1
|
Oliveira-Silva M, Goulart RS, Moraes MA, Nakamura-Silva R, Fujimoto RY, Sousa RC, Kobayashi RKT, Medeiros LP, Nakazato G, Pitondo-Silva A. Multidrug-resistant Escherichia coli strains isolated from swine manure biofertilizer in Brazil. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:534. [PMID: 38727864 DOI: 10.1007/s10661-024-12658-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/30/2024] [Indexed: 06/21/2024]
Abstract
Escherichia coli is one of the key bacteria responsible for a variety of diseases in humans and livestock-associated infections around the globe. It is the leading cause of mortality in neonatal and weaned piglets in pig husbandry, causing diarrhea and significant harm to the industry. Furthermore, the frequent and intensive use of antimicrobials for the prevention of diseases, particularly gastrointestinal diseases, may promote the selection of multidrug-resistant (MDR) strains. These resistant genotypes can be transmitted through the excrement of animals, including swine. It is common practice to use porcine manure processed by biodigesters as fertilizer. This study aimed to examine the antimicrobial susceptibility, the presence of virulence genes frequently associated with pathotypes of intestinal pathogenic E. coli (InPEC), and antimicrobial resistance genes (ARGs) of 28 E. coli isolates collected from swine manure fertilizers. In addition, the enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) technique was used to investigate the genetic relationship among the strains. Using disk diffusion, the antimicrobial susceptibility profiles of the strains were determined. Using polymerase chain reaction (PCR), 14 distinct virulence genes associated with the most prevalent diarrhea and intestinal pathogenic E. coli (DEC/InPEC) and five ARGs were analyzed. All isolates tested positive for multidrug resistance. There was no detection of any of the 14 virulence genes associated with InPECs, indicating the presence of an avirulent commensal microbiota. Molecular classification by ERIC-PCR revealed that the majority of isolates (27 isolates) coalesced into a larger cluster with a genetic similarity of 47.7%; only one strain did not cluster in this cluster, indicating a high level of genetic diversity among the analyzed isolates. Thus, it is of the utmost importance to conduct epidemiological surveillance of animal breeding facilities in order to determine their microbiota and formulate plans to reduce the use of antimicrobials and improve animal welfare.
Collapse
Affiliation(s)
- Mariana Oliveira-Silva
- Universidade de Ribeirão Preto (UNAERP), Avenida Costábile Romano, N° 2201. Bloco J, Lab. 1, Ribeirânia., Ribeirão Preto, SP, CEP 14096-900, Brazil
| | - Rafael Silva Goulart
- Universidade de Ribeirão Preto (UNAERP), Avenida Costábile Romano, N° 2201. Bloco J, Lab. 1, Ribeirânia., Ribeirão Preto, SP, CEP 14096-900, Brazil
| | - Miguel Augusto Moraes
- Universidade de Ribeirão Preto (UNAERP), Avenida Costábile Romano, N° 2201. Bloco J, Lab. 1, Ribeirânia., Ribeirão Preto, SP, CEP 14096-900, Brazil
| | - Rafael Nakamura-Silva
- Universidade de Ribeirão Preto (UNAERP), Avenida Costábile Romano, N° 2201. Bloco J, Lab. 1, Ribeirânia., Ribeirão Preto, SP, CEP 14096-900, Brazil
| | - Rodrigo Yudi Fujimoto
- Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA, Unidade Tabuleiros Costeios, Av. Beira Mar, 3250 Jardins, Aracaju, Sergipe, CEP 49025040, Brazil
| | - Ricardo Coelho Sousa
- Empresa Brasileira de Pesquisa Agropecuária-EMBRAPA, Unidade Tabuleiros Costeios, Av. Beira Mar, 3250 Jardins, Aracaju, Sergipe, CEP 49025040, Brazil
| | - Renata Katsuko Takayama Kobayashi
- Laboratório de Bacteriologia Básica E Aplicada, Departamento de Microbiologia, Universidade Estadual de Londrina, Rod. Celso Garcia Cid PR 445 Km 380, Londrina, PR, CEP 86057-970, Brazil
| | - Leonardo Pinto Medeiros
- Laboratório de Bacteriologia Básica E Aplicada, Departamento de Microbiologia, Universidade Estadual de Londrina, Rod. Celso Garcia Cid PR 445 Km 380, Londrina, PR, CEP 86057-970, Brazil
| | - Gerson Nakazato
- Laboratório de Bacteriologia Básica E Aplicada, Departamento de Microbiologia, Universidade Estadual de Londrina, Rod. Celso Garcia Cid PR 445 Km 380, Londrina, PR, CEP 86057-970, Brazil
| | - André Pitondo-Silva
- Universidade de Ribeirão Preto (UNAERP), Avenida Costábile Romano, N° 2201. Bloco J, Lab. 1, Ribeirânia., Ribeirão Preto, SP, CEP 14096-900, Brazil.
| |
Collapse
|
2
|
Ma L, Song Y, Lyu W, Chen Q, Xiao X, Jin Y, Yang H, Wang W, Xiao Y. Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime. Anim Microbiome 2023; 5:55. [PMID: 37941060 PMCID: PMC10634126 DOI: 10.1186/s42523-023-00279-z] [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: 06/20/2023] [Accepted: 11/02/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The dissemination of antibiotic resistance genes (ARGs) poses a substantial threat to environmental safety and human health. Herein, we present a longitudinal paired study across the swine lifetime from birth to market, coupled with metagenomic sequencing to explore the dynamics of ARGs and their health risk in the swine fecal microbiome. RESULTS We systematically characterized the composition and distribution of ARGs among the different growth stages. In total, 829 ARG subtypes belonging to 21 different ARG types were detected, in which tetracycline, aminoglycoside, and MLS were the most abundant types. Indeed, 134 core ARG subtypes were shared in all stages and displayed a growth stage-associated pattern. Furthermore, the correlation between ARGs, gut microbiota and mobile genetic elements (MGEs) revealed Escherichia coli represented the main carrier of ARGs. We also found that in most cases, the dominant ARGs could be transmitted to progeny piglets, suggesting the potential ARGs generation transmission. Finally, the evaluation of the antibiotic resistance threats provides us some early warning of those high health risk ARGs. CONCLUSIONS Collectively, this relatively more comprehensive study provides a primary overview of ARG profile in swine microbiome across the lifetime and highlights the health risk and the intergenerational spread of ARGs in pig farm.
Collapse
Affiliation(s)
- Lingyan Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yuanyuan Song
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wentao Lyu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qu Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xingning Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yuanxiang Jin
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310032, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wen Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yingping Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
3
|
Martín-Valls GE, Li Y, Díaz I, Cano E, Sosa-Portugal S, Mateu E. Diversity of respiratory viruses present in nasal swabs under influenza suspicion in respiratory disease cases of weaned pigs. Front Vet Sci 2022; 9:1014475. [PMID: 36337208 PMCID: PMC9627340 DOI: 10.3389/fvets.2022.1014475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/29/2022] [Indexed: 11/15/2022] Open
Abstract
Respiratory diseases in weaned pigs are a common problem, with a complex etiology involving both viruses and bacteria. In the present study, we investigated the presence of eleven viruses in nasal swabs, collected from nurseries (55 cases) under the suspicion of swine influenza A virus (swIAV) and submitted by swine veterinarians for diagnosis. The other ten viruses included in the study were influenza B (IBV) and D (IDV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcine respiratory coronavirus (PRCV), Porcine cytomegalovirus (PCMV), Porcine circovirus 2 (PCV2), 3 (PCV3) and 4 (PCV), Porcine parainfluenza 1 (PPIV1) and Swine orthopneumovirus (SOV). Twenty-six swIAV-positive cases and twenty-nine cases of swIAV-negative respiratory disease were primarily established. While IBV, IDV, PCV4 and PPIV1 were not found in any of the cases, PRCV, SOV, and PCMV were more likely to be found in swIAV-positive nurseries with respiratory disease (p < 0.05). Overall, PCV3, PRRSV, and PCMV were the most frequently detected agents at herd level. Taken individually, virus prevalence was: swIAV, 48.6%; PRCV, 48.0%; PRRSV, 31.6%; SOV, 33.8%; PCMV, 48.3%, PCV2, 36.0%; and PCV3, 33.0%. Moreover, low Ct values (<30) were common for all agents, except PCV2 and PCV3. When the correlation between pathogens was individually examined, the presence of PRRSV was negatively correlated with swIAV and PRCV, while was positively associated to PCMV (p < 0.05). Also, PRCV and SOV were positively correlated between them and negatively with PCMV. Besides, the analysis of suckling pig samples, collected in subclinically infected farrowing units under an influenza monitoring program, showed that circulation of PRCV, PCMV, SOV, and PCV3 started during the early weeks of life. Interestingly, in those subclinically infected units, none of the pathogens was found to be correlated to any other. Overall, our data may contribute to a better understanding of the complex etiology and epidemiology of respiratory diseases in weaners. This is the first report of SOV in Spain and shows, for the first time, the dynamics of this pathogen in swine farms.
Collapse
Affiliation(s)
- Gerard E. Martín-Valls
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- *Correspondence: Gerard E. Martín-Valls
| | - Yanli Li
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ivan Díaz
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Esmeralda Cano
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Silvana Sosa-Portugal
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Enric Mateu
- Department de Sanitat i Anatomia Animals, Faculty of Veterinària, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| |
Collapse
|
4
|
Toya R, Sasaki Y, Uemura R, Sueyoshi M. Optimizing antimicrobial use by improving medication adherence among pig producers. Anim Sci J 2022; 93:e13713. [PMID: 35417067 DOI: 10.1111/asj.13713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022]
Abstract
In Japan, many pig producers buy antimicrobials using veterinarians' prescriptions. Even if veterinarians prescribe antimicrobials for treatments and metaphylaxis, producers may be using them for prophylaxis on farms with a high incidence of chronic diseases. To reduce the frequency of antimicrobial use, we applied the concept of medication adherence and launched an intervention in eight farrow-to-finish farms. For the intervention farms, we attempted to implement measures for preventing the repeated onset of chronic infections that interfered with adherence, confirmed the need to continue medications, and discontinued medications if possible. For each farm, these interventions began at different time points after 2017 and continued until 2020. We evaluated the effectiveness of this intervention based on the amount of active ingredients/population correction unit and the total number of defined daily doses for the weight group/slaughter pig. The ratio of antimicrobial use for both indicators in the year 2020 compared with the start of the intervention decreased on all farms. Among the eight non-intervention farms, six showed an increase in both indicators. These results suggest that interventions for chronic diseases administered by producers and veterinarians lead to high adherence to prescriptions and responsible and prudent use of antimicrobials on pig farms.
Collapse
Affiliation(s)
- Ryohei Toya
- Production Medicine Center, Agricultural Mutual Aid Association in Miyazaki Prefecture, Miyazaki, Japan.,Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yosuke Sasaki
- Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ryoko Uemura
- Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Masuo Sueyoshi
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan.,Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| |
Collapse
|