Centre for Functional Ecology - Science for People and The Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Ivânia Esteves
- Centre for Functional Ecology - Science for People and The Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, Faculdade de Medicina, University of Coimbra, Coimbra, Portugal
- Biocant-Transfer Technology Center, BiocantPark, Cantanhede, Portugal
| | - Mara E. M. Braga
- Chemical Process Engineering and Forest Products Research Centre, Department of Chemical Engineering, University of Coimbra, Coimbra, Portugal
| | - Hermínio C. de Sousa
- Chemical Process Engineering and Forest Products Research Centre, Department of Chemical Engineering, University of Coimbra, Coimbra, Portugal
| | - Isabel Abrantes
- Centre for Functional Ecology - Science for People and The Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Carla Maleita
- Centre for Functional Ecology - Science for People and The Planet, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Chemical Process Engineering and Forest Products Research Centre, Department of Chemical Engineering, University of Coimbra, Coimbra, Portugal
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Pate LA, Milne CE, McMorran R, Roberts DJ, Macrae AI. Factors influencing Scottish dairy farmers' antibiotic use. Vet Rec 2023; 192:e2997. [PMID: 37183187 DOI: 10.1002/vetr.2997] [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: 06/26/2022] [Revised: 03/15/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND Good stewardship of antibiotics can reduce the development and impact of antimicrobial resistance (AMR); therefore, understanding farmers' antibiotic use is of interest to stakeholders. To date, few qualitative studies have looked at farmers' antibiotic use on dairy farms in the UK. METHODS Semi-structured interviews were used to explore 15 Scottish dairy farmers' antibiotic use behaviours and the factors influencing their antibiotic use on farms. RESULTS Using an inductive process, the results from the interviews were analysed, and four key themes were extracted: use of antibiotics, awareness of AMR, determinants of antibiotic use and future aspirations. LIMITATIONS Some of the farmers interviewed were wary about discussing their antibiotic use, which could mean that some contentious issues were not discussed. The farmers also all belonged to a single milk-buying group, which may limit the generalisability of the findings. CONCLUSIONS The quantities of antibiotics used were felt to be driven by the disease prevalence on farms, cows being indoors more, increasing herd sizes resulting in increased stocking densities, retention of poorer cows and substandard housing. Farmer knowledge of antibiotics varied, and not all farmers interviewed were aware of AMR. The farm veterinarian, the press and peers were found to be the main sources of antibiotic information.
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Affiliation(s)
| | | | | | - David J Roberts
- Department of Agriculture and Business Management, SRUC, Dumfries, UK
| | - Alastair I Macrae
- Dairy Herd Health and Productivity Service, The Royal (Dick) School of Veterinary Studies and the Roslin Institute, Midlothian, UK
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22
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Lu SY, Liu S, Patel MH, Glenzinski KM, Skory CD. Saccharomyces cerevisiae surface display of endolysin LysKB317 for control of bacterial contamination in corn ethanol fermentations. Front Bioeng Biotechnol 2023; 11:1162720. [PMID: 37091344 PMCID: PMC10117863 DOI: 10.3389/fbioe.2023.1162720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023] Open
Abstract
Control of bacterial contamination in bioethanol fermentation facilities has traditionally relied on chemical-based products such as hop acids and use of antibiotics. Recent emphasis on antibiotic stewardship has prompted new research into the development of alternative approaches to microbial remediation strategies. We recently described a recombinant peptidoglycan hydrolase, endolysin LysKB317, which inhibited Limosilactobacillus fermentum strains in corn mash fermentation. Here, Saccharomyces cerevisiae EBY100 was used to anchor recombinant LysKB317 using cell surface display with the a-agglutinin proteins Aga1p–Aga2p. Immunostaining and confocal fluorescence were used for localization of the extracellular interface of the cells. Yeast surface-expressed endolysin demonstrated an 83.8% decrease in bacterial cell counts compared to a 9.5% decrease in control yeast. Recombinant S. cerevisiae expressing LysKB317 used for small-scale corn mash fermentation, when infected with L. fermentum, could proactively control bacterial infection for 72 h with at least 1-log fold reduction. Analysis of fermentation products showed improved ethanol concentrations from 3.4% to at least 5.9% compared to the infection-only control and reduced levels of lactic and acetic acid from 34.7 mM to 13.8 mM and 25.5 mM to 18.1 mM, respectively. In an optimized yeast surface display system, proactive treatment of bacterial contaminants by endolysin LysKB317 can improve fermentation efficiency in the presence of L. fermentum contamination.
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Affiliation(s)
- Shao-Yeh Lu
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
- *Correspondence: Shao-Yeh Lu,
| | - Siqing Liu
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
| | - Maulik H. Patel
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
| | - Kristina M. Glenzinski
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
| | - Christopher D. Skory
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, Agricultural Research Service, Peoria, IL, United States
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Manetsberger J, Caballero Gómez N, Benomar N, Christie G, Abriouel H. Characterization of the Culturable Sporobiota of Spanish Olive Groves and Its Tolerance toward Environmental Challenges. Microbiol Spectr 2023; 11:e0401322. [PMID: 36719235 PMCID: PMC10100736 DOI: 10.1128/spectrum.04013-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 01/09/2023] [Indexed: 02/01/2023] Open
Abstract
Olive agriculture presents an integral economic and social pillar of the Mediterranean region with 95% of the world's olive tree population concentrated in this area. A diverse ecosystem consisting of fungi, archaea, viruses, protozoa, and microbial communities-the soil microbiome-plays a central role in maintaining healthy soils while keeping up productivity. Spore-forming organisms (i.e., the sporobiota) have been identified as one of the predominant communities of the soil microbiome and are known for the wide variety of antimicrobial properties and extraordinary resistance. Hence, the aim of this work was to determine the culturable sporobiota of Spanish olive orchards and characterize its phenotypic properties toward common environmental challenges. A collection of 417 heat-resistant bacteria were isolated from five Spanish olive orchards. This collective was termed the "olive sporobiota." Rep-PCR clustering of representative isolates revealed that they all belonged to the group of Bacillus spp., or closely related species, showing a great variety of species and strains. Representative isolates showed susceptibility to common antibiotics, as well as good resistance to heavy metal exposure, with an order of metal tolerance determined as iron > copper > nickel > manganese > zinc > cadmium. Finally, we showed that the application of mineral fertilizer can in several cases enhance bacterial growth and thus potentially increase the relative proportion of the sporobiota in the olive grove ecosystem. In summary, the identification of the culturable olive sporobiota increases our understanding of the microbial diversity in Spanish olive groves, while tolerance and resistance profiles provide important insights into the phenotypic characteristics of the microbial community. IMPORTANCE Microbial communities are a key component of healthy soils. Spore-forming microorganisms represent a large fraction of this community-termed the "sporobiota"-and play a central role in creating a conducive environment for plant growth and food production. In addition, given their unique features, such as extraordinary stability and antimicrobial properties, members of the sporobiota present interesting candidates for biotechnological applications, such as sustainable plant protection products or in a clinical setting. For this, however, more information is needed on the spore-forming community of agricultural installations, ultimately promoting a transition toward a more sustainable agriculture.
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Affiliation(s)
- Julia Manetsberger
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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Zhang J, Yu H, Zhang H, Zhao Q, Si W, Qin Y, Zhang J. Dietary Epimedium extract supplementation improves intestinal functions and alters gut microbiota in broilers. J Anim Sci Biotechnol 2023; 14:14. [PMID: 36653873 PMCID: PMC9847172 DOI: 10.1186/s40104-022-00812-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/27/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Growth-promoting antibiotics have been banned by law in the livestock and poultry breeding industry in many countries. Various alternatives to antibiotics have been investigated for using in livestock. Epimedium (EM) is an herb rich in flavonoids that has many beneficial effects on animals. Therefore, this study was planned to explore the potential of EM as a new alternative antibiotic product in animal feed. METHODS A total of 720 1-day-old male broilers (Arbor Acres Plus) were randomly divided into six groups and fed basal diet (normal control; NC), basal diet supplemented with antibiotic (75 mg/kg chlortetracycline; CTC), and basal diet supplemented with 100, 200, 400 or 800 mg/kg EM extract for 6 weeks (EM100, EM200, EM400 and EM800 groups). The growth performance at weeks 3 and 6 was measured. Serum, intestinal tissue and feces were collected to assay for antioxidant indexes, intestinal permeability, lactic acid and short-chain fatty acids (SCFAs) profiles, microbial composition, and expression of intestinal barrier genes. RESULTS The average daily feed intake in CTC group at 1-21 d was significantly higher than that in the NC group, and had no statistical difference with EM groups. Compared with NC group, average daily gain in CTC and EM200 groups increased significantly at 1-21 and 1-42 d. Compared with NC group, EM200 and EM400 groups had significantly decreased levels of lipopolysaccharide and D-lactic acid in serum throughout the study. The concentrations of lactic acid, acetic acid, propionic acid, butyric acid and SCFAs in feces of birds fed 200 mg/kg EM diet were significantly higher than those fed chlortetracycline. The dietary supplementation of chlortetracycline and 200 mg/kg EM significantly increased ileal expression of SOD1, Claudin-1 and ZO-1 genes. Dietary supplemented with 200 mg/kg EM increased the relative abundances of g_NK4A214_group and Lactobacillus in the jejunal, while the relative abundances of Microbacterium, Kitasatospora, Bacteroides in the jejunal and Gallibacterium in the ileum decreased. CONCLUSION Supplementation with 200 mg/kg EM extract improved the composition of intestinal microbiota by regulating the core bacterial genus Lactobacillus, and increased the concentration of beneficial metabolites lactic acid and SCFAs in the flora, thereby improving the antioxidant capacity and intestinal permeability, enhancing the function of tight junction proteins. These beneficial effects improved the growth performance of broilers.
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Affiliation(s)
- Jiaqi Zhang
- grid.410727.70000 0001 0526 1937State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193 Beijing, China ,grid.464332.4Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Haitao Yu
- grid.410727.70000 0001 0526 1937State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193 Beijing, China ,grid.464332.4Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Huiyan Zhang
- grid.410727.70000 0001 0526 1937State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193 Beijing, China ,grid.464332.4Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Qingyu Zhao
- grid.410727.70000 0001 0526 1937State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193 Beijing, China ,grid.464332.4Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Wei Si
- grid.410727.70000 0001 0526 1937State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193 Beijing, China ,grid.464332.4Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Yuchang Qin
- grid.410727.70000 0001 0526 1937State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193 Beijing, China ,grid.464332.4Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, 100193 Beijing, China
| | - Junmin Zhang
- grid.410727.70000 0001 0526 1937State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, 100193 Beijing, China ,grid.464332.4Scientific Observing and Experiment Station of Animal Genetic Resources and Nutrition in North China of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, 100193 Beijing, China
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Abjani F, Madhavan P, Chong PP, Chinna K, Rhodes CA, Lim YAL. Urbanisation and its Associated Factors Affecting Human Gut Microbiota: Where are we Heading to? Ann Hum Biol 2023; 50:137-147. [PMID: 36650931 DOI: 10.1080/03014460.2023.2170464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
ContextThe continuous rise in urbanisation and its associated factors have been reflected in the structure of the human gut ecosystem.ObjectiveThe main focus of the review is to discuss and summarise the major risk factors associated with urbanisation that affects human gut microbiota thus affecting human health.MethodsMultiple medical literature databases, namely PubMed, Google, Google Scholar, and Web of Science were used to find relevant materials for urbanization and its major factors affecting human gut microbiota/microbiome. Both layman and Medical Subject Headings (MeSH) terms were used in the search. Due to the scarcity of the data, no limitation was set on the publication date. Relevant material in the English language which includes case reports, chapters of books, journal articles, online news reports and medical records was included in this review.ResultsBased on the data discussed in the review, it is quite clear that urbanisation and its associated factors have long-standing effects on the human gut microbiota that result in alterations of gut microbial diversity and composition. This is a matter of serious concern as chronic inflammatory diseases are on the rise in urbanised societies.ConclusionA better understanding of the factors associated with urbanisation will help us to identify and implement new biological and social approaches to prevent and treat diseases and improve health globally by deepening our understanding of these relationships and increasing studies across urbanisation gradients.HIGHLIGHTSHuman gut microbiota has been linked to almost every important function, including metabolism, intestinal homeostasis, immune system, biosynthesis of vitamins, brain processes, and its behaviour.However, dysbiosis i.e., alteration in the composition and diversity of gut microbiota is associated with the pathogenesis of many chronic conditions.In the 21st century, urbanisation represents a major demographic shift in developed and developing countries.During this period of urbanisation, humans have been exposed to many environmental exposures, all of which have led to the dysbiosis of human gut microbiota.The main focus of the review is to discuss and summarize the major risk factors associated with urbanisation and how it affects the diversity and composition of gut microbiota which ultimately affects human health.
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Affiliation(s)
- Farhat Abjani
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, Jalan Taylors, 47500 Subang Jaya, Selangor, Malaysia
| | - Priya Madhavan
- School of Medicine, Faculty of Health & Medical Sciences, Taylor's University, Jalan Taylors, 47500 Subang Jaya, Selangor, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health & Medical Sciences, Taylor's University, Jalan Taylors, 47500 Subang Jaya, Selangor, Malaysia
| | - Karuthan Chinna
- Faculty of Business and Management, UCSI University 56100 Cheras, Kuala Lumpur, Malaysia
| | - Charles Anthony Rhodes
- Department of Parasitology, University Malaya Medical Centre, 50603 Kuala Lumpur, Federal Territory of Kuala Lumpur, Malaysia
| | - Yvonne Ai Lian Lim
- Department of Parasitology, Faculty of Medicine, University of Malaya. 50603 Kuala Lumpur, Federal Territory of Kuala Lumpur, Malaysia
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Nemati G, Romanó A, Wahl F, Berger T, Rojo LV, Graber HU. Bovine Staphylococcus aureus: a European study of contagiousness and antimicrobial resistance. Front Vet Sci 2023; 10:1154550. [PMID: 37206433 PMCID: PMC10188956 DOI: 10.3389/fvets.2023.1154550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/04/2023] [Indexed: 05/21/2023] Open
Abstract
In dairy herds managements, mastitis is the leading cause of economic losses. One of the most important pathogens responsible for intra-mammary infections is Staphylococcus aureus. The genetic properties of S. aureus have a strong influence on its pathogenicity and contagiousness. In this study, we aimed to obtain a comprehensive overview of the key bovine S. aureus clinical properties, such as contagiousness and antimicrobial resistance, present in European strains. For this, 211 bovine S. aureus strains from ten European countries that were used in a previous study were used in this study. Contagiousness was assessed using qPCR for the detection of the marker gene adlb. Antimicrobial resistance was evaluated using a broth microdilution assay and mPCR for the detection of genes involved in penicillin resistance (blaI, blaR1, and blaZ). It was found that adlb was present in CC8/CLB strains; however, in Germany, it was found in CC97/CLI and in an unknown CC/CLR strains. CC705/CLC strains from all countries were found to be susceptible to all tested antibiotics. Major resistance to penicillin/ampicillin, chloramphenicol, clindamycin and tetracycline was detected. Resistance to oxacillin, trimethoprim/sulfamethoxazole and cephalosporins was rarely observed. In addition, contagiousness and antibiotic resistance seem to correlate with different CCs and genotypic clusters. Hence, it is recommended that multilocus sequence typing or genotyping be utilized as a clinical instrument to identify the most appropriate antibiotic to use in mastitis treatment. Actualization of the breakpoints of veterinary strains is necessary to address the existing antibiotic resistance of the bacteria involved in veterinary mastitis.
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Affiliation(s)
- Ghazal Nemati
- Food Microbial Systems, Risk Assessment and Mitigation Group, Agroscope, Bern, Switzerland
- Food Microbial Systems, Microbiological Safety of Foods of Animal Origin Group, Agroscope, Bern, Switzerland
- *Correspondence: Ghazal Nemati
| | - Alicia Romanó
- Food Microbial Systems, Microbiological Safety of Foods of Animal Origin Group, Agroscope, Bern, Switzerland
| | - Fabian Wahl
- Food Microbial Systems, Agroscope, Bern, Switzerland
| | - Thomas Berger
- Food Microbial Systems, Risk Assessment and Mitigation Group, Agroscope, Bern, Switzerland
| | - Laura Vazquez Rojo
- Food Microbial Systems, Microbiological Safety of Foods of Animal Origin Group, Agroscope, Bern, Switzerland
| | - Hans Ulrich Graber
- Food Microbial Systems, Microbiological Safety of Foods of Animal Origin Group, Agroscope, Bern, Switzerland
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Lima-Noronha MA, Fonseca DLH, Oliveira RS, Freitas RR, Park JH, Galhardo RS. Sending out an SOS - the bacterial DNA damage response. Genet Mol Biol 2022; 45:e20220107. [PMID: 36288458 PMCID: PMC9578287 DOI: 10.1590/1678-4685-gmb-2022-0107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022] Open
Abstract
The term “SOS response” was first coined by Radman in 1974, in an intellectual effort to put together the data suggestive of a concerted gene expression program in cells undergoing DNA damage. A large amount of information about this cellular response has been collected over the following decades. In this review, we will focus on a few of the relevant aspects about the SOS response: its mechanism of control and the stressors which activate it, the diversity of regulated genes in different species, its role in mutagenesis and evolution including the development of antimicrobial resistance, and its relationship with mobile genetic elements.
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Affiliation(s)
- Marco A. Lima-Noronha
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Douglas L. H. Fonseca
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Renatta S. Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rúbia R. Freitas
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Jung H. Park
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rodrigo S. Galhardo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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Siddique MH, Hayat S, Muzammil S, Ashraf A, Khan AM, Ijaz MU, Khurshid M, Afzal M. Ecofriendly phytosynthesized zirconium oxide nanoparticles as antibiofilm and quorum quenching agents against Acinetobacter baumannii. Drug Dev Ind Pharm 2022; 48:502-509. [PMID: 36191015 DOI: 10.1080/03639045.2022.2132260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The worldwide increase of multi-drug resistance has directed the researchers to focus on ecofriendly ways of nanoparticles synthesis with effective antivirulence properties. Here, we report the antibiofilm and quorum quenching potential of zirconium oxide nanoparticles (ZrO2 NPs) synthesized from aqueous ginger extract against multi drug resistant (MDR) Acinetobacter baumannii. The results indicated that ZrO2 NPs were of tetragonal shape with average diameter of 16 nm. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values for A. baumannii were 15.6 µg/ml and 62.5 µg/ml respectively as revealed by broth microdilution assay. Exposure of bacterial cells to ZrO2 NPs resulted in reactive oxygen species (ROS) generation which in turn led to cellular membrane disruption as observed by an increase in leakage of cellular contents such as proteins, sugars and DNA. The antibiofilm activity was evaluated by microtiter plate assay and the results revealed that the percentage inhibition of biofilm was found to be 14.3-80.6%. ZrO2 NPs also obstructed the chemical composition of biofilms matrix by reducing the proteins and carbohydrate contents. Molecular docking studies of ZrO2 NPs with four proteins (2NAZ, 4HKG, 5D6H and 5HM6) involved in biofilm formation of A. baumannii revealed the interaction of zirconium with target proteins. These findings suggested the in vitro efficacy of phytosynthesized ZrO2 NPs as antibiofilm and quorum quenching agents that can be exploited in the development of alternative therapeutic options against MDR A. baumannii.
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Affiliation(s)
| | - Sumreen Hayat
- Department of Microbiology, Government College University, Faisalabad
| | - Saima Muzammil
- Department of Microbiology, Government College University, Faisalabad
| | - Asma Ashraf
- Department of Zoology, Government College University, Faisalabad
| | | | - Muhammad Umar Ijaz
- Department of Zoology, Wildlife and Fisheries, University of Agriculture, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University, Faisalabad
| | - Muhammad Afzal
- Department of Bioinformatics and Biotechnology, Govt. College University, Faisalabad
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Grakh K, Mittal D, Kumar T, Thakur S, Panwar D, Singh L, Kumar M, Jindal N. Attitude, Opinions, and Working Preferences Survey among Pet Practitioners Relating to Antimicrobials in India. Antibiotics (Basel) 2022; 11:antibiotics11101289. [PMID: 36289947 PMCID: PMC9599001 DOI: 10.3390/antibiotics11101289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/28/2022] [Accepted: 06/28/2022] [Indexed: 01/17/2023] Open
Abstract
The indiscriminate usage and overuse of antimicrobials in pets or companion animals are underlying causes of antimicrobial resistance (AMR). Despite the multi-faceted global challenge presented by antimicrobial resistance, very few studies have appraised pet practitioners’ factors, such as written policy on antimicrobials, dose rate prescribed, use of critically important antimicrobials, and antimicrobial prescription in clean surgical procedures, which can contribute to AMR. In the present study, an online cross-sectional survey among randomly selected pet practitioners (n = 104) of various Indian provinces and union territories was conducted using a questionnaire comprising 33 closed-ended questions on different parameters, viz., the dosage regimen and level of compliance towards guidelines of the World Health Organization (WHO), other relevant veterinary associations, and their opinion while prescribing antimicrobials. Almost every practitioner of the 104 respondents had revealed the difficulties with owner compliance; i.e., incomplete course of the antibiotics, inappropriate follow-ups, and improper care of the sick animals. The majority of practitioners (95%) reported self-prescription of antimicrobials by the owner before presenting the pet(s) to the veterinary clinic, whereas more than half of the respondents (64%) revealed unavailability of antibiogram facilities. Furthermore, a large number (76%) of practitioners stated empirical treatment based on their experience as the main criteria for antimicrobial choice in the absence of timely results from the laboratory. Although non-necessitated use of antimicrobials in clean surgical procedures has been claimed, surprisingly, the majority of pet practitioners (97%) reported their use to reduce the post-operative complications. The use of the highest priority, critically important antimicrobials (HPCIA) listed by the WHO for humans, particularly quinolones and third-generation cephalosporin, also has been reported for different infections. The treatment durations were nearly as per the recommended guidelines issued by the Danish Small Animal Veterinary Association (DSAVA) for different ailments. Analysis using chi-square tests exhibited a significant correlation between less experienced veterinarians (less than 5 years) and prescription of antimicrobials restricted for critically important infections in human medicine. However, there seems to be no association between the experience of the practitioner and the further studied parameters, namely, antimicrobial regimen prescription, weighing the animals before prescription, dose rate calculation, and antimicrobial selection and use after clean surgical operations. The findings suggest periodic awareness campaigns among practitioners regarding the implementation of the official guidelines, the need for systematic surveillance of AMR, awareness among pet owners about antimicrobial resistance, and the importance of rational use of antimicrobials on their pets.
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Affiliation(s)
- Kushal Grakh
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Dinesh Mittal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
- Correspondence:
| | - Tarun Kumar
- Department of Veterinary Clinical Complex (VCC), Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Swati Thakur
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Diksha Panwar
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Lokender Singh
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Manesh Kumar
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar 125004, India
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Analysis of the Distribution and Antibiotic Resistance of Pathogens Causing Infections in Hospitals from 2017 to 2019. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:3512582. [PMID: 36159558 PMCID: PMC9507740 DOI: 10.1155/2022/3512582] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/18/2022]
Abstract
Background. Antibiotic resistance is a global public health problem, leading to high mortality and treatment costs. To achieve more efficient treatment protocols and better patient recovery, the distribution and drug resistance of pathogens in our hospital were investigated, allowing significant clinical guidance for the use of antimicrobials. Methods. In this retrospective study (2017–2019), 3482 positive samples were isolated from 43,981 specimens in 2017; 3750 positive specimens were isolated from 42,923 specimens in 2018; and 3839 positive pathogens were isolated from 46,341 specimens in 2019. These samples were from various parts of the patients, including the respiratory tract, urine, blood, wound secretions, bile, and puncture fluids. The distribution and antibiotic resistance of these isolated pathogens from the whole hospital were analyzed. Results. The results from pathogen isolation showed that Escherichia coli (12.8%), Staphylococcus aureus (11%), Klebsiella pneumoniae (10.8%), Pseudomonas aeruginosa (10.7%), and Acinetobacter baumannii (6.4%) represented the five main pathogenic bacteria in our hospital. Pseudomonas aeruginosa (16.2% and 17.5%) occupied the largest proportion in the central intensive care unit (central ICU) and respiratory intensive care unit (RICU), while Acinetobacter baumannii (15.4%) was the most common pathogen in the emergency intensive care unit (EICU). The resistance rate of Escherichia coli to trimethoprim and minocycline was 100%, and the sensitivity rate to ertapenem, furantoin, and amikacin was above 90%. The resistance rate of Pseudomonas aeruginosa to all antibiotics, such as piperacillin and ciprofloxacin, was under 40%. The sensitivity rate of Acinetobacter baumannii to tigecycline and minocycline was less than 30%, and the resistance rate to many drugs such as piperacillin, ceftazidime, and imipenem was above 60%. Extended-spectrum β-lactamases (ESBLs)-producing Klebsiella pneumoniae (ESBLs-KPN) and carbapenem-resistant Klebsiella pneumoniae (CRE-KPN), ESBLs-producing Escherichia coli (ESBLs-ECO) and carbapenem-resistant Escherichia coli (CRE-ECO), multidrug-resistant Acinetobacter baumannii (MDR-AB), multidrug-resistant Pseudomonas aeruginosa (MDR-PAE), and methicillin-resistant Staphylococcus aureus (MRSA) are all important multidrug-resistant bacteria found in our hospital. The resistance rate of ESBLs-producing Enterobacteriaceae to ceftriaxone and amcarcillin-sulbactam was above 95%. CRE Enterobacteriaceae bacteria showed the highest resistance to amcarcillin-sulbactam (97.1%), and the resistance rates of MDR-AB to cefotaxime, cefepime, and aztreonam were 100%. The resistance rates of MDR-PAE to ceftazidime, imipenem, and levofloxacin were 100%, and the sensitivity rate to polymyxin B was above 98%. The resistance rate of MRSA to oxacillin was 100%, and the sensitivity rate to linezolid and vancomycin was 100%. Conclusion. The distribution of pathogenic bacteria in different hospital departments and sample sources was markedly different. Therefore, targeted prevention and control of key pathogenic bacteria in different hospital departments is necessary, and understanding both drug resistance and multiple drug resistance of the main pathogenic bacteria may provide guidance for the rational use of antibiotics in the clinic.
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Wang X, Bodirsky BL, Müller C, Chen KZ, Yuan C. The triple benefits of slimming and greening the Chinese food system. NATURE FOOD 2022; 3:686-693. [PMID: 37118140 DOI: 10.1038/s43016-022-00580-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/22/2022] [Indexed: 04/30/2023]
Abstract
The Chinese food system has undergone a transition of unprecedented speed, leading to complex interactions with China's economy, health and environment. Structural changes experienced by the country over the past few decades have boosted economic development but have worsened the mismatch between food supply and demand, deteriorated the environment, driven obesity and overnutrition levels up, and increased the risk for pathogen spread. Here we propose a strategy for slimming and greening the Chinese food system towards sustainability targets. This strategy takes into account the interlinkages between agricultural production and food consumption across the food system, going beyond agriculture-focused perspectives. We call for a food-system approach with integrated analysis of potential triple benefits for the economy, health and the environment, as well as multisector collaboration in support of evidence-based policymaking.
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Affiliation(s)
- Xiaoxi Wang
- China Academy for Rural Development, Department of Agricultural Economics and Management, Zhejiang University, Hangzhou, China.
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany.
| | - Benjamin Leon Bodirsky
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany.
| | - Christoph Müller
- China Academy for Rural Development, Department of Agricultural Economics and Management, Zhejiang University, Hangzhou, China
- Potsdam Institute for Climate Impact Research, Member of the Leibniz Association, Potsdam, Germany
| | - Kevin Z Chen
- China Academy for Rural Development, Department of Agricultural Economics and Management, Zhejiang University, Hangzhou, China
- International Food Policy Research Institute, Washington, DC, USA
| | - Changzheng Yuan
- School of Public Health, the Children's Hospital, and National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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Dmitrović S, Pajčin I, Lukić N, Vlajkov V, Grahovac M, Grahovac J, Jokić A. Taguchi Grey Relational Analysis for Multi-Response Optimization of Bacillus Bacteria Flocculation Recovery from Fermented Broth by Chitosan to Enhance Biocontrol Efficiency. Polymers (Basel) 2022; 14:polym14163282. [PMID: 36015554 PMCID: PMC9413004 DOI: 10.3390/polym14163282] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 02/05/2023] Open
Abstract
Degradation of environment is a challenge to crop production around the world. Biological control of various plant diseases using antagonistic bacteria is an encouraging alternative to traditionally used chemical control strategies. Chitosan as a well-known natural flocculation agent also exhibits antimicrobial activity. The goal of this study was to investigate a dual nature of chitosan in flocculation of Bacillus sp. BioSol021 cultivation broth intended for biocontrol applications. Experiments were performed based on L18 standard Taguchi orthogonal array design with five input parameters (chitosan type and dosage, pH value, rapid and slow mixing rates). In this study, the grey relational analysis was used to perform multi-objective optimization of the chosen responses, i.e., flocculation efficiency and four inhibition zone diameters against the selected phytopathogens. The results have indicated a great potential of a highly efficient method for removal of the Bacillus bacteria from the cultivation broth using chitosan. The good flocculation efficiency and high precipitate antimicrobial activity against the selected phytopathogens were achieved. It has been shown that multiple flocculation performance parameters were improved, resulting in slightly improved response values.
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Affiliation(s)
- Selena Dmitrović
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar cara Lazara 1, 21000 Novi Sad, Serbia
| | - Ivana Pajčin
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar cara Lazara 1, 21000 Novi Sad, Serbia
- Correspondence: (I.P.); (J.G.)
| | - Nataša Lukić
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar cara Lazara 1, 21000 Novi Sad, Serbia
| | - Vanja Vlajkov
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar cara Lazara 1, 21000 Novi Sad, Serbia
| | - Mila Grahovac
- Faculty of Agriculture, University of Novi Sad, Trg Dositeja Obradovića 8, 21000 Novi Sad, Serbia
| | - Jovana Grahovac
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar cara Lazara 1, 21000 Novi Sad, Serbia
- Correspondence: (I.P.); (J.G.)
| | - Aleksandar Jokić
- Faculty of Technology Novi Sad, University of Novi Sad, Bulevar cara Lazara 1, 21000 Novi Sad, Serbia
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Melgarejo T, Sharp N, Krumbeck JA, Wu G, Kim YJ, Linde A. The Urinary Resistome of Clinically Healthy Companion Dogs: Potential One Health Implications. Antibiotics (Basel) 2022; 11:antibiotics11060780. [PMID: 35740186 PMCID: PMC9220278 DOI: 10.3390/antibiotics11060780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/02/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
An interdisciplinary approach to antimicrobial resistance (AMR) is essential to effectively address what is projected to soon become a public health disaster. Veterinary medicine accounts for a majority of antimicrobial use, and mainly in support of industrial food animal production (IFAP), which has significant exposure implications for human and nonhuman animals. Companion dogs live in close proximity to humans and share environmental exposures, including food sources. This study aimed to elucidate the AMR-gene presence in microorganisms recovered from urine from clinically healthy dogs to highlight public health considerations in the context of a species-spanning framework. Urine was collected through cystocentesis from 50 companion dogs in Southern California, and microbial DNA was analyzed using next-generation sequencing. Thirteen AMR genes in urine from 48% of the dogs {n=24} were detected. The most common AMR genes were aph(3')Ia, and ermB, which confer resistance to aminoglycosides and MLS (macrolides, lincosamides, streptogramins) antibiotics, respectively. Antibiotic-resistance profiles based on the AMR genes detected, and the intrinsic resistance profiles of bacterial species, were inferred in 24% of the samples {n=12} for 57 species, with most belonging to Streptococcus, Staphylococcus, and Corynebacterium genera. The presence of AMR genes that confer resistance to medically important antibiotics suggests that dogs may serve as reservoirs of clinically relevant resistomes, which is likely rooted in excessive IFAP antimicrobial use.
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Affiliation(s)
- Tonatiuh Melgarejo
- Veterinary Clinical Center, College of Veterinary Medicine, Western University of Health Sciences, 611 E. Second Street, Pomona, CA 91766, USA; (N.S.); (Y.J.K.)
- Correspondence: (T.M.); (A.L.)
| | - Nathan Sharp
- Veterinary Clinical Center, College of Veterinary Medicine, Western University of Health Sciences, 611 E. Second Street, Pomona, CA 91766, USA; (N.S.); (Y.J.K.)
| | | | - Guangxi Wu
- MiDOG LLC, 14672 Bentley Cir, Tustin, CA 92780, USA; (J.A.K.); (G.W.)
| | - Young J. Kim
- Veterinary Clinical Center, College of Veterinary Medicine, Western University of Health Sciences, 611 E. Second Street, Pomona, CA 91766, USA; (N.S.); (Y.J.K.)
| | - Annika Linde
- Veterinary Clinical Center, College of Veterinary Medicine, Western University of Health Sciences, 611 E. Second Street, Pomona, CA 91766, USA; (N.S.); (Y.J.K.)
- Correspondence: (T.M.); (A.L.)
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Váradi G, Galgóczy L, Tóth GK. Rationally Designed Antimicrobial Peptides Are Potential Tools to Combat Devastating Bacteria and Fungi. Int J Mol Sci 2022; 23:ijms23116244. [PMID: 35682921 PMCID: PMC9181708 DOI: 10.3390/ijms23116244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/01/2023] Open
Affiliation(s)
- Györgyi Váradi
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, 6720 Szeged, Hungary;
| | - László Galgóczy
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Temesvári krt. 62, 6726 Szeged, Hungary
| | - Gábor K. Tóth
- Department of Medical Chemistry, Albert Szent-Györgyi Medical School, University of Szeged, Dóm tér 8, 6720 Szeged, Hungary;
- MTA-SZTE Biomimetic Systems Research Group, Department of Medical Chemistry, University of Szeged, Dóm tér 8, 6720 Szeged, Hungary
- Correspondence:
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Flater JS, Alt LM, Soupir M, Moorman TB, Howe A. Prairie strips' effect on transport of antimicrobial resistance indicators in poultry litter. JOURNAL OF ENVIRONMENTAL QUALITY 2022; 51:260-271. [PMID: 35112354 DOI: 10.1002/jeq2.20333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Poultry litter is a valuable nutrient resource for agricultural production but is also a potential source for introducing antibiotic resistance genes (ARGs) and litter-associated bacteria (LAB) to the environment. Prairie strips have been demonstrated as an effective conservation practice to improve environmental quality in agroecosystems. This research aims to assess prairie strips' potential for reducing the transport of LAB and ARGs in runoff after litter application. Plot-scale rainfall simulations were performed using a replicated block design, with soil and surface runoff samples taken during the rainfall event. Microbial taxa and ARGs were characterized in the litter, soil, and water samples. In plots with litter application, LAB and ARGs were mainly detected in runoff, with very low detection in soils. Detection of ARGs in runoff, irrespective of strip installations, is consistent with previous observations of litter as a source of antimicrobial resistance (AMR) risks. The effectiveness of prairie strips to remove LAB and ARGs varied. In two of the three prairie strip plots, fewer AMR indicators were detected relative to control plots, suggesting that the prairie strips can potentially reduce these risks. In one plot, which was also associated with increased flow rate, we observed increased AMR indicators despite the installation of a prairie strip. Our observations highlight the need to prioritize understanding of soil properties even within the same site. Although we show that prairie strips can potentially reduce AMR risks, further research is needed to better understand the influence of rainfall timing, soil, and litter characteristics.
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Affiliation(s)
- Jared S Flater
- Dep. of Agriculture and Biosystems Engineering, Iowa State Univ., Elings Hall, 605 Bissell Rd, Ames, IA, 50011, USA
| | - Laura M Alt
- Dep. of Agriculture and Biosystems Engineering, Iowa State Univ., Elings Hall, 605 Bissell Rd, Ames, IA, 50011, USA
| | - Michelle Soupir
- Dep. of Agriculture and Biosystems Engineering, Iowa State Univ., Elings Hall, 605 Bissell Rd, Ames, IA, 50011, USA
| | - Thomas B Moorman
- USDA-ARS, National Laboratory for Agriculture and the Environment, 1015 N University Blvd., Ames, IA, 50011, USA
| | - Adina Howe
- Dep. of Agriculture and Biosystems Engineering, Iowa State Univ., Elings Hall, 605 Bissell Rd, Ames, IA, 50011, USA
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Quorum-Sensing Inhibition by Gram-Positive Bacteria. Microorganisms 2022; 10:microorganisms10020350. [PMID: 35208805 PMCID: PMC8875677 DOI: 10.3390/microorganisms10020350] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/27/2022] [Accepted: 01/28/2022] [Indexed: 12/01/2022] Open
Abstract
The modern paradigm assumes that interspecies communication of microorganisms occurs through precise regulatory mechanisms. In particular, antagonism between bacteria or bacteria and fungi can be achieved by direct destruction of the targeted cells through the regulated production of antimicrobial metabolites or by controlling their adaptive mechanisms, such as the formation of biofilms. The quorum-quenching phenomenon provides such a countermeasure strategy. This review discusses quorum-sensing suppression by Gram-positive microorganisms, the underlying mechanisms of this process, and its molecular intermediates. The main focus will be on Gram-positive bacteria that have practical applications, such as starter cultures for food fermentation, probiotics, and other microorganisms of biotechnological importance. The possible evolutionary role of quorum-quenching mechanisms during the development of interspecies interactions of bacteria is also considered. In addition, the review provides possible practical applications for these mechanisms, such as the control of pathogens, improving the efficiency of probiotics, and plant protection.
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Sobierajski T, Mazińska B, Chajęcka-Wierzchowska W, Śmiałek M, Hryniewicz W. Antimicrobial and Antibiotic Resistance from the Perspective of Polish Veterinary Students: An Inter-University Study. Antibiotics (Basel) 2022; 11:antibiotics11010115. [PMID: 35052992 PMCID: PMC8772817 DOI: 10.3390/antibiotics11010115] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
The phenomenon of antibiotic resistance is a global problem that affects the use of antibiotics by humans and animal husbandry. One of the primary reasons for the growing phenomenon of antibiotic resistance is the over-prescription of antibiotics by doctors in human medicine and the overuse of antibiotics in industrial animal farming. Adequate education of veterinary medical students on the use of antibiotics in animal husbandry may reduce antibiotic resistance. For this reason, a survey was conducted among students at four primary research and didactic centers teaching veterinary medicine in Poland. The survey aimed to find out the knowledge and attitude of students towards the use of antibiotics and antibiotic resistance. The survey was conducted in May/June 2021. Four hundred and sixty-seven students participated in the study. The study positively verified that antibiotics and antibiotic resistance knowledge increase with successive years of veterinary studies/education. For most students (82.2%), antibiotic resistance is a significant problem, but only 58.7% believe it is global, and one in three respondents heard about the One Health approach.
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Affiliation(s)
- Tomasz Sobierajski
- Faculty of Applied Social Sciences and Resocialization, Warsaw University, Krakowskie Przedmieście 26/28, 00-927 Warsaw, Poland
- Correspondence:
| | - Beata Mazińska
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (B.M.); (W.H.)
| | - Wioleta Chajęcka-Wierzchowska
- Department of Industrial and Food Microbiology, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, 10-726 Olsztyn, Poland;
| | - Marcin Śmiałek
- Department of Poultry Diseases, Faculty of Veterinary Medicine, University of Warmia and Mazury, 10-719 Olsztyn, Poland;
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725 Warsaw, Poland; (B.M.); (W.H.)
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Banakar PS, Kumar S, Vinay VV, Dixit S, Tyagi N, Tyagi AK. Supplementation of Aloe vera extract in lactating goats' diet: effects on rumen fermentation efficiency, nutrient utilization, lactation performance, and antioxidant status. Trop Anim Health Prod 2021; 53:517. [PMID: 34657226 DOI: 10.1007/s11250-021-02894-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/10/2021] [Indexed: 11/28/2022]
Abstract
The present work was conducted to investigate the effects of supplementing Aloe vera extract on rumen fermentation efficiency, nutrient utilization, lactation performance, and antioxidant status of goats. Twenty-four crossbreed lactating goats (Alpine × Beetal) were divided into three experimental groups (AV0, AV2, and AV4). AV0 had no supplementation, groups AV2 and AV4 received ready to feed aqueous extract of Aloe vera at 20 and 40 g/kg dry matter intake, respectively, along with basal diet and experiment lasted for 100 days. Average DMI did not vary (P > 0.05) among treatment groups; however, the metabolic bodyweight of AV4 was significantly lower (P < 0.05) than the AV0 and AV2 groups (AV0 = AV2 > AV4). Intake and digestibility of DM, OM, CP, NDF, ADF, and EE were unaffected (P > 0.05) by Aloe vera supplementation. The milk production, yield of milk fat, protein, lactose, and solid not fat (SNF) of goats in the AV4 group were significantly higher (P < 0.05) than other groups (AV4 > AV2 = AV0). The activity of superoxide dismutase and catalase enzymes and levels of plasma ferric reducing total antioxidant power were high (P < 0.01) in the Aloe vera supplemented group (AV4 = AV2 > AV0). There was no significant difference (P = 0.979) in the pH, acetic acid (P = 0.449), and butyric acid (P = 0.864) concentration of the rumen liquor among the treatment groups. The propionic acid concentration was similar between AV2 and AV4 and significantly higher (P = 0.024) than the AV0 group (AV4 = AV2 > AV0). Moreover, C2:C3 values were significantly lower (P = 0.037) in the AV4 group compared to the control (AV0). Thus, Aloe vera supplementation enhanced milk yield, propionic acid production, and antioxidant status without affecting nutrient utilization; however, results were better in the AV4 group. The inclusion of Aloe vera at 40 g/kg of DMI would improve the rumen fermentation efficiency, lactation performance, and overall health status of the dairy goats.
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Affiliation(s)
- P S Banakar
- Rumen Biotechnology Lab, Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Sachin Kumar
- Rumen Biotechnology Lab, Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - V V Vinay
- Rumen Biotechnology Lab, Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Sonam Dixit
- Rumen Biotechnology Lab, Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Nitin Tyagi
- Rumen Biotechnology Lab, Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Amrish Kumar Tyagi
- Rumen Biotechnology Lab, Animal Nutrition Division, ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India. .,Present Address: Animal Nutrition and Physiology, Indian Council of Agricultural Research, New Delhi, India.
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