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Bogomazova A, Krylova E, Soltynskaya I, Prasolova O, Ivanova O. In silico analysis to develop PCR assays for identification of bacterial pathogens in animals: what can we improve? Front Vet Sci 2023; 10:1235837. [PMID: 37645677 PMCID: PMC10461052 DOI: 10.3389/fvets.2023.1235837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Affiliation(s)
- Alexandra Bogomazova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), Moscow, Russia
- Laboratory of Cell Biology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of FMBA of Russia (Lopukhin FRCC PCM), Moscow, Russia
| | - Ekaterina Krylova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), Moscow, Russia
| | - Irina Soltynskaya
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), Moscow, Russia
| | - Olga Prasolova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), Moscow, Russia
| | - Olga Ivanova
- Department of Molecular Biology, Russian State Center for Quality and Standardization of Veterinary Drugs and Feed (VGNKI), Moscow, Russia
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Rao J, Wei X, Li H, Zhang Z, Liu J, Lian M, Cao W, Yuan L, Dou B, Tian Y, Chen H, Li J, Bei W. Novel Multiplex PCR Assay and Its Application in Detecting Prevalence and Antibiotic Susceptibility of Porcine Respiratory Bacterial Pathogens in Guangxi, China. Microbiol Spectr 2023; 11:e0397122. [PMID: 36916923 PMCID: PMC10100844 DOI: 10.1128/spectrum.03971-22] [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: 10/08/2022] [Accepted: 01/27/2023] [Indexed: 03/15/2023] Open
Abstract
Porcine respiratory disease complex (PRDC) is a serious disease caused by multiple pathogens which inflicts huge economic losses on the pig industry. Investigating the epidemiology of porcine respiratory bacterial pathogens (PRBPs) in specific geographic areas and exploring the antibiotic susceptibility of local strains will contribute to the prevention and control of PRDC. However, the epidemiology of PRBPs in Guangxi Province remains unclear, and existing diagnostic methods have multiple limitations, such as high costs and the detection of only a single pathogen at a time. In this study, we developed a multiplex PCR assay for Streptococcus suis, Glaesserella parasuis, Actinobacillus pleuropneumoniae, Pasteurella multocida, and Mycoplasma hyopneumoniae, and investigated the prevalence of PRBPs in pigs with respiratory symptoms in Guangxi Province. The isolates from positive samples were subjected to susceptibility tests to 16 antibiotics. Our results indicated that of the 664 samples from pigs with respiratory symptoms, 433 (65.21%), 320 (48.19%), 282 (42.47%), 23 (3.46%), and 9 (1.36%), respectively, carried each of these 5 pathogens; 533 samples were positive; and 377 (56.78%) carried multiple pathogens simultaneously. The dominant PRBPs in pigs with respiratory symptoms in Guangxi province were S. suis, G. parasuis, and A. pleuropneumoniae, which frequently co-infected swine herds. Most of the isolates (A. pleuropneumoniae, G. parasuis, S. suis, and P. multocida) were sensitive to cefquinome, ceftiofur, trimethoprim-sulfamethoxazole (TMP-SMX), and tiamulin antibiotics. We developed a rapid specific multiplex PCR assay for PRBPs. Our findings provide new information on the epidemiology of PRBPs in Guangxi Province and offer a reference for developing drug targets against PRDC. IMPORTANCE Pigs are closely associated with humans as the most common food animals and the vectors of numerous pathogens. PRDC, caused by multiple pathogens, is a serious disease that can cause growth retardation in swine and even sudden death. Due to the droplet transmission of PRBP and the similar clinical signs of different pathogen infections, most pig farms struggle to identify and control PRBPs, leading to the abuse of antibiotics. In addition, some PRBPs have the potential to infect humans and threaten human health. Therefore, this study developed a multiplex PCR method targeting PRBPs, investigated the prevalence of these pathogens, and tested their antibiotic susceptibility. Our studies have important implications for public health safety and the development of the pig industry.
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Affiliation(s)
- Jing Rao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xinchen Wei
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Huan Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zhewei Zhang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jiahui Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Mengjie Lian
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Weiwei Cao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Long Yuan
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Beibei Dou
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yanhong Tian
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Weicheng Bei
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Yi L, Jin M, Gao M, Wang H, Fan Q, Grenier D, Sun L, Wang S, Wang Y. Specific quantitative detection of Streptococcus suis and Actinobacillus pleuropneumoniae in co-infection and mixed biofilms. Front Cell Infect Microbiol 2022; 12:898412. [PMID: 35992166 PMCID: PMC9381733 DOI: 10.3389/fcimb.2022.898412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory infections seriously affect the swine industry worldwide. Co-infections of two vital pathogenic bacteria Streptococcus suis (S. suis) and Actinobacillus pleuropneumoniae (A. pleuropneumoniae), colonizing the respiratory tract often occurs in veterinary clinical practice. Moreover, our previous research found that S. suis and A. pleuropneumoniae can form biofilm in vitro. The formation of a mixed biofilm not only causes persistent infections, but also increases the multiple drug resistance of bacteria, which brings difficulties to disease prevention and control. However, the methods for detecting S. suis and A. pleuropneumoniae in co-infection and biofilm are immature. Therefore, in this study, primers and probes were designed based on the conservative sequence of S. suis gdh gene and A. pleuropneumoniae apxIVA gene. Then, a TaqMan duplex real-time PCR method for simultaneous detection of S. suis and A. pleuropneumoniae was successfully established via optimizing the reaction system and conditions. The specificity analysis results showed that this TaqMan real-time PCR method had strong specificity and high reliability. The sensitivity test results showed that the minimum detection concentration of S. suis and A. pleuropneumoniae recombinant plasmid was 10 copies/μL, which is 100 times more sensitive than conventional PCR methods. The amplification efficiencies of S. suis and A. pleuropneumoniae were 95.9% and 104.4% with R2 value greater than 0.995, respectively. The slopes of the calibration curves of absolute cell abundance of S. suis and A. pleuropneumoniae were 1.02 and 1.09, respectively. The assays were applied to cultivated mixed biofilms and approximately 108 CFUs per biofilm were quantified when 108 CFUs planktonic bacteria of either S. suis or A. pleuropneumoniae were added to biofilms. In summary, this study developed a TaqMan real-time PCR assay for specific, accurate quantification of S. suis or A. pleuropneumoniae in mixed biofilms, which may help for the detection, prevention and control of diseases caused by a bacterial mixed infection involving S. suis and A. pleuropneumoniae.
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Affiliation(s)
- Li Yi
- College of Life Science, Luoyang Normal University, Luoyang, China
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Manyu Jin
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Mengxia Gao
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Haikun Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Qingying Fan
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Daniel Grenier
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de Médecine Dentaire, Université Laval, Quebec City, QC, Canada
| | - Liyun Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Shaohui Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Yang Wang, ; Shaohui Wang,
| | - Yang Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
- *Correspondence: Yang Wang, ; Shaohui Wang,
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Stringer OW, Li Y, Bossé JT, Forrest MS, Hernandez-Garcia J, Tucker AW, Nunes T, Costa F, Mortensen P, Velazquez E, Penny P, Rodriguez-Manzano J, Georgiou P, Langford PR. Rapid Detection of Actinobacillus pleuropneumoniae From Clinical Samples Using Recombinase Polymerase Amplification. Front Vet Sci 2022; 9:805382. [PMID: 35400111 PMCID: PMC8990124 DOI: 10.3389/fvets.2022.805382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/25/2022] [Indexed: 11/30/2022] Open
Abstract
Actinobacillus pleuropneumoniae (APP) is the causative agent of porcine pleuropneumonia, resulting in high economic impact worldwide. There are currently 19 known serovars of APP, with different ones being predominant in specific geographic regions. Outbreaks of pleuropneumonia, characterized by sudden respiratory difficulties and high mortality, can occur when infected pigs are brought into naïve herds, or by those carrying different serovars. Good biosecurity measures include regular diagnostic testing for surveillance purposes. Current gold standard diagnostic techniques lack sensitivity (bacterial culture), require expensive thermocycling machinery (PCR) and are time consuming (culture and PCR). Here we describe the development of an isothermal point-of-care diagnostic test - utilizing recombinase polymerase amplification (RPA) for the detection of APP, targeting the species-specific apxIVA gene. Our APP-RPA diagnostic test achieved a sensitivity of 10 copies/μL using a strain of APP serovar 8, which is the most prevalent serovar in the UK. Additionally, our APP-RPA assay achieved a clinical sensitivity and specificity of 84.3 and 100%, respectively, across 61 extracted clinical samples obtained from farms located in England and Portugal. Using a small subset (n = 14) of the lung tissue samples, we achieved a clinical sensitivity and specificity of 76.9 and 100%, respectively) using lung imprints made on FTA cards tested directly in the APP-RPA reaction. Our results demonstrate that our APP-RPA assay enables a suitable rapid and sensitive screening tool for this important veterinary pathogen.
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Affiliation(s)
- Oliver W. Stringer
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Yanwen Li
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Janine T. Bossé
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Juan Hernandez-Garcia
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Tiago Nunes
- Ceva Animal Health Ltd., Saúde Animal, Algés, Portugal
| | | | | | | | - Paul Penny
- Ceva Animal Health Ltd., Amersham, United Kingdom
| | - Jesus Rodriguez-Manzano
- Section of Adult Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Imperial College London, London, United Kingdom
| | - Paul R. Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
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