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Kimbell LK, LaMartina EL, Kohls S, Wang Y, Newton RJ, McNamara PJ. Impact of corrosion inhibitors on antibiotic resistance, metal resistance, and microbial communities in drinking water. mSphere 2023; 8:e0030723. [PMID: 37681947 PMCID: PMC10597465 DOI: 10.1128/msphere.00307-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023] Open
Abstract
Corrosion inhibitors, including zinc orthophosphate, sodium orthophosphate, and sodium silicate, are commonly used to prevent the corrosion of drinking water infrastructure. Metals such as zinc are known stressors for antibiotic resistance selection, and phosphates can increase microbial growth in drinking water distribution systems (DWDS). Yet, the influence of corrosion inhibitor type on antimicrobial resistance in DWDS is unknown. Here, we show that sodium silicates can decrease antibiotic resistant bacteria (ARB) and antibiotic-resistance genes (ARGs), while zinc orthophosphate increases ARB and ARGs in source water microbial communities. Based on controlled bench-scale studies, zinc orthophosphate addition significantly increased the abundance of ARB resistant to ciprofloxacin, sulfonamides, trimethoprim, and vancomycin, as well as the genes sul1, qacEΔ1, an indication of resistance to quaternary ammonium compounds, and the integron-integrase gene intI1. In contrast, sodium silicate dosage at 10 mg/L resulted in decreased bacterial growth and antibiotic resistance selection compared to the other corrosion inhibitor additions. Source water collected from the drinking water treatment plant intake pipe resulted in less significant changes in ARB and ARG abundance due to corrosion inhibitor addition compared to source water collected from the pier at the recreational beach. In tandem with the antibiotic resistance shifts, significant microbial community composition changes also occurred. Overall, the corrosion inhibitor sodium silicate resulted in the least selection for antibiotic resistance, which suggests it is the preferred corrosion inhibitor option for minimizing antibiotic resistance proliferation in DWDS. However, the selection of an appropriate corrosion inhibitor must also be appropriate for the water chemistry of the system (e.g., pH, alkalinity) to minimize metal leaching first and foremost and to adhere to the lead and copper rule. IMPORTANCE Antibiotic resistance is a growing public health concern across the globe and was recently labeled the silent pandemic. Scientists aim to identify the source of antibiotic resistance and control points to mitigate the spread of antibiotic resistance. Drinking water is a direct exposure route to humans and contains antibiotic-resistant bacteria and associated resistance genes. Corrosion inhibitors are added to prevent metallic pipes in distribution systems from corroding, and the type of corrosion inhibitor selected could also have implications on antibiotic resistance. Indeed, we found that sodium silicate can minimize selection of antibiotic resistance while phosphate-based corrosion inhibitors can promote antibiotic resistance. These findings indicate that sodium silicate is a preferred corrosion inhibitor choice for mitigation of antibiotic resistance.
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Affiliation(s)
- Lee K. Kimbell
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Emily Lou LaMartina
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Stan Kohls
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
| | - Yin Wang
- Department of Civil and Environmental Engineering, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ryan J. Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Patrick J. McNamara
- Department of Civil, Construction and Environmental Engineering, Marquette University, Milwaukee, Wisconsin, USA
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Raut R, Maharjan P, Fouladkhah AC. Practical Preventive Considerations for Reducing the Public Health Burden of Poultry-Related Salmonellosis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6654. [PMID: 37681794 PMCID: PMC10487474 DOI: 10.3390/ijerph20176654] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/20/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023]
Abstract
With poultry products as one of the leading reservoirs for the pathogen, in a typical year in the United States, it is estimated that over one million individuals contract non-typhoidal Salmonella infections. Foodborne outbreaks associated with Salmonella infections in poultry, thus, continue to remain a significant risk to public health. Moreover, the further emergence of antimicrobial resistance among various serovars of Salmonella is an additional public health concern. Feeding-based strategies (such as use of prebiotics, probiotics, and/or phytobiotics as well as essential oils), non-feeding-based strategies (such as use of bacteriophages, vaccinations, and in ovo strategies), omics tools and surveillance for identifying antibiotic-resistance genes, post-harvest application of antimicrobials, and biosecurity measures at poultry facilities are practical interventions that could reduce the public health burden of salmonellosis and antibiotic resistance associated with poultry products. With the escalating consumption of poultry products around the globe, the fate, prevalence, and transmission of Salmonella in agricultural settings and various poultry-processing facilities are major public health challenges demanding integrated control measures throughout the food chain. Implementation of practical preventive measures discussed in the current study could appreciably reduce the public health burden of foodborne salmonellosis associated with poultry products.
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Affiliation(s)
- Rabin Raut
- Cooperative Extension Program, Tennessee State University, Nashville, TN 37209, USA;
- Public Health Microbiology Laboratory, Tennessee State University, Nashville, TN 37209, USA
| | - Pramir Maharjan
- Cooperative Extension Program, Tennessee State University, Nashville, TN 37209, USA;
| | - Aliyar Cyrus Fouladkhah
- Public Health Microbiology Laboratory, Tennessee State University, Nashville, TN 37209, USA
- Public Health Microbiology FoundationSM, Nashville, TN 37209, USA
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Oxendine A, Walsh AA, Young T, Dixon B, Hoke A, Rogers EE, Lee MD, Maurer JJ. Conditions Necessary for the Transfer of Antimicrobial Resistance in Poultry Litter. Antibiotics (Basel) 2023; 12:1006. [PMID: 37370325 DOI: 10.3390/antibiotics12061006] [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: 04/26/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Animal manures contain a large and diverse reservoir of antimicrobial resistance (AMR) genes that could potentially spillover into the general population through transfer of AMR to antibiotic-susceptible pathogens. The ability of poultry litter microbiota to transmit AMR was examined in this study. Abundance of phenotypic AMR was assessed for litter microbiota to the antibiotics: ampicillin (Ap; 25 μg/mL), chloramphenicol (Cm; 25 μg/mL), streptomycin (Sm; 100 μg/mL), and tetracycline (Tc; 25 μg/mL). qPCR was used to estimate gene load of streptomycin-resistance and sulfonamide-resistance genes aadA1 and sul1, respectively, in the poultry litter community. AMR gene load was determined relative to total bacterial abundance using 16S rRNA qPCR. Poultry litter contained 108 CFU/g, with Gram-negative enterics representing a minor population (<104 CFU/g). There was high abundance of resistance to Sm (106 to 107 CFU/g) and Tc (106 to 107 CFU/g) and a sizeable antimicrobial-resistance gene load in regards to gene copies per bacterial genome (aadA1: 0.0001-0.0060 and sul1: 0.0355-0.2455). While plasmid transfer was observed from Escherichia coli R100, as an F-plasmid donor control, to the Salmonella recipient in vitro, no AMR Salmonella were detected in a poultry litter microcosm with the inclusion of E. coli R100. Confirmatory experiments showed that isolated poultry litter bacteria were not interfering with plasmid transfer in filter matings. As no R100 transfer was observed at 25 °C, conjugative plasmid pRSA was chosen for its high plasmid transfer frequency (10-4 to 10-5) at 25 °C. While E. coli strain background influenced the persistence of pRSA in poultry litter, no plasmid transfer to Salmonella was ever observed. Although poultry litter microbiota contains a significant AMR gene load, potential to transmit resistance is low under conditions commonly used to assess plasmid conjugation.
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Affiliation(s)
- Aaron Oxendine
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Allison A Walsh
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Tamesha Young
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Brandan Dixon
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Alexa Hoke
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Eda Erdogan Rogers
- Department of Biomedical Science and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Margie D Lee
- Department of Biomedical Science and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - John J Maurer
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
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Tan Y, Cao X, Chen S, Ao X, Li J, Hu K, Liu S, Penttinen P, Yang Y, Yu X, Liu A, Liu C, Zhao K, Zou L. Antibiotic and heavy metal resistance genes in sewage sludge survive during aerobic composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161386. [PMID: 36608829 DOI: 10.1016/j.scitotenv.2023.161386] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
Municipal sewage sludge has been generated in increasing amounts with the acceleration of urbanization and economic development. The nutrient rich sewage sludge can be recycled by composting that has a great potential to produce stabilized organic fertilizer and substrate for plant cultivation. However, little is known about the metals, pathogens and antibiotic resistance transfer risks involved in applying the composted sludge in agriculture. We studied changes in and relationships between heavy metal contents, microbial communities, and antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) in aerobic composting of sewage sludge. The contents of most of the analyzed heavy metals were not lower after composting. The bacterial α-diversity was lower, and the community composition was different after composting. Firmicutes were enriched, and Proteobacteria and potential pathogens in the genera Arcobacter and Acinetobacter were depleted in the composted sludge. The differences in bacteria were possibly due to the high temperature phase during the composting which was likely to affect temperature-sensitive bacteria. The number of detected ARGs, HMRGs and MGEs was lower, and the relative abundances of several resistance genes were lower after composting. However, the abundance of seven ARGs and six HMRGs remained on the same level after composting. Co-occurrence analysis of bacterial taxa and the genes suggested that the ARGs may spread via horizontal gene transfer during composting. In summary, even though aerobic composting is effective for managing sewage sludge and to decrease the relative abundance of potential pathogens, ARGs and HMRGs, it might include a potential risk for the dissemination of ARGs in the environment.
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Affiliation(s)
- Yulan Tan
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuedi Cao
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Shujuan Chen
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xiaoling Ao
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Jianlong Li
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Kaidi Hu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Shuliang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Petri Penttinen
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yong Yang
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Xiumei Yu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Aiping Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, Sichuan 625014, China
| | - Chengxi Liu
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Ke Zhao
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Likou Zou
- College of Resource, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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Prevalence of Class 1 Integron and In Vitro Effect of Antibiotic Combinations of Multidrug-Resistant Enterococcus Species Recovered from the Aquatic Environment in the Eastern Cape Province, South Africa. Int J Mol Sci 2023; 24:ijms24032993. [PMID: 36769316 PMCID: PMC9917988 DOI: 10.3390/ijms24032993] [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: 01/12/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Enterococci are regarded as a better indication of faecal pollution in freshwater and marine waters. Their levels in seawater are positively connected with swimming-related gastrointestinal disorders. This study used an Enterococcus-specific polymerase chain reaction (PCR) to characterize the isolates. Classes 1 and 2 integrons were examined for environmental Enterococcus isolates using a standard biological procedure. All strains were assessed against a panel of 12 antibiotics from various classes using disc diffusion methods. The microdilution method was used to work out the minimum inhibitory concentration (MIC) according to the CLSI guiding principles. The combination therapy of the resistant drugs was evaluated using a checkerboard assay and a time-dependent test for assessing their bactericidal or bacteriostatic activity. The gene diversity of the tested organisms was analyzed with the aid of Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR. In total, 57 Enterococcus spp. environmental samples were recovered, in which Enterococcus faecalis (33.33%) and Enterococcus faecium (59.65%) were the dominant species. Resistance to linezolid, ciprofloxacin, erythromycin, gentamicin, vancomycin, rifampicin, and tetracycline was prevalent. Fifty (50) strains tested positive for class 1 integron, more frequent in Enterococcus faecium and Enterococcus faecalis isolates, with no gene cassette array discovered. A combination of gentamicin (MIC 4 µg/mL) with vancomycin (MIC 256 µg/mL) antibiotics against Enterococcus faecalis showed antibacterial activity. In contrast, the combination of ciprofloxacin (1 µg/mL) with Ampicillin (16 µg/mL) antibiotics against Enterococcus faecalis showed a bacteriostatic effect. The ERIC-PCR analysis pointed out that most of the assessed isolates have close genetic similarities.
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Magdy H, Rady MH, Salama MS, Sayed HAE, Hamza D, Azzam M, Essa EE. Isolation of Multidrug-Resistant Helicobacter pylori from Wild Houseflies Musca domestica with a New Perspective for the Treatment. Vector Borne Zoonotic Dis 2023; 23:63-74. [PMID: 36577051 DOI: 10.1089/vbz.2022.0033] [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: 12/29/2022] Open
Abstract
Background: High frequency of Helicobacter pylori infection and the unknown mode of transmission prompted us to investigate H. pylori-wild housefly relationship. H. pylori causes chronic gastritis, peptic ulcers, and stomach cancer. H. pylori persists in the gut of the experimentally infected houseflies. The existence of H. pylori strains isolated from wild houseflies, on the other hand, has never been documented. Materials and Methods: In this study, 902 wild houseflies from different sites were identified as Musca domestica, then 60 flies were screened by traditional microbiological techniques and H. pylori-specific 16S rRNA gene. The antibiotic resistance (ART) was investigated phenotypically. Wild housefly gut bacterial isolates were further evaluated genotypically to have 23S rRNA gene mutation related to clarithromycin resistance. To find efficient therapeutic alternatives, the potency of three plant extracts (garlic, ginger, and lemon) and the wasp, Vespa orientalis venom was evaluated against H. pylori. The cytotoxic effect of the crude wasp venom, the most potent extract, against Vero and Colon cancer (Caco2) cell lines was investigated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. Results: All isolates from houseflies were positive. The isolated bacteria have variable resistance to frequently used antibiotics in all isolates. Minimum inhibitory concentration values of 15.625 mg/mL for both ginger and lemon extracts, 7.8125 mg/mL for garlic extract, and 0.0313 mg/mL for wasp venom were recorded. Wasp venom has the most potent antibacterial activity compared with the four antibiotics that are currently used in therapies against H. pylori. Conclusion: We conclude that wild houseflies can play a role in disseminating H. pylori. The housefly gut may be a suitable environment for the horizontal transfer of ART genes among its associated microbiome and H. pylori. Wasp venom proved its potential activity as a new and effective anti-H. pylori drug for both therapeutic and preventative usage.
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Affiliation(s)
- Hadeer Magdy
- Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Magda H Rady
- Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed S Salama
- Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Hayam A E Sayed
- Department of Microbiology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Dalia Hamza
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - May Azzam
- Department of Biochemistry, Faculty of Pharmacology, Cairo University, Giza, Egypt
| | - Eman E Essa
- Department of Entomology, Faculty of Science, Ain Shams University, Cairo, Egypt
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Semedo M, Song B. Sediment metagenomics reveals the impacts of poultry industry wastewater on antibiotic resistance and nitrogen cycling genes in tidal creek ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159496. [PMID: 36257428 DOI: 10.1016/j.scitotenv.2022.159496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
The intensification of the poultry industry may lead to the increased spread of antibiotic resistance genes (ARGs) in the environment. However, the impacts of wastewater discharge from poultry processing plants on the sediment resistome are relatively unexplored. Furthermore, its relationships with important biogeochemical pathways, such as the N cycle, are virtually unknown. The overall objective of this study was to examine the abundance and diversity of antibiotic resistance and N cycling genes in sediment microbial communities impacted by poultry industry wastewater. We performed a metagenomic investigation of sediments in an impacted and a reference tidal creek. We also quantified the abundance of the clinical class 1 integron-integrase gene (intI1) through qPCR as a secondary marker of anthropogenic contamination. Abundance and diversity of ARGs were substantially higher in the impacted tidal creek, especially near the wastewater discharge. Abundances of ARGs conferring resistance to macrolides, tetracyclines, and streptogramins were also higher in the impacted creek than the reference creek. From the N cycling genes detected in the metagenomes, nrfA, the genetic marker for dissimilatory nitrate reduction to ammonia (DNRA), had the strongest positive relationship with the total abundance of ARGs, which may indicate an increased potential of eutrophication in ARG-impacted ecosystems due to nitrogen retention. This study demonstrates that wastewater discharge from a poultry processing plant can increase the spread of ARGs, which may result in negative impacts on ecosystem health.
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Affiliation(s)
- Miguel Semedo
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA 23062, USA; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal.
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & Mary, Gloucester Point, VA 23062, USA
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Hu J, Afayibo DJA, Zhang B, Zhu H, Yao L, Guo W, Wang X, Wang Z, Wang D, Peng H, Tian M, Qi J, Wang S. Characteristics, pathogenic mechanism, zoonotic potential, drug resistance, and prevention of avian pathogenic Escherichia coli (APEC). Front Microbiol 2022; 13:1049391. [PMID: 36583051 PMCID: PMC9793750 DOI: 10.3389/fmicb.2022.1049391] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022] Open
Abstract
Although most Escherichia coli (E. coli) strains are commensal and abundant, certain pathogenic strains cause severe diseases from gastroenteritis to extraintestinal infections. Extraintestinal pathogenic E. coli (ExPEC) contains newborn meningitis E. coli (NMEC), uropathogenic E. coli (UPEC), avian pathogenic E. coli (APEC), and septicemic E. coli (SEPEC) based on their original host and clinical symptom. APEC is a heterogeneous group derived from human ExPEC. APEC causes severe respiratory and systemic diseases in a variety of avians, threatening the poultry industries, food security, and avian welfare worldwide. APEC has many serotypes, and it is a widespread pathogenic bacterium in poultry. In addition, ExPEC strains share significant genetic similarities and similar pathogenic mechanisms, indicating that APEC potentially serves as a reservoir of virulence and resistance genes for human ExPEC, and the virulence and resistance genes can be transferred to humans through food animals. Due to economic losses, drug resistance, and zoonotic potential, APEC has attracted heightened awareness. Various virulence factors and resistance genes involved in APEC pathogenesis and drug resistance have been identified. Here, we review the characteristics, epidemiology, pathogenic mechanism zoonotic potential, and drug resistance of APEC, and summarize the current status of diagnosis, alternative control measures, and vaccine development, which may help to have a better understanding of the pathogenesis and resistance of APEC, thereby reducing economic losses and preventing the spread of multidrug-resistant APEC to humans.
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Zhu P, Wu Y, Ru Y, Hou Y, San KW, Yu X, Guo W. Industrial-scale aerobic composting of livestock manures with the addition of biochar: Variation of bacterial community and antibiotic resistance genes caused by various composting stages. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 314:120270. [PMID: 36162559 DOI: 10.1016/j.envpol.2022.120270] [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: 07/27/2022] [Revised: 09/04/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
The presence of large amounts of antibiotic resistance genes (ARGs) in livestock manures poses an impending, tough safety risk to ecosystems. To investigate more comprehensively the mechanisms of ARGs removal from industrial-scale composting of livestock manure based on biochar addition, we tracked the dynamics of bacterial community and ARGs at various stages of aerobic composting of livestock manures with 10% biochar. There were no significant effects of biochar on the bacterial community and the profiles of ARGs. During aerobic composting, the relative abundance of ARGs and mobile genetic elements (MGEs) showed overall trends of decreasing and then increasing. The key factor driving the dynamics of ARGs was bacterial community composition, and the potential hosts of ARGs were Caldicoprobacter, Tepidimicrobium, Ignatzschineria, Pseudogracilibacillus, Actinomadura, Flavobacterium and Planifilum. The retention of the thermophilic bacteria and the repopulation of the initial bacteria were the dominant reasons for the increase in ARGs at maturation stage. Additionally, among the MGEs, the relative abundance of transposon gene was substantially removed, while the integron genes remained at high relative abundance. Our results highlighted that the suitability of biochar addition to industrial-scale aerobic composting needs to be further explored and that effective measures are needed to prevent the increase of ARGs content on maturation stage.
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Affiliation(s)
- Pengcheng Zhu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, 266237, PR China
| | - Yuxin Wu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, 266237, PR China
| | - Yuning Ru
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, 266237, PR China
| | - Yihang Hou
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, 266237, PR China
| | - Kim Woon San
- Tounong Organic Fertilizer Co. Ltd., Qingdao, 266733, PR China
| | - Xiaona Yu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, 266237, PR China
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, 266237, PR China.
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Rao S, Linke L, Magnuson R, Jaunch L, Hyatt DR. Antimicrobial resistance and genetic diversity of Staphylococcus aureus collected from livestock, poultry and humans. One Health 2022; 15:100407. [PMID: 36277090 PMCID: PMC9582408 DOI: 10.1016/j.onehlt.2022.100407] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 05/13/2022] [Accepted: 06/05/2022] [Indexed: 10/30/2022] Open
Abstract
Staphylococcus aureus is one of the most prominent nosocomial, community and farm acquired bacterial infections among animals and human populations. The main purpose of our study was to identify and characterize antimicrobial resistance (AMR) among Staphylococcus aureus isolated from livestock, poultry and humans and to further identify the associated genes. Staphylococcus aureus isolates from human, bovine, swine and poultry were collected from different laboratories across the United States collected between 2003 and 2016. Antimicrobial susceptibility testing for 13 antimicrobials was performed and conventional PCR was used to detect the presence of the nuc gene, mec gene, and to detect int1 gene. Associations between the presence of mec and intl and specific AMR profiles were determined. Antimicrobial resistance was detected in all four host categories, with the highest overall rates found in swine, 100% resistant to tetracycline, 88% to penicillin and 64% clindamycin. The next highest was found among humans with 81.6% of isolates resistant to penicillin followed by 44% to clindamycin and 43% to erythromycin. Among beef cattle isolates, 63.2% were resistant to penicillin, 15.8% resistant to clindamycin and 15.8% to erythromycin. No isolates from any of the hosts were resistant to linezolid. Among poultry isolates, the highest AMR was found to clindamycin, followed by erythromycin and penicillin. Among dairy cattle, highest resistance was found to penicillin, followed by chloramphenicol and gentamicin. Dairy cattle were the only host category with isolates that are resistant to trimethoprim-sulfamethoxazole. Of the 220 isolates detected by latex agglutination, 217 were confirmed to be S. aureus via PCR of the nuc gene, 21.4% were positive for the mecA gene. Swine had the highest prevalence of the mecA gene, followed by humans, poultry and beef cattle. This study has demonstrated a high occurrence of penicillin resistance among all S. aureus isolates. There were differences observed between host species with tetracycline resistance being the highest among swine isolates and clindamycin being highest in poultry isolates. No detection of oxacillin resistance was found in isolates from dairy cattle but was found in isolates from all of the other host species, 94% of which contained the mecA gene. High occurrence of penicillin resistance in Staphylococcus aureus isolates collected from livestock, poultry and humans. Tetracycline resistance was the highest among swine isolates and clindamycin was the highest in poultry isolates. Oxacillin resistance was not detected among dairy cattle isolates but was found in isolates from other host species. Ninety four percent of the S. aureus isolates were resistant to oxacillin contained the mecA gene.
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Sultan I, Siddiqui MT, Gogry FA, Haq QMR. Molecular characterization of resistance determinants and mobile genetic elements of ESBL producing multidrug-resistant bacteria from freshwater lakes in Kashmir, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154221. [PMID: 35245551 DOI: 10.1016/j.scitotenv.2022.154221] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Antibiotic resistance conceded as a global concern is a phenomenon that emerged from the bacterial response to the extensive utilization of antimicrobials. The expansion of resistance determinants through horizontal transfer is linked with mobile genetic elements (MGEs) like transposons, insertion sequences, and integrons. Heavy metals also create consequential health hazards. Metal resistance gene in alliance with antibiotic resistance genes (ARGs) and MGEs is assisting bacteria to attain exalted quantity of resistance. METHODOLOGY The present work was carried out to study ARGs blaCTX-M, AmpC, qnrS, MGEs like ISecp1, TN3, TN21, and Int I by performing PCR and sequencing from Wular and Dal lakes of Kashmir; India. The genetic environment analysis of blaCTX-M-15 was carried out using PCR amplification, and sequencing approach followed by in-silico docking and mutational studies. Co-occurrence of ARGs and HMRGs was determined. Plasmid typing was done using PCR-based replicon typing (PBRT) and conjugation assay was also performed. RESULTS Out of 201 isolates attained from 16 locations, 33 were ESBLs producers. 30 ESBL displaying isolates were perceived positive for CTX-M gene, followed by AmpC (17), qnrS (13), ISecp1 (15), TN3 (11), TN21 (11), Int I (18), and SulI (14). The genetic environment of blaCTX-M-15 was observed as (ISEcp1-blaCTX-M-15-orf477), classical promoter-10 TACAAT and -35 TTGAA was found at the 3' region. The 3D structure of CTX-M-15 and ISEcp1 was generated and CTX-M-15-ISEcp1 (R299L) docking and mutation showed a reduction in hydrogen bonds. Co-occurrence of antibiotics and HMRGs (mer, sil, and ars) was found in 18, 14, and 8 isolates. PBRT analysis showed the presence of Inc. groups- B/O, F, I1, HI1, FIA, HI2, N, FIB, L/M. Molecular analysis of transconjugants showed the successful transfer of ARGs, MGEs, and HMRGs in the E. coli J53 AZR strain. CONCLUSION This study highlights the occurrence of ESBL producing bacteria in the aquatic environment of Kashmir India that can serve as a reservoir of ARGs. It also discussed the molecular mechanisms of MGEs which can help in containing the spread of antibiotic resistance.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
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Ayala Nuñez T, Cerbino GN, Rapisardi MF, Quiroga C, Centrón D. Novel Mobile Integrons and Strain-Specific Integrase Genes within Shewanella spp. Unveil Multiple Lateral Genetic Transfer Events within The Genus. Microorganisms 2022; 10:microorganisms10061102. [PMID: 35744620 PMCID: PMC9229058 DOI: 10.3390/microorganisms10061102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Shewanella spp. are Gram-negative bacteria that thrive in aquatic niches and also can cause infectious diseases as opportunistic pathogens. Chromosomal (CI) and mobile integrons (MI) were previously described in some Shewanella isolates. Here, we evaluated the occurrence of integrase genes, the integron systems and their genetic surroundings in the genus. We identified 22 integrase gene types, 17 of which were newly described, showing traits of multiple events of lateral genetic transfer (LGT). Phylogenetic analysis showed that most of them were strain-specific, except for Shewanella algae, where SonIntIA-like may have co-evolved within the host as typical CIs. It is noteworthy that co-existence of up to five different integrase genes within a strain, as well as their wide dissemination to Alteromonadales, Vibrionales, Chromatiales, Oceanospirillales and Enterobacterales was observed. In addition, identification of two novel MIs suggests that continuous LGT events may have occurred resembling the behavior of class 1 integrons. The constant emergence of determinants associated to antimicrobial resistance worldwide, concomitantly with novel MIs in strains capable to harbor several types of integrons, may be an alarming threat for the recruitment of novel antimicrobial resistance gene cassettes in the genus Shewanella, with its consequent contribution towards multidrug resistance in clinical isolates.
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Affiliation(s)
- Teolincacihuatl Ayala Nuñez
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - Gabriela N. Cerbino
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - María Florencia Rapisardi
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
- Laboratorio de Investigación en Biología del ARN Bacteriano IMPaM (UBA/CONICET), Faculty of Medicine, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina
- Correspondence: or (C.Q.); (D.C.); Tel.: +54-11-5285-3500 (C.Q.); +54-911-50987496 (D.C.)
| | - Daniela Centrón
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM, UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina; (T.A.N.); (G.N.C.); (M.F.R.)
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos IMPaM (UBA/CONICET), Faculty of Medicine, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires CP1121, Argentina
- Correspondence: or (C.Q.); (D.C.); Tel.: +54-11-5285-3500 (C.Q.); +54-911-50987496 (D.C.)
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Ramful R, Sunthar TPM, Kamei K, Pezzotti G. Investigating the Antibacterial Characteristics of Japanese Bamboo. Antibiotics (Basel) 2022; 11:antibiotics11050569. [PMID: 35625213 PMCID: PMC9137583 DOI: 10.3390/antibiotics11050569] [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: 01/31/2022] [Revised: 02/21/2022] [Accepted: 04/20/2022] [Indexed: 11/16/2022] Open
Abstract
Natural materials, such as bamboo, is able to withstand the rough conditions posed by its environment, such as resistance to degradation by microorganisms, due to notable antibacterial characteristics. The methods of extraction exert a significant influence on the effectiveness of bamboo-derived antibacterial agents. In this study, the antibacterial characteristics of various types of Japanese bamboo, namely, Kyoto-Moso, Kyushu-Moso and Kyushu-Madake were investigated by considering an extraction and a non-extraction method. The characterization of the efficacy of antibacterial agents of various bamboo samples derived from both methods of extractions was conducted using an in vitro cultured bacteria technique consisting of E. coli and S. aureus. Antibacterial test results based on colony-forming units showed that antibacterial agents derived from the non-extraction method yielded better efficacy when tested against E. coli and S. aureus. Most specimens displayed maximum antibacterial efficacy following a 48-h period. The antibacterial agents derived from thermally modified bamboo powder via the non-extraction method showed improved antibacterial activity against S. aureus specifically. In contrast, absorbance results indicated that antibacterial agents derived from the extraction method yielded poor efficacy when tested against both E. coli and S. aureus. From FTIR analysis, characteristic bands assigned to the C-O and C-H functional groups in lignin were recognized as responsible for the antibacterial trait observed in both natural and thermally modified Japanese bamboo powder. Techniques to exploit the antibacterial characteristics present in bamboo by identification of antibacterial source and adoption of adequate methods of extraction are key steps in taking advantage of this attribute in numerous applications involving bamboo-derived products such as laminates and textile fabrics.
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Affiliation(s)
- Raviduth Ramful
- Graduate School of Science and Technology, Kyoto Institute of Technology (KIT), Kyoto 606-8585, Japan
- Mechanical and Production Engineering Department, Faculty of Engineering, University of Mauritius, Reduit 80837, Mauritius
- Correspondence:
| | - Thefye P. M. Sunthar
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (T.P.M.S.); (G.P.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-0841, Japan
| | - Kaeko Kamei
- Department of Biomolecular Engineering, Kyoto Institute of Technology, Kyoto 606-8585, Japan;
| | - Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto 606-8585, Japan; (T.P.M.S.); (G.P.)
- Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-0841, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
- Department of Orthopedic Surgery, Tokyo Medical University, Tokyo 105-8461, Japan
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Néron B, Littner E, Haudiquet M, Perrin A, Cury J, Rocha EPC. IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms 2022; 10:700. [PMID: 35456751 PMCID: PMC9024848 DOI: 10.3390/microorganisms10040700] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023] Open
Abstract
Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4000 Klebsiella pneumoniae genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that K. pneumoniae has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available on multiple public platforms.
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Affiliation(s)
- Bertrand Néron
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris Cité, 75015 Paris, France; (B.N.); (A.P.)
| | - Eloi Littner
- Microbial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, France; (E.L.); (M.H.)
- DGA CBRN Defence, 91710 Vert-le-Petit, France
- Collège Doctoral, Sorbonne Université, 75005 Paris, France
| | - Matthieu Haudiquet
- Microbial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, France; (E.L.); (M.H.)
- Ecole Doctorale FIRE–Programme Bettencourt, CRI, 75004 Paris, France
| | - Amandine Perrin
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris Cité, 75015 Paris, France; (B.N.); (A.P.)
- Microbial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, France; (E.L.); (M.H.)
- Collège Doctoral, Sorbonne Université, 75005 Paris, France
| | - Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, France; (E.L.); (M.H.)
- Laboratoire Interdisciplinaire des Sciences du Numérique, Université Paris-Saclay, CNRS UMR 9015, INRIA, 91400 Orsay, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, France; (E.L.); (M.H.)
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Gontar Ł, Sitarek-Andrzejczyk M, Kochański M, Buła M, Drutowska A, Zych D, Markiewicz J. Dynamics and Diversity of Microbial Contamination in Poultry Bedding Materials Containing Parts of Medicinal Plants. MATERIALS 2022; 15:ma15041290. [PMID: 35207831 PMCID: PMC8877630 DOI: 10.3390/ma15041290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/31/2022] [Accepted: 02/05/2022] [Indexed: 12/10/2022]
Abstract
Microorganisms thriving in poultry bedding materials during their exploitation are involved in the development of several diseases and disfunctions of animals. They can also contaminate food products and pose risks to the environment and human health. This study provides an analysis of dynamics and diversity in microbiological contamination observed during the exploitation of poultry bedding materials containing parts of medicinal plants: Satureja hortensis, Origanum vulgare, Melissa officinalis, Salvia officinalis, and Thymus vulgaris, compared with standard types of beddings: straw chaff and straw pellets. The research was carried out in two 42-day experimental cycles involving in total 2400 broiler chickens. Each week, the total count of mesophilic bacteria, fungi and yeasts, the presumptive presence and count of Staphylococcus sp., Escherichia sp., Listeria sp., Salmonella sp., and Candida sp. were determined by culturing on selective media, along with pH and moisture measurements. After 35 days of the experiment, a reduction of the total count of mesophilic bacteria above 1 log compared to the control (11.86 vs. 13.02 log CFU/g) was observed. As the count of yeasts decreased after 21 days, an increase in the total count of bacteria was reported, which indicates a strong competition between microorganisms. The results improve our understanding of the temporal effects of using materials containing parts of medicinal plants on the microbial contamination in poultry litter.
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Affiliation(s)
- Łukasz Gontar
- Correspondence: (Ł.G.); (M.S.-A.); Tel.: +48-42-636-12-59 (Ł.G.); +48-42-636-12-26 (M.S.-A.)
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Song L, Wang C, Jiang G, Ma J, Li Y, Chen H, Guo J. Bioaerosol is an important transmission route of antibiotic resistance genes in pig farms. ENVIRONMENT INTERNATIONAL 2021; 154:106559. [PMID: 33864959 DOI: 10.1016/j.envint.2021.106559] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/04/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Although pig farms are hotspots of antibiotic resistance due to intensive use of antibiotics, little is known about the abundance, diversity and transmission of airborne antibiotic resistance genes (ARGs). This study reports that bioaerosol is an important spread route of ARGs in pig farms. ARGs, mobile genetic elements (MGEs), and bacterial communities were investigated in both air and feces samples during winter and summer. The average concentration of airborne ARGs and MGEs during winter is higher than that during summer when using the ventilation system. The tetM is identified as the predominant airborne ARG with abundance of 6.3 ± 1.2 log copies/m3. Clostridium and Streptococcus are two dominant bacteria and several opportunistic pathogens are detected in air samples. High temperature is favorable for more diverse bacterial communities, but relative humidity has negative effects. The wind speed promotes the spread of airborne ARGs. The network analysis results show the average fecal contribution to airborne bacteria is 19.9% and 59.4% during summer and winter, respectively. Horizontal gene transfer plays an important role in the dissemination of airborne ARGs during winter (77.8% possibility), while a lower possibility of 12.0% in summer.
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Affiliation(s)
- Lu Song
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - Can Wang
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China.
| | - Guanyu Jiang
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - Jinbiao Ma
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - Yunfei Li
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - Hong Chen
- Tianjin Key Lab of Indoor Air Environmental Quality Control, Tianjin, PR China; School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia.
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Mohammadi-Aragh MK, Stokes CE. Assessing Class 1 Integron Presence in Poultry Litter Amended with Wood Biochar and Wood Vinegar. Curr Microbiol 2021; 78:3733-3740. [PMID: 34459936 DOI: 10.1007/s00284-021-02640-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/20/2021] [Indexed: 11/26/2022]
Abstract
Class 1 integrons are mobile genetic elements that facilitate the spread of antibiotic resistance genes among bacteria. The use of prophylactic antibiotics has resulted in the rise of antibiotic resistance genes accumulating in a wide range of settings, including poultry houses and the agricultural fields where poultry litter is applied as a fertilizer. Biochar and wood vinegar are forest products wastes that have generated increasing attention as additives to agricultural soils. The objectives of this study were to observe the prevalence of class 1 integrons in poultry litter blended with biochar and wood vinegar over time and to verify a modified class 1 integron screening assay. Poultry litter blends were sampled and screened for class 1 integrons using polymerase chain reaction, and 80 products, 79 of which showed positive, were sent for DNA sequencing. The GenBank® BLAST database was used to verify the presence of the class 1 integron-integrase gene (intI1). There was no change in prevalence over time in poultry litter blends. Out of 79 PCR products that were intI1 positive, 78 showed at least 95% sequence identity to intI1 encoding bacteria and 64 showed at least 97% sequence identity. This indicates that this method was effective for conducting baseline surveillance of class 1 integrons in poultry litter and poultry litter-blended biochar and/or wood vinegar. Most significantly, class 1 integron prevalence did not decrease over time, further supporting the recalcitrance of these elements and the need for improved monitoring systems.
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Affiliation(s)
- Maryam K Mohammadi-Aragh
- Department of Agricultural and Biological Engineering, Mississippi State University, Starkville, MS, USA.
| | - C Elizabeth Stokes
- Department of Sustainable Bioproducts, Mississippi State University, Starkville, MS, USA
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Pereira AR, Paranhos AGDO, de Aquino SF, Silva SDQ. Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:26380-26403. [PMID: 33835340 DOI: 10.1007/s11356-021-13784-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.
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Affiliation(s)
- Andressa Rezende Pereira
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil
| | - Aline Gomes de Oliveira Paranhos
- Graduate Program in Environmental Engineering, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil
| | - Sérgio Francisco de Aquino
- Department of Chemistry, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil
| | - Silvana de Queiroz Silva
- Department of Biological Sciences, Federal University of Ouro Preto, Campus Morro do Cruzeiro, Ouro Preto, State of Minas Gerais, CEP: 35.400-000, Brazil.
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Singh NS, Singhal N, Kumar M, Virdi JS. High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk. Front Microbiol 2021; 12:621564. [PMID: 33633708 PMCID: PMC7899961 DOI: 10.3389/fmicb.2021.621564] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/05/2021] [Indexed: 11/16/2022] Open
Abstract
Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of blaCTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, blaTEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), blaCTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where blaCTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of blaCTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of blaCTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.
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Affiliation(s)
- Nambram Somendro Singh
- Department of Microbiology, University of Delhi South Campus, New Delhi, India.,Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Neelja Singhal
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi South Campus, New Delhi, India
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Mazhar SH, Li X, Rashid A, Su J, Xu J, Brejnrod AD, Su JQ, Wu Y, Zhu YG, Zhou SG, Feng R, Rensing C. Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 755:142702. [PMID: 33049532 DOI: 10.1016/j.scitotenv.2020.142702] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Environmental selection of antibiotic resistance genes (ARGs) is considered to be caused by antibiotic or metal residues, frequently used in livestock. In this study we examined three commercial poultry farms to correlate the co-occurrence patterns of antibiotic and metal residues to the presence of ARGs. We quantified 283 ARGs, 12 mobile genetic elements (MGEs), 49 targeted antibiotics, 7 heavy metals and sequenced 16S rRNA genes. The abundance and type of ARG were significantly enriched in manure while soil harbored the most diverse bacterial community. Procrustes analysis displayed significant correlations between ARGs/MGEs and the microbiome. Cadmium (Cd), arsenic (As), zinc (Zn), copper (Cu) and lead (Pb) were responsible for a majority of positive correlations to ARGs when compared to antibiotics. Integrons and transposons co-occurred with ARGs corresponding to 9 classes of antibiotics, especially Class1 integrase intI-1LC. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that antibiotics, metals, MGEs and bacteria explain solely 0.7%, 5.7%, 12.4%, and 21.9% of variances of ARGs in the microbial community, respectively. These results suggested that bacterial composition and horizontal gene transfer were the major factors shaping the composition of ARGs; Metals had a bigger effect on ARG profile than detected antibiotics in this study.
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Affiliation(s)
- Sohaib H Mazhar
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanji Li
- Section of Microbiology, University of Copenhagen, Denmark
| | - Azhar Rashid
- Nuclear Institute for Food and Agriculture (PAEC), Tarnab, Peshawar 25000, Pakistan
| | - JunMing Su
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junqiang Xu
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Asker Daniel Brejnrod
- Skaggs School of Pharmacy, University of California San Diego, La Jolla, United States
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China
| | - Yijian Wu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shun Gui Zhou
- Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China; Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
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21
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Gambino D, Vicari D, Vitale M, Schirò G, Mira F, Giglia ML, Riccardi A, Gentile A, Giardina S, Carrozzo A, Cumbo V, Lastra A, Gargano V. Study on Bacteria Isolates and Antimicrobial Resistance in Wildlife in Sicily, Southern Italy. Microorganisms 2021; 9:203. [PMID: 33478101 PMCID: PMC7835999 DOI: 10.3390/microorganisms9010203] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/20/2022] Open
Abstract
Wild environments and wildlife can be reservoirs of pathogens and antibiotic resistance. Various studies have reported the presence of zoonotic bacteria, resistant strains, and genetic elements that determine antibiotic resistance in wild animals, especially near urban centers or agricultural and zootechnical activities. The purpose of this study was the analysis, by cultural and molecular methods, of bacteria isolated from wild animals in Sicily, Italy, regarding their susceptibility profile to antibiotics and the presence of antibiotic resistance genes. Bacteriological analyses were conducted on 368 wild animals, leading to the isolation of 222 bacterial strains identified by biochemical tests and 16S rRNA sequencing. The most isolated species was Escherichia coli, followed by Clostridium perfringens and Citrobacter freundii. Antibiograms and the determination of resistance genes showed a reduced spread of bacteria carrying antibiotic resistance among wild animals in Sicily. However, since several wild animals are becoming increasingly close to residential areas, it is important to monitor their health status and to perform microbiological analyses following a One Health approach.
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Affiliation(s)
- Delia Gambino
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Domenico Vicari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Maria Vitale
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Giorgia Schirò
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Francesco Mira
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Maria La Giglia
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Alessandra Riccardi
- Department of Veterinary Science, University of Pisa, Viale delle Piagge n. 2, 56124 Pisa, Italy;
| | - Antonino Gentile
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Susanna Giardina
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Anna Carrozzo
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Valentina Cumbo
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Antonio Lastra
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
| | - Valeria Gargano
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Via Gino Marinuzzi n. 3, 90129 Palermo, Italy; (D.G.); (M.V.); (G.S.); (F.M.); (M.L.G.); (A.G.); (S.G.); (A.C.); (V.C.); (A.L.); (V.G.)
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22
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Guo W, Huang C, Xi B, Tang Z, Tan W, Li W, Zhang Y, Li W. The maturity period is the main stage of antibiotic resistance genes reduction in aerobic composting process of swine manure in sub-scale farms. BIORESOURCE TECHNOLOGY 2021; 319:124139. [PMID: 32971337 DOI: 10.1016/j.biortech.2020.124139] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/12/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
This study was focused on the changes of antibiotic resistance genes (ARGs) and their potential host bacteria during the swine manure composting on sub-scale farms. Eight target ARGs increased 427% on average, with a trend of increase at early stage and decrease at later stage, and the main reduction stage appeared in maturity stage. The abundance of ARGs was mainly affected by the community succession of potential host bacteria. Composting could reduce the abundance of potential host bacteria of ARGs as well as pathogens such as Pseudomonas, and reduce the environmental risks of swine manure. N/C and S levels had a positive effect on the potential host of most ARGs. Prolonging the maturity period would inhibit the growth of potential host bacteria of ARGs during composting, therefore inhibiting the transmission of ARGs.
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Affiliation(s)
- Wei Guo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Caihong Huang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Zhurui Tang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Key Laboratory of Urban Water Resource and Environment (SKLUWRE), School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenxuan Li
- Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Republic of Singapore
| | - Ying Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wei Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
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23
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Cao R, Ben W, Qiang Z, Zhang J. Removal of antibiotic resistance genes in pig manure composting influenced by inoculation of compound microbial agents. BIORESOURCE TECHNOLOGY 2020; 317:123966. [PMID: 32836032 DOI: 10.1016/j.biortech.2020.123966] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
The influence of compound microbial agents on antibiotic resistance genes (ARGs) in pig manure composting was investigated. The results show that the addition of microbial agents promoted the reduction of total ARGs and the maximum removal efficiencies for absolute abundance (77.2%) and relative abundance (64.5%) were observed in the repeated dose and high dose groups, respectively. Four categories of ARGs declined with the reduction of Firmicutes and Tn916/1545, whereas two categories increased with the proliferation of intI1 and various potential hosts in the composting. The ARG profiles and bacterial communities were shaped by composting stages (mesophilic-thermophilic and cooling-maturation stages) in all groups. However, the addition of microbial agents accelerated the variation of composting stages, and may change the potential ARG hosts which influences the removal of ARGs. Of note, intI1 and two potential pathogens (Mycobacterium and Bacillus) correlated positively to several increased ARGs, implying the possible risks of compost products.
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Affiliation(s)
- Rukun Cao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Weiwei Ben
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China.
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
| | - Junya Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, Department of Water Pollution Control Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing 100085, China
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24
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Gutierrez A, DE J, Schneider KR. Prevalence, Concentration, and Antimicrobial Resistance Profiles of Salmonella Isolated from Florida Poultry Litter. J Food Prot 2020; 83:2179-2186. [PMID: 32692820 DOI: 10.4315/jfp-20-215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/20/2020] [Indexed: 01/14/2023]
Abstract
ABSTRACT For over a decade, Salmonella contamination has increasingly led to outbreaks of foodborne illness associated with fresh produce. The use of untreated animal manures, or biological soil amendments of animal origin, to amend agricultural soils holds a risk of contamination from foodborne pathogens, such as Salmonella. This study was conducted to determine the prevalence, concentration, serotypes, and antimicrobial resistance profiles of Salmonella in poultry litter from Florida farms. Litter pH, total Kjeldahl nitrogen, total ammonia nitrogen, total phosphorus (P2O5), total potassium (K2O), moisture content, total solids, total ash, organic matter, and aerobic plate count (APC) were also measured. Litter samples (n = 54) were collected from 18 broiler farms across three seasons (spring, summer, and winter). Salmonella concentrations were enumerated using a most-probable-number (MPN) method, and antimicrobial susceptibility testing was performed. The prevalence of Salmonella in litter samples was 61.1%, with a geometric mean of 0.21 ± 20.7 MPN/g. Across all seasons, Salmonella concentrations were not influenced by the chemical, physical, or microbial properties measured. Recovered Salmonella isolates (n = 290) were grouped into serogroups O:4 (43.1%), O:7 (26.9%), O:8 (11.0%), O:1,3,10,19 (7.9%), and O:9,46 (7.2%). Serotyping Salmonella isolates (n = 47) resulted in 12 serotypes, with the most common being Typhimurium (27.7%), Kentucky (17.0%), Enteritidis (14.9%), and Mbandaka (14.9%). Antimicrobial resistance to tetracycline (29.8%), sulfisoxazole (23.4%), and streptomycin (14.9%) was observed. No isolates were resistant to more than two antimicrobial agents. This study provides valuable information for future risk assessments for the use of poultry litter as an untreated biological soil amendment of animal origin. HIGHLIGHTS
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Affiliation(s)
- Alan Gutierrez
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida 32611, USA
| | - Jaysankar DE
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida 32611, USA
| | - Keith R Schneider
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida 32611, USA.,(ORCID: https://orcid.org/0000-0003-0145-3418 [K.R.S.])
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25
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El-Gohary FA, Abdel-Hafez LJM, Zakaria AI, Shata RR, Tahoun A, El-Mleeh A, Abo Elfadl EA, Elmahallawy EK. Enhanced Antibacterial Activity of Silver Nanoparticles Combined with Hydrogen Peroxide Against Multidrug-Resistant Pathogens Isolated from Dairy Farms and Beef Slaughterhouses in Egypt. Infect Drug Resist 2020; 13:3485-3499. [PMID: 33116668 PMCID: PMC7550212 DOI: 10.2147/idr.s271261] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/11/2020] [Indexed: 12/20/2022] Open
Abstract
Purpose The last few decades have witnessed a rapid and global increase in multidrug-resistant bacteria (MDR) emergence. Methods The aim of the current study is to isolate the most common MDR bacteria from dairy farms and beef slaughterhouses followed by evaluation of their antimicrobial resistance pattern and assessment of the antibacterial activity of AgNPs-H2O2 as an alternative to conventional antibiotics. In this regard, 200 samples were collected from two dairy farms and one beef slaughterhouse located in Dakhliya Governorate, Egypt. Results Interestingly, out of 120 collected samples from dairy farms, the prevalence of the isolated strains was 26.7, 23.3, 21.7, 16.7, and 11.7% for S. typhimurium, E. coli O157:H7, L. monocytogenes, K. pneumoniae and P. aeruginosa, respectively. Meanwhile, the overall prevalence was 30, 25, 22.5, 17.5, and 5% for E. coli O157:H7, L. monocytogenes, S. typhimurium, P. aeruginosa, and K. pneumoniae, respectively, for the 80 samples collected from a beef slaughterhouse. The antimicrobial susceptibility pattern elucidated that all isolated strains exhibited resistance to at least four of the tested antimicrobials, with multiple-antibiotic resistance index values (MAR) ranging between 0.44 and 0.88. Furthermore, the commercial AgNPs-H2O2 product was characterized by transmission electron microscopy (TEM) and zeta potential that showed spherical particles with a surface charge of -0.192 mV. The antimicrobial activity of synergized nano-silver (AgNP) with H2O2 product toward MDR strains was assessed via measuring minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and time-kill curve. Conclusion The present data report high prevalence rates of MDR pathogens in dairy farms and abattoirs. More importantly, AgNPs-H2O2 exerted broad-spectrum bactericidal activity toward MDR bacterial strains, suggesting their promising usage as safe, ecofriendly, cost-effective antibacterial agents. To our knowledge, this study is a pioneer in investigating the potential alternative antimicrobial role of silver nanoparticles for control of multiple drug-resistant pathogens in Egypt.
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Affiliation(s)
- Fatma A El-Gohary
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Lina Jamil M Abdel-Hafez
- Department of Microbiology and Immunology, Faculty of Pharmacy, October 6 University, October 6 City, Giza, Egypt
| | - Amira I Zakaria
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Radwa Reda Shata
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Amin Tahoun
- Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelshkh University, Kafrelsheikh 33511, Egypt
| | - Amany El-Mleeh
- Department of Pharmacology, Faculty of Veterinary Medicine, Menoufia University, Sheibin Elkom 32511, Egypt
| | - Eman A Abo Elfadl
- Department of Animal Husbandry and Development of Animal Wealth (Biostatistics), Faculty of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Ehab Kotb Elmahallawy
- Department of Biomedical Sciences, University of León (ULE), León 24071, Spain.,Department of Zoonoses, Faculty of Veterinary Medicine, Sohag University, Sohag 82524, Egypt
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26
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Prevalence and Characterisation of Class 1 and 2 Integrons in Multi-drug Resistant Staphylococcus Aureus Isolates from Pig Farms in Chongqing, China. J Vet Res 2020; 64:381-386. [PMID: 32984627 PMCID: PMC7497750 DOI: 10.2478/jvetres-2020-0061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/24/2020] [Indexed: 12/23/2022] Open
Abstract
Introduction Integrons are mobile DNA elements that allow for acquisition and dissemination of antibiotic-resistance genes among pig farm-derived bacteria. Limited information is available on integrons of Staphylococcus aureus from pig farms. The aim of this study was to characterise and investigate the prevalence of class 1 and 2 integrons in multi-drug resistant (MDR) S. aureus isolates from pig farms. Material and Methods A total of 724 swabs were collected from 12 pig farms in Chongqing, China, and examined by conventional microbial and molecular methods. Results In total, 68 isolates were S. aureus, 57 of which were methicillin resistant (MRSA). All 68 isolates were MDR strains and carried integrons, of which 88.2% (60/68) harboured both class 1 and 2. In addition, 85.3% (58/68) of the class 2 integron-positive isolates carried the β-lactam resistance gene (blaTEM-1 ), and 66.7% (40/60) of the class 1 integron-positive isolates carried the aadA1c, aadA1 or dfrA1 gene for respective streptomycin and spectinomycin or trimethoprim resistance. Conclusions Class 1 and 2 integrons are common among the pig farm-derived S. aureus isolates. On account of their significance for public health, the prevalence of the integrons and their associated resistance genes in pig farm-derived S. aureus isolates should be paid special attention.
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27
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Walker GK, Suyemoto MM, Gall S, Chen L, Thakur S, Borst LB. The role of Enterococcus faecalis during co-infection with avian pathogenic Escherichia coli in avian colibacillosis. Avian Pathol 2020; 49:589-599. [PMID: 32674609 DOI: 10.1080/03079457.2020.1796926] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Enterococcus spp. (ENT) are frequently co-isolated with avian pathogenic E. coli (APEC) from poultry with colibacillosis, a leading cause of flock mortality. Although largely overlooked, ENT may play an active role in these infections. To assess the frequency of ENT co-isolation in colibacillosis, cultures were collected from birds with gross lesions of omphalitis, polyserositis, and septicaemia over a 3-year period from three turkey flocks and three broiler flocks. In birds diagnosed with colibacillosis based on gross findings and isolation of E. coli, ENT were co-isolated with APEC in 35.7% (n = 41/115) of colibacillosis mortality and 3.7% of total mortality (n = 41/1122). Co-isolated APEC and ENT pairs (n = 41) were further characterized using antimicrobial resistance phenotyping and in vitro co-culture assays. E. faecalis (EF) was the most commonly co-isolated species (68% n = 28/41) and tetracycline resistance was the resistance phenotype most commonly found among APEC (51% n = 21/41) and ENT (93% n = 38/41). Under iron-restricted conditions, EF enhanced APEC growth in a proximity-dependent manner and APEC grown in mixed culture with EF exhibited a significant growth and survival advantage (P ≤ 0.01). In an embryo lethality assay, APEC co-infection with EF resulted in decreased survival of broiler embryos compared to mono-infections (P ≤ 0.05). These data demonstrate that EF augmented APEC survival and growth under iron limiting conditions, possibly translating to the increased virulence of APEC in broiler embryos. Thus, ENT co-infections may be a previously unrecognized contributor to colibacillosis-related mortality. Further investigations into the mechanism of this interaction are warranted. RESEARCH HIGHLIGHTS Enterococcus is frequently co-isolated with avian pathogenic E. coli (APEC). Enterococcus faecalis (EF) enhances survival of APEC in iron restricted conditions. EF co-infection increases APEC virulence in broiler embryos.
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Affiliation(s)
- Grayson K Walker
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - M Mitsu Suyemoto
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Sesny Gall
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Laura Chen
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Luke B Borst
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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28
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Ali N, Lin Y, Qing Z, Xiao D, Ud Din A, Ali I, Lian T, Chen B, Wen R. The Role of Agriculture in the Dissemination of Class 1 Integrons, Antimicrobial Resistance, and Diversity of Their Gene Cassettes in Southern China. Genes (Basel) 2020; 11:genes11091014. [PMID: 32872161 PMCID: PMC7564866 DOI: 10.3390/genes11091014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
Integrons are hot spots for acquiring gene cassettes from the environment and play a major role in the bacterial evolution and dissemination of antimicrobial resistance (AMR), thus posing a serious threat. There are currently studies on integrons and antibiotic resistance genes; however, the presence and association of integrons in different agricultural crops and their subsequent dissemination and role in AMR have not been reported previously. This study examines the abundance of integrons, their gene cassette diversity in various crop soils, and their role in the dissemination of AMR in the southern region of China. Samples from different agri-crop soil, such as rice (R.S), sugarcane (S.S), citrus (C.S), banana (B.S), agricultural runoff (the point where the runoff of all sites meet (R.O)), and wild (non-agricultural) soil (W.S), were collected. Quantitative PCR was used to determine the abundance of integrons, and clone libraries were constructed to examine the gene cassette arrays. All the tested samples were found positive for Class-I (CL1) integrons and revealed a higher concentration and higher relative abundance of R.S than the others, with the least found at the W.S site. The W.S CL1 cassette arrays were found empty, and no putative conserved domains were found. The R.O was found to contain a high number of gene cassettes with various functions, while the smallest number of gene cassettes was found in the S.S among the crop soils. Most of the gene cassettes presented by the R.O were primarily shared with other sites, and the antibiotic-resistant genes were consistently observed to be dominant. The constructed clone libraries represented a diverse gene cassette array with 16% novel gene cassettes that play a vital role in pathogenesis, transportation, biosynthesis, and AMR. Most resistance-related gene cassettes were associated with the genes encoding resistance to quaternary ammonium compound (QAC) and aminoglycosides. This study highlights the significant differences in the abundance of integrons among various agricultural soils and offers deep insight into the pools of gene cassettes that play a key role in the dissemination of integrons and AMR.
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Affiliation(s)
- Niyaz Ali
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Yinfu Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Zhen Qing
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Dan Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Ahmad Ud Din
- Drug Discovery Research Center, South West Medical University, Luzhou 646000, China;
| | - Izhar Ali
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
| | - Tengxiang Lian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, South China Agricultural University, Guangzhou 510642, China;
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
- Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ronghui Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bio-Resources, College of Life Science and Technology, Guangxi University, Nanning 530004, China; (N.A.); (Y.L.); (Z.Q.); (D.X.); (I.A.); (B.C.)
- Correspondence: ; Tel.: +86-13669614062
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Hedman HD, Vasco KA, Zhang L. A Review of Antimicrobial Resistance in Poultry Farming within Low-Resource Settings. Animals (Basel) 2020; 10:E1264. [PMID: 32722312 PMCID: PMC7460429 DOI: 10.3390/ani10081264] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 12/28/2022] Open
Abstract
The emergence, spread, and persistence of antimicrobial resistance (AMR) remain a pressing global health issue. Animal husbandry, in particular poultry, makes up a substantial portion of the global antimicrobial use. Despite the growing body of research evaluating the AMR within industrial farming systems, there is a gap in understanding the emergence of bacterial resistance originating from poultry within resource-limited environments. As countries continue to transition from low- to middle income countries (LMICs), there will be an increased demand for quality sources of animal protein. Further promotion of intensive poultry farming could address issues of food security, but it may also increase risks of AMR exposure to poultry, other domestic animals, wildlife, and human populations. Given that intensively raised poultry can function as animal reservoirs for AMR, surveillance is needed to evaluate the impacts on humans, other animals, and the environment. Here, we provide a comprehensive review of poultry production within low-resource settings in order to inform future small-scale poultry farming development. Future research is needed in order to understand the full extent of the epidemiology and ecology of AMR in poultry within low-resource settings.
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Affiliation(s)
- Hayden D. Hedman
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
| | - Karla A. Vasco
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.A.V.); (L.Z.)
| | - Lixin Zhang
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (K.A.V.); (L.Z.)
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA
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30
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Zhou Y, Li Y, Zhang L, Wu Z, Huang Y, Yan H, Zhong J, Wang LJ, Abdullah HM, Wang HH. Antibiotic Administration Routes and Oral Exposure to Antibiotic Resistant Bacteria as Key Drivers for Gut Microbiota Disruption and Resistome in Poultry. Front Microbiol 2020; 11:1319. [PMID: 32733394 PMCID: PMC7358366 DOI: 10.3389/fmicb.2020.01319] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 05/25/2020] [Indexed: 01/05/2023] Open
Abstract
Previous studies have identified oral administration of antibiotics and gut-impacting drugs as critical drivers for fecal antibiotic resistance (AR) and microbiome disruption in lab mice, but the practical implications of these findings have yet to be validated in hosts nurtured in conventional environment. Using ampicillin (Amp) as a way to extrapolate the general effect of antibiotics, this project examined the impact of drug administration routes on fecal microbiota and resistome using poultry raised in a teaching farm. AR genes were found to be abundant in the feces of young Leghorn chicks without previous antibiotic treatment. In chickens seeded with bla CMY-2 + Escherichia coli, 300 mg/kg body weight of Amp was orally administered for 5 days. This led to the fecal microbiota switching from Firmicutes occupied (95.60 ± 2.62%) and Lactobacillus rich, to being dominated by Proteobacteria (70.91 ± 28.93%), especially Escherichia/Shigella. However, when Amp was given via muscle injection, Firmicutes was mostly retained (i.e., from 83.6 ± 24.4% pre- to 90.4 ± 15.2% post-treatment). In control chickens without seeding with bla CMY-2 + E. coli, oral Amp also led to the increase of Proteobacteria, dominated by Klebsiella and Escherichia/Shigella, and a reduction of Firmicutes. Specifically within Firmicutes, Enterococcus, Clostridium, etc. were enriched but Lactobacillus was diminished. The fecal resistome including Ampr genes was more abundant in chickens receiving oral Amp than those treated with muscle injection, but the difference was primarily within 1 log. The data illustrated that both drug administration routes and pre-existing gut microbiota have profound impacts on gut microbiome disruption when antibiotic treatment is given. In hosts nurtured in a conventional environment, drug administration route has the most evident impact on gut microbiota rather than the size of the targeted bla CMY-2 + gene pool, likely due to the pre-existing bacteria that are (i) less susceptible to Amp, and/or (ii) with Ampr- or multidrug resistance-encoding genes other than bla CMY-2 +. These results demonstrated the critical interplay among drug administration routes, microbiota seeded through the gastrointestinal tract, AR, gut microbiota disruption, and the rise of common opportunistic pathogens in hosts. The potential implications in human and animal health are discussed.
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Affiliation(s)
- Yang Zhou
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Li
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Lu Zhang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Zuowei Wu
- College of Veterinary Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Ying Huang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - He Yan
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,College of Food Science and Engineering of Technology, Guangzhou, China
| | - Jiang Zhong
- Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China
| | - Li-Ju Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States
| | - Hafiz M Abdullah
- Department of Animal Science Poultry Facility, OARDC, Wooster, OH, United States
| | - Hua H Wang
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
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31
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Cao R, Wang J, Ben W, Qiang Z. The profile of antibiotic resistance genes in pig manure composting shaped by composting stage: Mesophilic-thermophilic and cooling-maturation stages. CHEMOSPHERE 2020; 250:126181. [PMID: 32109697 DOI: 10.1016/j.chemosphere.2020.126181] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
The variation of antibiotic resistance genes (ARGs) and influential factors in pig manure composting were investigated by conducting simulated composting tests using four different supplement materials (wheat straw, corn straw, poplar sawdust and spent mushroom). The results show that the relative abundance of total ARGs increased by 0.19-1.61 logs after composting, and tetX, sulI, sulII, dfrA1 and aadA were the major contributors. The variations of ARG profiles and bacterial communities throughout the composting were clearly divided into mesophilic-thermophilic and cooling-maturation stages in all tests, while different supplement materials did not exert a noticeable influence. Network analysis demonstrated the diversity of bacterial hosts for ARGs, the existence of multiple antibiotic resistant bacteria, and the weak correlations between ARGs and physicochemical factors in the composting piles. Of note, integron intI1 and Mycobacterium (a potential pathogen) were positively correlated with eight and four ARGs, respectively, that displayed increased abundance after composting.
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Affiliation(s)
- Rukun Cao
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085, China
| | - Jian Wang
- Institute of Rural Energy and Environmental Protection, Academy of Agricultural Planning and Engineering, Ministry of Agriculture and Rural Affairs, Beijing, 100121, China; Key Laboratory of Technologies and Models for Cyclic Utilization from Agricultural Resources, Ministry of Agriculture and Rural Affairs, Beijing, 100121, China
| | - Weiwei Ben
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085, China.
| | - Zhimin Qiang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 18 Shuang-qing Road, Beijing, 100085, China.
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32
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Oluwadare M, Lee MD, Grim CJ, Lipp EK, Cheng Y, Maurer JJ. The Role of the Salmonella spvB IncF Plasmid and Its Resident Entry Exclusion Gene traS on Plasmid Exclusion. Front Microbiol 2020; 11:949. [PMID: 32499773 PMCID: PMC7242723 DOI: 10.3389/fmicb.2020.00949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/21/2020] [Indexed: 11/30/2022] Open
Abstract
Salmonella enterica cause significant illnesses worldwide. There has been a marked increase in resistance to fluoroquinolones and β-lactams/cephalosporins, antibiotics commonly used to treat salmonellosis. However, S. enterica serovars vary in their resistance to these and other antibiotics. The systemic virulence of some Salmonella serovars is due to a low copy number, IncF plasmid (65-100 kb) that contains the ADP-ribosylating toxin, SpvB. This virulence plasmid is present in only nine Salmonella serovars. It is possible that the spvB-virulence plasmid excludes other plasmids and may explain why antibiotic resistance is slow to develop in certain Salmonella serovars such as S. Enteritidis. The distribution of plasmid entry exclusion genes traS/traT and traY/excA are variable in Salmonella IncF and IncI plasmids, respectively and may account for differences in emergent antimicrobial resistance for some Salmonella serovars. The goal of this study is to determine the contribution of the Salmonella spvB-virulence plasmid in F-plasmid exclusion. From conjugation experiments, S. Typhimurium exhibited lower conjugation frequency with incFI and incFII plasmids when the spvB-virulence plasmid is present. Furthermore, introduction of cloned incFI traS into a "plasmidless" S. Typhimurium LT2 strain and Escherichia coli DH5α excluded incFI plasmid. However, deletion of the virulence plasmid traS did not affect plasmid exclusion significantly compared to a spvB control deletion. In addition, differences in F plasmid conjugation in natural Salmonella isolates did not correlate with IncF or SpvB-virulence plasmid genotype. There appear to be other plasmid or chromosomal genes at play in plasmid exclusion that may be responsible for the slow development of antibiotic resistance in certain serovars.
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Affiliation(s)
- Mopelola Oluwadare
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - Margie D. Lee
- Department of Population Health, University of Georgia, Athens, GA, United States
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, United States
| | - Erin K. Lipp
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Ying Cheng
- Department of Population Health, University of Georgia, Athens, GA, United States
| | - John J. Maurer
- Department of Population Health, University of Georgia, Athens, GA, United States
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
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33
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Vrancianu CO, Popa LI, Bleotu C, Chifiriuc MC. Targeting Plasmids to Limit Acquisition and Transmission of Antimicrobial Resistance. Front Microbiol 2020; 11:761. [PMID: 32435238 PMCID: PMC7219019 DOI: 10.3389/fmicb.2020.00761] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is a significant global threat to both public health and the environment. The emergence and expansion of AMR is sustained by the enormous diversity and mobility of antimicrobial resistance genes (ARGs). Different mechanisms of horizontal gene transfer (HGT), including conjugation, transduction, and transformation, have facilitated the accumulation and dissemination of ARGs in Gram-negative and Gram-positive bacteria. This has resulted in the development of multidrug resistance in some bacteria. The most clinically significant ARGs are usually located on different mobile genetic elements (MGEs) that can move intracellularly (between the bacterial chromosome and plasmids) or intercellularly (within the same species or between different species or genera). Resistance plasmids play a central role both in HGT and as support elements for other MGEs, in which ARGs are assembled by transposition and recombination mechanisms. Considering the crucial role of MGEs in the acquisition and transmission of ARGs, a potential strategy to control AMR is to eliminate MGEs. This review discusses current progress on the development of chemical and biological approaches for the elimination of ARG carriers.
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Affiliation(s)
- Corneliu Ovidiu Vrancianu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
| | - Laura Ioana Popa
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- The National Institute of Research and Development for Biological Sciences, Bucharest, Romania
| | - Coralia Bleotu
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
- Stefan S. Nicolau Institute of Virology, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
- The Research Institute of the University of Bucharest, Bucharest, Romania
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34
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Al-Kadmy IMS, Ibrahim SA, Al-Saryi N, Aziz SN, Besinis A, Hetta HF. Prevalence of Genes Involved in Colistin Resistance in Acinetobacter baumannii: First Report from Iraq. Microb Drug Resist 2019; 26:616-622. [PMID: 31816255 DOI: 10.1089/mdr.2019.0243] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background and Aim: Colistin is increasingly being used as a "last-line" therapy to treat infections caused by multidrug-resistant (MDR) Acinetobacter baumannii isolates, when essentially no other options are available in these days. The aim of this study was to detect genes associated with colistin resistance in A. baumannii. Methods: One hundred twenty-one isolates of A. baumannii were collected from clinical and environmental samples during 2016 to 2018 in Baghdad. Isolates were diagnosed as A. baumannii by using morphological tests, Vitek-2 system, 16SrRNA PCR amplification, and sequencing. Antibiotic susceptibility test was carried out using disk diffusion method. Phenotypic detection of colistin resistance was performed by CHROMagar™ COL-APSE medium and broth microdilution method for the determination of the minimal inhibitory concentration. Molecular detection of genes responsible for colistin resistance in A. baumannii was performed by PCR. Results: Ninety-two (76%) of the 121 A. baumannii isolates were colistin resistant. Twenty-six (21.5%) of the 121 isolates showed positive growth on CHROMagar Acinetobacter base for MDR. PCR detected mcr-1, mcr-2, and mcr-3 genes in 89 (73.5%), 78 (64.5%), and 82 (67.8%) A. baumannii isolates, respectively. Seventy-eight (64.5%) of the 121 isolates harbored the integron intI2 gene and 81 (66.9%) contained intI3 gene. Moreover, 60 (49.6%) of the 121 isolates were positive for the quorum sensing lasI gene. Conclusion: The presence of a large percentage of colistin-resistant A. baumannii strains in Baghdad may be due to the presence of mobile genetic elements, and it is urgent to avoid unnecessary clinical use of colistin.
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Affiliation(s)
- Israa M S Al-Kadmy
- Faculty of Science and Engineering, School of Engineering, University of Plymouth, Plymouth, United Kingdom.,Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Susan A Ibrahim
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Nadal Al-Saryi
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Sarah Naji Aziz
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Alexandros Besinis
- Faculty of Science and Engineering, School of Engineering, University of Plymouth, Plymouth, United Kingdom
| | - Helal F Hetta
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt.,Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
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35
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Mahmoud MAM, Abdel-Mohsein HS. Hysterical tetracycline in intensive poultry farms accountable for substantial gene resistance, health and ecological risk in Egypt- manure and fish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113039. [PMID: 31521994 DOI: 10.1016/j.envpol.2019.113039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Although the poultry production sector plays a key role in sustaining the majority of animal protein demand in Egypt, the deleterious effects of widespread antibiotic resistance on health and environment are currently not well recognized. Litter and dropping samples from broiler and layer poultry farms as well as, tilapia samples from the Nile River and aquaculture farms were collected from Upper Egypt. Samples were extracted and examined for tetracycline residues [tetracycline (TC), chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC)] using HPLC. In addition, tetracycline resistance genes [tet (M), tet (W), tet (Q) and tet (G)] were screened from pooled intestinal contents collected from twelve broiler farms in Upper Egypt. The antibiotic resistance genes results revealed that tet (W) was confirmed to be expressed in all intestinal samples. In contrast, tet (Q) and tet (M) were detected only in 42% and 17% of the samples, respectively. CTC and OTC were the antimicrobial compounds with the highest concentrations in poultry litter and droppings, with concentrations of 6.05 and 2.47 μg g-1 (CTC) and 5.9 and 1.33 μg g-1 (OTC), respectively. However, the concentrations of DC were significantly higher than those of the other compounds in both aquaculture and Nile River tilapia. The tetracycline residue levels in aquaculture tilapia were significantly higher than those in Nile River tilapia. The hazard quotients (HQs) exceeded 1 for OTC, CTC and DC, which highlights the great risk of using broiler litter to fertilize agricultural land. Moreover, the presence of DC and CTC indicates that consumption of aquaculture tilapia poses a considerable health risk. Therefore, poultry litter or droppings containing tetracycline residues and tet resistance determinants used for aquaculture or as farmland fertilizers could be major sources of antibiotic resistance in fish, humans and environment.
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Affiliation(s)
- Manal A M Mahmoud
- Department of Animal, Poultry Hygiene and Environmental Sanitation, Faculty of Veterinary Medicine, Assiut University, 71526, Egypt.
| | - Hosnia S Abdel-Mohsein
- Department of Animal, Poultry Hygiene and Environmental Sanitation, Faculty of Veterinary Medicine, Assiut University, 71526, Egypt
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36
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Nnadozie CF, Odume ON. Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113067. [PMID: 31465907 DOI: 10.1016/j.envpol.2019.113067] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/13/2019] [Accepted: 08/15/2019] [Indexed: 05/12/2023]
Abstract
Freshwater environments are susceptible to possible contamination by residual antibiotics that are released through different sources, such as agricultural runoffs, sewage discharges and leaching from nearby farms. Freshwater environment can thus become reservoirs where an antibiotic impact microorganisms, and is an important public health concern. Degradation and dilution processes are fundamental for predicting the actual risk of antibiotic resistance dissemination from freshwater reservoirs. This study reviews major approaches for detecting and quantifying antibiotic resistance bacteria (ARBs) and genes (ARGs) in freshwater and their prevalence in these environments. Finally, the role of dilution, degradation, transmission and the persistence and fate of ARB/ARG in these environments are also reviewed. Culture-based single strain approaches and molecular techniques that include polymerase chain reaction (PCR), quantitative polymerase chain reaction (qPCR) and metagenomics are techniques for quantifying ARB and ARGs in freshwater environments. The level of ARBs is extremely high in most of the river systems (up to 98% of the total detected bacteria), followed by lakes (up to 77% of the total detected bacteria), compared to dam, pond, and spring (<1%). Of most concern is the occurrence of extended-spectrum β-lactamase producing Enterobacteriaceae, methicillin resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE), which cause highly epidemic infections. Dilution and natural degradation do not completely eradicate ARBs and ARGs in the freshwater environment. Even if the ARBs in freshwater are effectively inactivated by sunlight, their ARG-containing DNA can still be intact and capable of transferring resistance to non-resistant strains. Antibiotic resistance persists and is preserved in freshwater bodies polluted with high concentrations of antibiotics. Direct transmission of indigenous freshwater ARBs to humans as well as their transitory insertion in the microbiota can occur. These findings are disturbing especially for people that rely on freshwater resources for drinking, crop irrigation, and food in form of fish.
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Affiliation(s)
- Chika F Nnadozie
- Unilever Centre for Environmental Water Quality, Institute for Water Research, Rhodes University, PO Box 94, Grahamstown 6140, South Africa.
| | - Oghenekaro Nelson Odume
- Unilever Centre for Environmental Water Quality, Institute for Water Research, Rhodes University, PO Box 94, Grahamstown 6140, South Africa
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37
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Epidemiological significance of poultry litter for spreading the antibiotic-resistant strains of Escherichia coli. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s004393391600043x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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39
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Bythwood TN, Soni V, Lyons K, Hurley-Bacon A, Lee MD, Hofacre C, Sanchez S, Maurer JJ. Antimicrobial Resistant Salmonella enterica Typhimurium Colonizing Chickens: The Impact of Plasmids, Genotype, Bacterial Communities, and Antibiotic Administration on Resistance. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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40
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Hultman J, Tamminen M, Pärnänen K, Cairns J, Karkman A, Virta M. Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent. FEMS Microbiol Ecol 2019. [PMID: 29514229 PMCID: PMC5939699 DOI: 10.1093/femsec/fiy038] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Wastewater treatment plants (WWTPs) collect wastewater from various sources for a multi-step treatment process. By mixing a large variety of bacteria and promoting their proximity, WWTPs constitute potential hotspots for the emergence of antibiotic resistant bacteria. Concerns have been expressed regarding the potential of WWTPs to spread antibiotic resistance genes (ARGs) from environmental reservoirs to human pathogens. We utilized epicPCR (Emulsion, Paired Isolation and Concatenation PCR) to detect the bacterial hosts of ARGs in two WWTPs. We identified the host distribution of four resistance-associated genes (tetM, int1, qacEΔ1and blaOXA-58) in influent and effluent. The bacterial hosts of these resistance genes varied between the WWTP influent and effluent, with a generally decreasing host range in the effluent. Through 16S rRNA gene sequencing, it was determined that the resistance gene carrying bacteria include both abundant and rare taxa. Our results suggest that the studied WWTPs mostly succeed in decreasing the host range of the resistance genes during the treatment process. Still, there were instances where effluent contained resistance genes in bacterial groups not carrying these genes in the influent. By permitting exhaustive profiling of resistance-associated gene hosts in WWTP bacterial communities, the application of epicPCR provides a new level of precision to our resistance gene risk estimates.
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Affiliation(s)
- Jenni Hultman
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - Manu Tamminen
- Department of Biology, University of Turku, University Hill, 20014 University of Turku, Finland
| | - Katariina Pärnänen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - Johannes Cairns
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
| | - Antti Karkman
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, 41346 Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Guldhedsgatan 10, 41346 Gothenburg, Sweden.,Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014 University of Helsinki, Finland
| | - Marko Virta
- Department of Microbiology, University of Helsinki, Viikinkaari 9, 00014 University of Helsinki, Finland
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41
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Hurst JJ, Oliver JP, Schueler J, Gooch C, Lansing S, Crossette E, Wigginton K, Raskin L, Aga DS, Sassoubre LM. Trends in Antimicrobial Resistance Genes in Manure Blend Pits and Long-Term Storage Across Dairy Farms with Comparisons to Antimicrobial Usage and Residual Concentrations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2405-2415. [PMID: 30707579 DOI: 10.1021/acs.est.8b05702] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The use of antimicrobials by the livestock industry can lead to the release of unmetabolized antimicrobials and antimicrobial resistance genes (ARG) into the environment. However, the relationship between antimicrobial use, residual antimicrobials, and ARG prevalence within manure is not well understood, specifically across temporal and location-based scales. The current study determined ARG abundance in untreated manure blend pits and long-term storage systems from 11 conventional and one antimicrobial-free dairy farms in the Northeastern U.S. at six times over one-year. Thirteen ARGs corresponding to resistance mechanisms for tetracyclines, macrolides-lincosamides, sulfonamides, aminoglycosides, and β-lactams were quantified using a Custom qPCR Array or targeted qPCR. ARG abundance differed between locations, suggesting farm specific microbial resistomes. ARG abundance also varied temporally. Manure collected during the winter contained lower ARG abundances. Overall, normalized ARG concentrations did not correlate to average antimicrobial usage or tetracycline concentrations across farms and collection dates. Of the 13 ARGs analyzed, only four genes showed a higher abundance in samples from conventional farms and eight ARGs exhibited similar normalized concentrations in the conventional and antimicrobial-free farm samples. No clear trends were observed in ARG abundance between dairy manure obtained from blend pits and long-term storage collected during two drawdown periods (fall and spring), although higher ARG abundances were generally observed in spring compared to fall. This comprehensive study informs future studies needed to determine the contributions of ARGs from dairy manure to the environment.
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Affiliation(s)
- Jerod J Hurst
- Department of Chemistry , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
| | - Jason P Oliver
- Department of Animal Sciences , Cornell University , Ithaca , New York 14850 , United States
| | - Jenna Schueler
- Department of Environmental Science & Technology , University of Maryland , College Park , Maryland 20742 , United States
| | - Curt Gooch
- Department of Animal Sciences , Cornell University , Ithaca , New York 14850 , United States
| | - Stephanie Lansing
- Department of Environmental Science & Technology , University of Maryland , College Park , Maryland 20742 , United States
| | - Emily Crossette
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Krista Wigginton
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Lutgarde Raskin
- Department of Civil and Environmental Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Diana S Aga
- Department of Chemistry , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
| | - Lauren M Sassoubre
- Department of Civil, Structural, and Environmental Engineering , University at Buffalo, The State University of New York (SUNY) , Buffalo , New York 14260 , United States
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1189] [Impact Index Per Article: 198.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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Sultan I, Rahman S, Jan AT, Siddiqui MT, Mondal AH, Haq QMR. Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective. Front Microbiol 2018; 9:2066. [PMID: 30298054 PMCID: PMC6160567 DOI: 10.3389/fmicb.2018.02066] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022] Open
Abstract
History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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Oladeinde A, Cook K, Orlek A, Zock G, Herrington K, Cox N, Plumblee Lawrence J, Hall C. Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter. PLoS One 2018; 13:e0202286. [PMID: 30169497 PMCID: PMC6118388 DOI: 10.1371/journal.pone.0202286] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter (PL) as an important extra-intestinal environment that may have selected for specific S. Heidelberg strains. Poultry litter is a mixture of bedding materials and chicken excreta that contains chicken gastrointestinal (GI) bacteria, undigested feed, feathers, and other materials of chicken origin. In this study, we performed a series of controlled laboratory experiments which assessed the microevolution of two S. Heidelberg strains (SH-2813 and SH-116) in PL previously used to raise 3 flocks of broiler chickens. The strains are closely related at the chromosome level, differing from the reference genome by 109 and 89 single nucleotide polymorphisms/InDels, respectively. Whole genome sequencing was performed on 86 isolates recovered after 0, 1, 7 and 14 days of microevolution in PL. Only strains carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids survived more than 7 days in PL. Competition experiments showed that carriage of these plasmids was associated with increased fitness. This increased fitness was associated with an increased copy number of IncX1 and ColE1 plasmids. Further, all Col plasmid-bearing strains had hotspot mutations in 37 loci on the chromosome and in 3 loci on the IncX1 plasmid. Additionally, we observed a decrease in susceptibility to tobramycin, kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing strains. Our study demonstrates how positive selection from poultry litter can change the evolutionary path of S. Heidelberg.
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Affiliation(s)
- Adelumola Oladeinde
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Kimberly Cook
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Alex Orlek
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Greg Zock
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Kyler Herrington
- Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Nelson Cox
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Jodie Plumblee Lawrence
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
| | - Carolina Hall
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, USDA-ARS, Athens, GA, United States of America
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45
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Clavijo V, Flórez MJV. The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review. Poult Sci 2018; 97:1006-1021. [PMID: 29253263 PMCID: PMC5850219 DOI: 10.3382/ps/pex359] [Citation(s) in RCA: 277] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/29/2017] [Indexed: 12/23/2022] Open
Abstract
The microbiome of the broiler chicken gastrointestinal tract (GIT) has been extensively studied, and it has been amply demonstrated that it plays an important role in the health of the host, as it has a positive impact on the immune system, the physiology of the GIT, and productivity. Also, the microbiota is involved in reducing and preventing colonization by enteric pathogens through the process of competitive exclusion and the production of bacteriostatic and bactericidal substances. The taxonomic composition of the microbiota is affected by different factors, such as the organ, the age of the animal, diet and the use of antimicrobials. Different kinds of additives that regulate the microbial community in feed include probiotics (live microorganisms that when administered in adequate amounts confer a health benefit on the host), prebiotics (ingredients that stimulate increased beneficial microbial activity in the digestive system in order to improve the health of the host) and phytobiotics (primary or secondary components of plants that contain bioactive compounds that exert a positive effect on the growth and health of animals). Phages may potentially provide an integrated solution to modulate the intestinal microbiome of chicken intestines, as they reduce specific pathogenic microbial populations, permitting the proliferation of beneficial microbiota. Studies have shown that the use of cocktails of phages, especially in high concentrations and with short lapses of time between exposure to the bacteria and treatment with phages, optimize the reduction of Salmonella in chickens. Each of these technologies has demonstrable positive effects on the health of the host and the reduction of the pathogen load in controlled assays. This paper presents a comprehensive summary of the role of the microbiota in the broiler chicken gastrointestinal tract, and discusses the usefulness of different strategies for its modulation to control pathogens, with a particular emphasis on bacteriophages.
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Affiliation(s)
- Viviana Clavijo
- Department of Biological Sciences, Universidad de los Andes, Carrera 1 Este N° 19A-40, Bogotá, Colombia
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Barraud O, Peyre M, Couvé-Deacon E, Chainier D, Bahans C, Guigonis V, Ploy MC, Bedu A, Garnier F. Antibiotic Resistance Acquisition in the First Week of Life. Front Microbiol 2018; 9:1467. [PMID: 30022973 PMCID: PMC6039568 DOI: 10.3389/fmicb.2018.01467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
Objectives: The fetus is considered sterile but recent studies have suggested that gut colonization could start before birth. Scarce data are available for the acquisition of resistant Gram-negative bacteria (GNB) during the first days of life. Several studies have shown that integrons play a major role in antibiotic resistance acquisition. In this work, we studied the dynamics of human intestinal acquisition of GNB and integrons during the first days of life. Methods: Meconium was collected at birth and a stool sample before hospital discharge (days 2 or 3) on 185 term neonates. GNB were searched by culture on each sample and class 1, 2, and 3 integrons from each GNB or directly from samples. Eight risk factors for integron and GNB acquisition were studied. Results: We isolated 228 GNB, 46 from meconium and the remainder from stools. No link was found between GNB isolation and antibiotic exposure during delivery, but antibiotic exposure during labor significantly selected blaTEM-positive amoxicillin-resistant Enterobacteria. Two-thirds of GNB were antibiotic-susceptible and most of the resistant isolates were acquired after birth. Integrons were detected in 18 of the 228 GNB isolates from 3 meconium and 20 stools. Antibiotic administration during delivery and vaginal carriage of Streptococcus agalactiae appeared as risk factors for integron acquisition. Conclusion: Gram-negative bacteria and integrons are mostly acquired after birth during the first days of life even if for some term neonates, meconium was not sterile. Antibiotic administration during delivery is a major risk for integron acquisition and for selection of amoxicillin-resistant Enterobacteria.
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Affiliation(s)
- Olivier Barraud
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
| | - Marianne Peyre
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France
| | | | - Delphine Chainier
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
| | - Claire Bahans
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France.,Comité Hme REcherche Clinique, Hôpital Femme Mère Enfant, Limoges, France
| | - Vincent Guigonis
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France.,Comité Hme REcherche Clinique, Hôpital Femme Mère Enfant, Limoges, France
| | - Marie-Cécile Ploy
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
| | - Antoine Bedu
- Service de Pédiatrie, Hôpital Femme Mère Enfant, Limoges, France.,Comité Hme REcherche Clinique, Hôpital Femme Mère Enfant, Limoges, France
| | - Fabien Garnier
- INSERM, CHU Limoges, UMR 1092, Université de Limoges, Limoges, France
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Singh NS, Singhal N, Virdi JS. Genetic Environment of blaTEM-1, blaCTX-M-15, blaCMY-42 and Characterization of Integrons of Escherichia coli Isolated From an Indian Urban Aquatic Environment. Front Microbiol 2018; 9:382. [PMID: 29563901 PMCID: PMC5845874 DOI: 10.3389/fmicb.2018.00382] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/20/2018] [Indexed: 12/02/2022] Open
Abstract
The presence of antibiotic resistance genes (ARGs) including those expressing ESBLs and AmpC-β-lactamases in Escherichia coli inhabiting the aquatic environments is a serious health problem. The situation is further complicated by the fact that ARGs can be easily transferred among bacterial species with the help of mobile genetic elements – plasmids, integrons, insertion sequences (IS), and transposons. Therefore, the analysis of genetic environment and mobile genetic elements associated with ARGs is important as these provide useful information about the epidemiology of these genes. In our previous study, we had reported presence of various β-lactam resistance genes present in E. coli strains inhabiting the river Yamuna traversing the National Capital Territory of Delhi (India). In the present study, we have analyzed the genetic environment of three ARGs blaTEM-1, blaCTX-M-15, and blaCMY -42 of those E. coli strains. The structure of class 1 integrons and their gene cassettes was also analyzed. Insertion sequence IS26 was present upstream of blaTEM-1, ISEcp1 was present upstream of blaCTXM-15 gene and orf477 was present downstream of blaCTXM-15. ISEcp1 was also present upstream of blaCMY -42 and, blc and sugE genes were present in the downstream region of this gene. Thus, the overall genetic environment surrounding these genes was similar to that reported from E. coli strains isolated globally. Conjugation assays, isolation and analysis of plasmid DNA of the transconjugants indicated that blaTEM-1, blaCTX-M-15, blaCMY -42 and class 1 integron were plasmid-mediated and possibly transmit between genera through horizontal gene transfer (HGT). This might lead to dissemination of antimicrobial resistance genes in aquatic environment. The work embodied in this paper is the first describing the genetic environment of bla and integrons in aquatic E. coli isolated from India.
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Affiliation(s)
- Nambram S Singh
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi, New Delhi, India
| | - Neelja Singhal
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi, New Delhi, India
| | - Jugsharan S Virdi
- Microbial Pathogenicity Laboratory, Department of Microbiology, University of Delhi, New Delhi, India
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Moser KA, Zhang L, Spicknall I, Braykov NP, Levy K, Marrs CF, Foxman B, Trueba G, Cevallos W, Goldstick J, Trostle J, Eisenberg JNS. The Role of Mobile Genetic Elements in the Spread of Antimicrobial-Resistant Escherichia coli From Chickens to Humans in Small-Scale Production Poultry Operations in Rural Ecuador. Am J Epidemiol 2018; 187:558-567. [PMID: 29506196 DOI: 10.1093/aje/kwx286] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 07/25/2017] [Indexed: 11/15/2022] Open
Abstract
Small-scale production poultry operations are increasingly common worldwide. To investigate how these operations influence antimicrobial resistance and mobile genetic elements (MGEs), Escherichia coli isolates were sampled from small-scale production birds (raised in confined spaces with antibiotics in feed), household birds (no movement constraints; fed on scraps), and humans associated with these birds in rural Ecuador (2010-2012). Isolates were screened for genes associated with MGEs as well as phenotypic resistance to 12 antibiotics. Isolates from small-scale production birds had significantly elevated odds of resistance to 7 antibiotics and presence of MGE genes compared with household birds (adjusted odds ratio (OR) range = 2.2-87.9). Isolates from humans associated with small-scale production birds had elevated odds of carrying an integron (adjusted OR = 2.0; 95% confidence interval (CI): 1.06, 3.83) compared with humans associated with household birds, as well as resistance to sulfisoxazole (adjusted OR = 1.9; 95% CI: 1.01, 3.60) and trimethoprim/sulfamethoxazole (adjusted OR = 2.1; 95% CI: 1.13, 3.95). Stratifying by the presence of MGEs revealed antibiotic groups that are explained by biological links to MGEs; in particular, resistance to sulfisoxazole, trimethoprim/sulfamethoxazole, or tetracycline was highest among birds and humans when MGE exposures were present. Small-scale production poultry operations might select for isolates carrying MGEs, contributing to elevated levels of resistance in this setting.
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Affiliation(s)
- Kara A Moser
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Ian Spicknall
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Nikolay P Braykov
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Karen Levy
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Carl F Marrs
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - William Cevallos
- Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Jason Goldstick
- Department of Emergency Medicine, University of Michigan, Ann Arbor, Michigan
- Injury Research Center, University of Michigan, Ann Arbor, Michigan
| | - James Trostle
- Department of Anthropology, Trinity College, Hartford, Connecticut
| | - Joseph N S Eisenberg
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan
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Li L, Zhao X. Characterization of the resistance class 1 integrons in Staphylococcus aureus isolates from milk of lactating dairy cattle in Northwestern China. BMC Vet Res 2018; 14:59. [PMID: 29482565 PMCID: PMC5827992 DOI: 10.1186/s12917-018-1376-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/15/2018] [Indexed: 11/19/2022] Open
Abstract
Background Integrons are mobile DNA elements and they have an important role in acquisition and dissemination of antimicrobial resistance genes. However, there are limited data available on integrons of Staphylococcus aureus (S. aureus) from bovine mastitis, especially from Chinese dairy cows. To address this knowledge gap, bovine mastitis-inducing S. aureus isolates were investigated for the presence of integrons as well as characterization of gene cassettes. Integrons were detected using PCR reactions and then further characterized by a restriction fragment-length polymorphism analysis and amplicon sequencing. Results All 121 S. aureus isolates carried the class 1 integrase gene intI1, with no intI2 and intI3 genes detected. One hundred and three isolates were positive for the presence of 12 resistance genes, either alone or in combination with other gene cassettes. These resistance genes encoded resistance to trimethoprim (dhfrV, dfrA1, dfrA12), aminoglycosides (aadA1, aadA5, aadA4, aadA24, aacA4, aadA2, aadB), chloramphenicol (cmlA6) and quaternary ammonium compound (qacH) and were organized into 11 different gene cassettes arrangements (A-K). The gene cassette arrays dfrA1-aadA1 (D, 44.6%), aadA2 (K, 31.4%), dfrA12-orfX2-aadA2 (G, 27.3%) and aadA1 (A, 25.6%) were most prevalent. Furthermore, 74 isolates contained combinations of 2 to 4 gene cassette arrays. Finally, all of the integron/cassettes-positive isolates were resistant to aminoglycoside antibiotics. Conclusions This is the first study on the integrons and gene cassette arrays in S. aureus isolates from milk of mastitic cows from Northwestern China and provide the evidence for class 1 integron as possible antibiotic resistance determinants on dairy farms.
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Affiliation(s)
- Longping Li
- College of Animal Science and Technology, Northwest A&F University, YangLing, Shaanxi, People's Republic of China.,Life Science Research Center, Yulin University, Yulin, 719000, People's Republic of China.,Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goat, Yulin University, Yulin, 719000, People's Republic of China
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, YangLing, Shaanxi, People's Republic of China. .,Department of Animal Science, McGill University, 21,111 Lakeshore, Ste. Anne de Bellevue, Quebec, H9X 3V9, Canada.
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50
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Zhang M, Chen L, Ye C, Yu X. Co-selection of antibiotic resistance via copper shock loading on bacteria from a drinking water bio-filter. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 233:132-141. [PMID: 29059628 DOI: 10.1016/j.envpol.2017.09.084] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 09/13/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Heavy metal contamination of source water frequently occurred in developing countries as a result of accidents. To address the problems, most of the previous studies have focused on engineering countermeasures. In this study, we investigated the effects of heavy metals, particularly copper, on the development of antibiotic resistance by establishing a copper shock loading test. Results revealed that co-selection occurred rapidly within 6 h. Copper, at the levels of 10 and 100 mg/L, significantly increased bacterial resistance to the antibiotics tested, including rifampin, erythromycin, kanamycin, and a few others. A total of 117 antimicrobial-resistance genes were detected from 12 types of genes, and the relative abundance of most genes (particularly mobile genetic elements intⅠand transposons) was markedly enriched by at least one fold. Furthermore, the copper shock loading altered the bacterial community. Numerous heavy metal and antibiotic resistant strains were screened out and enriched. These strains are expected to enhance the overall level of resistance. More noticeably, the majority of the co-selected antibiotic resistance could sustain for at least 20 h in the absence of copper and antimicrobial drugs. Resistance to vancomycin, erythromycin and lincomycin even could remain for 7 days. The prominent selection pressure by the copper shock loading implies that a real accident most likely poses similar impacts on the water environment. An accidental release of heavy metals would not only cause harm to the ecological environment, but also contribute to the development of bacterial antibiotic resistance. Broader concerns should be raised about the biological risks caused by sudden releases of pollutants by accidents.
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Affiliation(s)
- Menglu Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Science, Beijing 100049, People's Republic of China
| | - Lihua Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China; University of Chinese Academy of Science, Beijing 100049, People's Republic of China
| | - Chengsong Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China
| | - Xin Yu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, People's Republic of China.
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