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Ke CH, Lai PY, Hsu FY, Hsueh PR, Chiou MT, Lin CN. Antimicrobial susceptibility and resistome of Actinobacillus pleuropneumoniae in Taiwan: a next-generation sequencing analysis. Vet Q 2024; 44:1-13. [PMID: 38688482 PMCID: PMC11064736 DOI: 10.1080/01652176.2024.2335947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
Actinobacillus pleuropneumoniae infection causes a high mortality rate in porcine animals. Antimicrobial resistance poses global threats to public health. The current study aimed to determine the antimicrobial susceptibilities and probe the resistome of A. pleuropneumoniae in Taiwan. Herein, 133 isolates were retrospectively collected; upon initial screening, 38 samples were subjected to next-generation sequencing (NGS). Over the period 2017-2022, the lowest frequencies of resistant isolates were found for ceftiofur, cephalexin, cephalothin, and enrofloxacin, while the highest frequencies of resistant isolates were found for oxytetracycline, streptomycin, doxycycline, ampicillin, amoxicillin, kanamycin, and florfenicol. Furthermore, most isolates (71.4%) showed multiple drug resistance. NGS-based resistome analysis revealed aminoglycoside- and tetracycline-related genes at the highest prevalence, followed by genes related to beta-lactam, sulfamethoxazole, florphenicol, and macrolide. A plasmid replicon (repUS47) and insertion sequences (IS10R and ISVAp11) were identified in resistant isolates. Notably, the multiple resistance roles of the insertion sequence IS10R were widely proposed in human medicine; however, this is the first time IS10R has been reported in veterinary medicine. Concordance analysis revealed a high consistency of phenotypic and genotypic susceptibility to florphenicol, tilmicosin, doxycycline, and oxytetracycline. The current study reports the antimicrobial characterization of A. pleuropneumoniae for the first time in Taiwan using NGS.
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Affiliation(s)
- Chiao-Hsu Ke
- Sustainable Swine Research Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pan-Yun Lai
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Feng-Yang Hsu
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ming-Tang Chiou
- Sustainable Swine Research Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Chao-Nan Lin
- Sustainable Swine Research Center, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Animal Disease Diagnostic Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
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Vilaró A, Karstensen KT, Cavaco LM, Angen Ø, Solé E, Seró I, Novell E, Enrique-Tarancón V, Guitart-Matas J, Migura-Garcia L, Fraile L. An investigation of the transmission of Actinobacillus pleuropneumoniae within vertically integrated systems using whole genome sequencing. Vet Microbiol 2024; 295:110157. [PMID: 38917664 DOI: 10.1016/j.vetmic.2024.110157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/01/2024] [Accepted: 06/16/2024] [Indexed: 06/27/2024]
Abstract
Actinobacillus pleuropneumoniae (APP) causes significant economic losses to the swine industry. Antibiotic treatment can be challenging due to its clinical urgency and the turnover of antimicrobial susceptibility results from the diagnostic laboratory. The aim of this study was to evaluate the vertical transmission of APP within integrated systems as a criterion for optimising antimicrobial treatment in the field, using whole genome sequencing (WGS). Additionally, the genetic variability of Spanish APP isolates has been assessed to decipher antimicrobial resistance (AMR) determinants, toxin presence, serotype, and phenotype/genotype concordance of AMR. A total of 169 isolates from clinical cases of porcine pleuropneumonia with known antimicrobial susceptibility profiles were sequenced. Additionally, 48 NCBI assemblies were included to perform a phylogenetic analysis. Phylogenetic analysis revealed high association between phylogenetic clusters, serotypes, and presence of toxins that are associated within vertically integrated systems by its epidemiological link. Concordance between presence of AMR determinants (genotype) vs in-vitro antimicrobial susceptibility pattern (phenotype) was acceptable for amoxicillin, florfenicol, oxytetracycline, and enrofloxacin using epidemiological cut-off values (ECOFFs), but low concordance was observed for doxycycline and trimethoprim-sulfamethoxazole (T/S). On the other hand, using CLSI clinical breakpoints (CBPs), concordance was acceptable for florfenicol and enrofloxacin and not evaluated for doxycycline, oxytetracycline, trimethoprim-sulfamethoxazole (T/S), and amoxicillin because no CBP are available for them. Finally, WGS has demonstrated the clonality between isolates that shared a common origin (grandmother's farm) and resistance phenotype, suggesting vertical transmission of this pathogen and supporting the use of the epidemiological approach as a good criterion to optimise the antimicrobial use.
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Affiliation(s)
- Anna Vilaró
- Grup de Sanejament Porcí (GSP), Partida Caparrella 97C, Lleida 25192, Spain
| | - Kasper T Karstensen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Lina M Cavaco
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Øystein Angen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Emma Solé
- Grup de Sanejament Porcí (GSP), Partida Caparrella 97C, Lleida 25192, Spain
| | - Ingrid Seró
- Grup de Sanejament Porcí (GSP), Partida Caparrella 97C, Lleida 25192, Spain
| | - Elena Novell
- Grup de Sanejament Porcí (GSP), Partida Caparrella 97C, Lleida 25192, Spain
| | | | - Judith Guitart-Matas
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain; IRTA, Animal Health Program, Animal Health Research Centre (CReSA), Collaborating Centre of the World Organisation for Animal Health for research and control of emerging and re-emerging pig diseases in Europe, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Lourdes Migura-Garcia
- Joint Research Unit IRTA-UAB in Animal Health, Animal Health Research Centre (CReSA), Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain; IRTA, Animal Health Program, Animal Health Research Centre (CReSA), Collaborating Centre of the World Organisation for Animal Health for research and control of emerging and re-emerging pig diseases in Europe, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Lorenzo Fraile
- Department of Animal Science, ETSEA, Universitat de Lleida-AGROTECNIO-CERCA Centre, Lleida 25198, Spain.
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Wang H, Zhang L. Susceptibility evaluation and PK/PD integration of tulathromycin against Actinobacillus pleuropneumoniae during the mutant selection window. Front Vet Sci 2024; 11:1407907. [PMID: 39051006 PMCID: PMC11267949 DOI: 10.3389/fvets.2024.1407907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Actinobacillus pleuropneumoniae (APP) is a serious pathogen that affects the development of livestock breeding. Due to excessive use of antimicrobial drugs, many multidrug-resistant bacteria have emerged and spread, which have threatened the livestock industry. Therefore, we established a peristaltic pump infection model (PPIM) to evaluate the susceptibility change and pharmacokinetic/pharmacodynamic (PK/PD) integration of tulathromycin against APP during the mutant selection window (MSW) for preventing the emergence of mutant-resistant bacteria. Methods The 99% minimum inhibitory concentration (MIC99) and mutant prevention concentration (MPC) of tulathromycin against APP were measured using the agar-plate method. After the model of dynamic infection had been established based on tulathromycin data in lungs, different dosages were administered to make the drug concentrations located in different parts of the MSW. The population and sensitivity of APP were monitored. Tulathromycin concentrations were measured by high-performance liquid chromatography-tandem mass spectrometry. Finally, a sigmoid Emax model was used to analyze the relationships between PK/PD parameters and antibacterial effects. Results and discussion The values of MIC, MIC99, and MPC of tulathromycin against APP were 2, 1.4, and 44.8 μg/mL, respectively. The PPIM was stable. An elimination effect without regrowth was observed at 5.6 to 44.8 μg/mL (-4.48 to -7.05 Log10 CFU/mL, respectively). The MIC of APP increased 32-fold at 8 MIC99. AUC168 h/MIC99 had the best fit with the antibacterial effect (R 2 = 0.9867). The AUC168 h/MIC99 required to achieve bacteriostatic, bactericidal, and clearance effects were 1.80, 87.42, and 198 h, respectively. Our results could provide guidance for the clinical application of tulathromycin to treat APP infection and avoid the generation of drug-resistant bacteria.
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Affiliation(s)
- Hongjuan Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Longfei Zhang
- Institute of Traditional Chinese Veterinary Medicine, College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
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Guarneri F, Romeo C, Scali F, Zoppi S, Formenti N, Maisano AM, Catania S, Gottschalk M, Alborali GL. Serotype diversity and antimicrobial susceptibility profiles of Actinobacillus pleuropneumoniae isolated in Italian pig farms from 2015 to 2022. Vet Res 2024; 55:48. [PMID: 38594744 PMCID: PMC11005290 DOI: 10.1186/s13567-024-01305-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
Actinobacillus pleuropneumoniae (APP) is a bacterium frequently associated with porcine pleuropneumonia. The acute form of the disease is highly contagious and often fatal, resulting in significant economic losses for pig farmers. Serotype diversity and antimicrobial resistance (AMR) of APP strains circulating in north Italian farms from 2015 to 2022 were evaluated retrospectively to investigate APP epidemiology in the area. A total of 572 strains isolated from outbreaks occurring in 337 different swine farms were analysed. The majority of isolates belonged to serotypes 9/11 (39.2%) and 2 (28.1%) and serotype diversity increased during the study period, up to nine different serotypes isolated in 2022. The most common resistances were against tetracycline (53% of isolates) and ampicillin (33%), followed by enrofloxacin, florfenicol and trimethoprim/sulfamethoxazole (23% each). Multidrug resistance (MDR) was common, with a third of isolates showing resistance to more than three antimicrobial classes. Resistance to the different classes and MDR varied significantly depending on the serotype. In particular, the widespread serotype 9/11 was strongly associated with florfenicol and enrofloxacin resistance and showed the highest proportion of MDR isolates. Serotype 5, although less common, showed instead a concerning proportion of trimethoprim/sulfamethoxazole resistance. Our results highlight how the typing of circulating serotypes and the analysis of their antimicrobial susceptibility profile are crucial to effectively manage APP infection and improve antimicrobial stewardship.
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Affiliation(s)
- Flavia Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Claudia Romeo
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy.
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Federico Scali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Simona Zoppi
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle D'Aosta, Turin, Italy
| | - Nicoletta Formenti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Antonio Marco Maisano
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | | | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - G Loris Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
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Ozawa M, Kawano M, Abo H, Issiki Y, Kumakawa M, Kawanishi M, Kojima A, Iwamoto S. Characterization of Actinobacillus pleuropneumoniae isolated from pigs in Japan using whole genome sequencing. Comp Immunol Microbiol Infect Dis 2023; 102:102062. [PMID: 37741218 DOI: 10.1016/j.cimid.2023.102062] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/25/2023]
Abstract
We conducted whole-genome sequencing to investigate the serotypes, the presence of virulence and antimicrobial resistance genes, and the genetic relationships among isolates of Actinobacillus. pleuropneumoniae derived from diseased pigs. Serotype 2 (71.2%) was the most common, but the prevalence of serotypes 6 (13.6%) and 15 (6.8%) increased. Existing vaccines are considered ineffective on the isolates belonging to serotypes 6 and 15. The phylogenetic tree based on core genome single nucleotide polymorphisms showed that the isolates were clustered by serotype. Of the isolates, 62.5% did not have an antimicrobial resistance gene, including a florfenicol resistance gene, but 32.2% had a tetracycline resistance gene. The antimicrobial resistant phenotype and genotype were almost identical. The plasmid-derived contigs harbored resistance genes of aminoglycosides, tetracyclines, β-lactams, phenicols, or sulfonamides. It has been suggested that isolates with different genetic properties from vaccine strains are circulating; however, antimicrobial resistance may not be widespread.
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Affiliation(s)
- Manao Ozawa
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan.
| | - Motoshi Kawano
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Hitoshi Abo
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Yukari Issiki
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Mio Kumakawa
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Michiko Kawanishi
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Akemi Kojima
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan
| | - Shoko Iwamoto
- National Veterinary Assay Laboratory, Ministry of Agriculture, Forestry and Fisheries, 1-15-1, Tokura, Kokubunji, Tokyo 185-8511, Japan
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6
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Zhang L, Wang H, Bai Y, Wang L, Bai Y, Hu J. Evaluation of the mutant selection window of danofloxacin against Actinobacillus pleuropneumoniae in an in vitro dynamic model. Front Vet Sci 2023; 10:1107608. [PMID: 36793382 PMCID: PMC9923107 DOI: 10.3389/fvets.2023.1107608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Introduction The rapid emergence and widespread spread of multidrug-resistant bacteria is a serious threat to the health of humans and animals. The pharmacokinetic/pharmacodynamic (PK/PD) integration model based on mutant selection window (MSW) theory is an important method to optimize the dosage regimen to prevent the emergence and spread of drug-resistant bacteria. Actinobacillus pleuropneumoniae (AP) is a pathogen that can cause pleuropneumonia in pigs. Methods We employed an in vitro dynamic infection model (DIM) to study the prevention of drug-resistant mutations of danofloxacin against AP. A peristaltic pump was applied to establish an in vitro DIM to simulate the PK of danofloxacin in plasma, and to study the MSW of danofloxacin against AP. A peristaltic-pump in vitro infection model was established to simulate dynamic changes in the danofloxacin concentration in pig plasma. PK and PD data were obtained. Then, the relationship between PK/PD parameters and antibacterial activity was analyzed by the sigmoid Emax model. Results and discussion The area under the curve during 24 h/ the minimum concentration that inhibits colony formation by 99% (AUC24h/MIC99) had the best-fitting relationship with antibacterial activity. The AUC24h/MIC99 values for a bacteriostatic effect, bactericidal effect, and eradication effect were 2.68, 33.67, and 71.58 h, respectively. We hope these results can provide valuable guidance when using danofloxacin to treat AP infection.
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Affiliation(s)
- Longfei Zhang
- College of Animal Science and Veterinary Medicine of Henan Institute of Science and Technology, Xinxiang, China
| | - Hongjuan Wang
- College of Animal Science and Veterinary Medicine of Henan Institute of Science and Technology, Xinxiang, China
| | - Yilin Bai
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lei Wang
- College of Animal Science and Veterinary Medicine of Henan Institute of Science and Technology, Xinxiang, China,*Correspondence: Lei Wang ✉
| | - Yueyu Bai
- College of Animal Science and Veterinary Medicine of Henan Institute of Science and Technology, Xinxiang, China,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China,Yueyu Bai ✉
| | - Jianhe Hu
- College of Animal Science and Veterinary Medicine of Henan Institute of Science and Technology, Xinxiang, China,Jianhe Hu ✉
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Revealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing. Microbiol Spectr 2022; 10:e0118522. [PMID: 35856711 PMCID: PMC9430968 DOI: 10.1128/spectrum.01185-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems. IMPORTANCE Pleuropneumonia is one of the most relevant respiratory infections in the swine industry. Despite Actinobacillus pleuropneumoniae (APP) being one of the most important pathogens in the pig production, this is the first comparative study including all available whole genome sequencing data from NCBI. Moreover, this study also includes 16 APP isolates of Spanish origin with known epidemiological relationships through vertical integrated systems. Genomic comparisons provided a deeper understanding of molecular and epidemiological knowledge between different APP serotypes. Furthermore, determination of resistance and toxin profiles allowed correlation with the presence of mobile genetic elements and specific serotype, respectively.
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Li SC, Huang JF, Hung YT, Wu HH, Wang JP, Lin JH, Chen ZW, Hsuan SL. In silico capsule locus typing for serovar prediction of Actinobacillus pleuropneumoniae. Microb Genom 2022; 8:000780. [PMID: 35404221 PMCID: PMC9453067 DOI: 10.1099/mgen.0.000780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 01/16/2022] [Indexed: 12/01/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a causative agent of pleuropneumonia in pigs of all ages. A . pleuropneumoniae is divided into 19 serovars based on capsular polysaccharides (CPSs) and lipopolysaccharides. The serovars of isolates are commonly determined by serological tests and multiplex PCR. This study aimed to develop a genomic approach for in silico A. pleuropneumoniae typing by screening for the presence of the species-specific apxIV gene in whole-genome sequencing (WGS) reads and identifying capsule locus (KL) types in genome assemblies. A database of the A . pleuropneumoniae KL, including CPS synthesis and CPS export genes, was established and optimized for Kaptive. To test the developed genomic approach, WGS reads of 189 A . pleuropneumoniae isolates and those of 66 samples from 14 other bacterial species were analysed. ariba analysis showed that apxIV was detected in all 189 A . pleuropneumoniae samples. These apxIV -positive WGS reads were de novo assembled into genome assemblies and assessed. A total of 105 A . pleuropneumoniae genome assemblies that passed the quality assessment were analysed by Kaptive analysis against the A . pleuropneumoniae KL database. The results showed that 97 assemblies were classified and predicted as 13 serovars, which matched the serovar information obtained from the literature. The six genome assemblies from previously nontypable isolates were typed and predicted as serovars 17 and 18. Notably, one of the two “Actinobacillus porcitonsillarum ” samples was apxIV positive, and its genome assembly was typed as KL03 with high identity and predicted as A . pleuropneumoniae serovar 3. Collectively, a genomic approach was established and could accurately determine the KL type of A . pleuropneumoniae isolates using WGS reads. This approach can be used with high-quality genome assemblies for predicting A . pleuropneumoniae serovars and for retrospective analysis.
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Affiliation(s)
- Siou-Cen Li
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Jing-Fang Huang
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Yu-Ting Hung
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Hsiu-Hui Wu
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Jyh-Perng Wang
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Jiunn-Horng Lin
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Zeng-Weng Chen
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Shih-Ling Hsuan
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC
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9
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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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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2022; 10:80. [PMID: 35847383 PMCID: PMC9243550 DOI: 10.12688/f1000research.39214.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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Affiliation(s)
| | - Marco Fabbri
- European Commission Joint Research Centre, Ispra, Italy
| | | | | | - Guy Van den Eede
- European Commission Joint Research Centre, Ispra, Italy
- European Commission Joint Research Centre, Geel, Belgium
| | - Erik Alm
- The European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Derya Aytan-Aktug
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | | | - Catherine Carrillo
- Ottawa Laboratory – Carling, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | | | - Kok-Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Teresa Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Health Institute, Madrid, Spain
| | | | - Ivo Gut
- Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CNAG-CRG), Barcelona Institute of Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paul Hammer
- BIOMES. NGS GmbH c/o Technische Hochschule Wildau, Wildau, Germany
| | - Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, Lyon, France
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich, UK
| | | | - Thierry Naas
- French-NRC for CPEs, Service de Bactériologie-Hygiène, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | | | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Arthur Pightling
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | | | - John Rossen
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Lukas M. Weber
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
- Present address: Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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11
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Stringer OW, Li Y, Bossé JT, Langford PR. JMM Profile: Actinobacillus pleuropneumoniae: a major cause of lung disease in pigs but difficult to control and eradicate. J Med Microbiol 2022; 71. [PMID: 35262474 PMCID: PMC9176268 DOI: 10.1099/jmm.0.001483] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Gram-negative bacterium Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia in pigs, its only known natural host. Typical symptoms of peracute disease include fever, apathy and anorexia, and time from infection to death may only be 6 h. Severe lung lesions result from presence of one or two of the ApxI-III toxins. Control is through good husbandry practice, vaccines and antibiotic use. Culture and presence of the species-specific apxIV gene by PCR confirms diagnosis, and identification of serovar, of which 19 are known, informs on appropriate vaccine use and epidemiology.
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Affiliation(s)
- Oliver W Stringer
- Department of Infectious Disease, Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London, W2 1PG, UK
| | - Yanwen Li
- Department of Infectious Disease, Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London, W2 1PG, UK
| | - Janine T Bossé
- Department of Infectious Disease, Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London, W2 1PG, UK
| | - Paul R Langford
- Department of Infectious Disease, Section of Paediatric Infectious Disease, Imperial College London, St Mary's Campus, London, W2 1PG, UK
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12
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Donà V, Ramette A, Perreten V. Comparative genomics of 26 complete circular genomes of 18 different serotypes of Actinobacillus pleuropneumoniae. Microb Genom 2022; 8. [PMID: 35196217 PMCID: PMC8942016 DOI: 10.1099/mgen.0.000776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a Gram-negative, rod-shaped bacterium of the family Pasteurellaceae causing pig pleuropneumonia associated with great economic losses worldwide. Nineteen serotypes with distinctive lipopolysaccharide (LPS) and capsular (CPS) compositions have been described so far, yet complete circular genomes are publicly available only for the reference strains of serotypes 1, 4 and 5b, and for field strains of serotypes 1, 3, 7 and 8. We aimed to complete this picture by sequencing the reference strains of 17 different serotypes with the MinION sequencer (Oxford Nanopore Technologies, ONT) and on an Illumina HiSeq (Illumina) platform. We also included two field isolates of serotypes 2 and 3 that were PacBio- and MinION-sequenced, respectively. Genome assemblies were performed following two different strategies, i.e. PacBio- or ONT-only de novo assemblies polished with Illumina reads or a hybrid assembly by directly combining ONT and Illumina reads. Both methods proved successful in obtaining accurate circular genomes with comparable qualities. blast-based genome comparisons and core-genome phylogeny based on core genes, SNP typing and multi-locus sequence typing (cgMLST) of the 26 circular genomes indicated well-conserved genomes across the 18 different serotypes, differing mainly in phage insertions, and CPS, LPS and RTX-toxin clusters, which, consistently, encode serotype-specific antigens. We also identified small antibiotic resistance plasmids, and complete subtype I-F and subtype II-C CRISPR-Cas systems. Of note, highly similar clusters encoding all those serotype-specific traits were also found in other pathogenic and commensal Actinobacillus species. Taken together with the presence of transposable elements surrounding these loci, we speculate a dynamic intra- and interspecies exchange of such virulence-related factors by horizontal gene transfer. In conclusion, our comprehensive genomics analysis provides useful information for diagnostic test and vaccine development, but also for whole-genome-based epidemiological studies, as well as for the surveillance of the evolution of antibiotic resistance and virulence genes in A. pleuropneumoniae.
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Affiliation(s)
- Valentina Donà
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Vincent Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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13
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da Silva GC, Gonçalves OS, Rosa JN, França KC, Bossé JT, Santana MF, Langford PR, Bazzolli DMS. Mobile Genetic Elements Drive Antimicrobial Resistance Gene Spread in Pasteurellaceae Species. Front Microbiol 2022; 12:773284. [PMID: 35069478 PMCID: PMC8777487 DOI: 10.3389/fmicb.2021.773284] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/10/2021] [Indexed: 11/24/2022] Open
Abstract
Mobile genetic elements (MGEs) and antimicrobial resistance (AMR) drive important ecological relationships in microbial communities and pathogen-host interaction. In this study, we investigated the resistome-associated mobilome in 345 publicly available Pasteurellaceae genomes, a large family of Gram-negative bacteria including major human and animal pathogens. We generated a comprehensive dataset of the mobilome integrated into genomes, including 10,820 insertion sequences, 2,939 prophages, and 43 integrative and conjugative elements. Also, we assessed plasmid sequences of Pasteurellaceae. Our findings greatly expand the diversity of MGEs for the family, including a description of novel elements. We discovered that MGEs are comparable and dispersed across species and that they also co-occur in genomes, contributing to the family's ecology via gene transfer. In addition, we investigated the impact of these elements in the dissemination and shaping of AMR genes. A total of 55 different AMR genes were mapped to 721 locations in the dataset. MGEs are linked with 77.6% of AMR genes discovered, indicating their important involvement in the acquisition and transmission of such genes. This study provides an uncharted view of the Pasteurellaceae by demonstrating the global distribution of resistance genes linked with MGEs.
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Affiliation(s)
- Giarlã Cunha da Silva
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Osiel Silva Gonçalves
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Jéssica Nogueira Rosa
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Kiara Campos França
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Janine Thérèse Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Mateus Ferreira Santana
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Paul Richard Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Denise Mara Soares Bazzolli
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
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14
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Cohen LM, Bossé JT, Stegger M, Li Y, Langford PR, Kielland C, Klem TB, Gulliksen SM, Ranheim B, Grøntvedt CA, Angen Ø. Comparative Genome Sequence Analysis of Actinobacillus pleuropneumoniae Serovar 8 Isolates From Norway, Denmark, and the United Kingdom Indicates Distinct Phylogenetic Lineages and Differences in Distribution of Antimicrobial Resistance Genes. Front Microbiol 2021; 12:729637. [PMID: 34566934 PMCID: PMC8461171 DOI: 10.3389/fmicb.2021.729637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Actinobacillus pleuropneumoniae is the etiological agent of porcine pleuropneumonia, a disease of major impact on pig health, welfare, and productivity globally. Serovar 8 (APP) is the predominant clinical serovar in Norway and the United Kingdom (UK), and has been isolated from clinical cases in Denmark. The primary objective of this study was to characterize the genetic variability of isolates of A. pleuropneumoniae APP8 in the Norwegian population. The secondary objectives were to determine the within-host variability of APP8; to compare the APP8 bacterial populations in Norway, Denmark, and the UK, including antimicrobial resistance (AMR) gene profiles and to assess the effect of national differences in antimicrobial drug use and restricted animal movement on the occurrence of resistance. Isolates of APP8 from the UK (n=67), Denmark (n=22), and Norway (n=123) collected between 1983 and 2020 were compared using whole genome sequencing. To investigate genetic variability within individual hosts, an additional 104 APP8 isolates from the lungs of six Norwegian pigs were compared. Very low within-host variation was observed (≤ 2 single nucleotide polymorphisms). The phylogeny of 123 Norwegian APP8 isolates from 76 herds revealed some within-herd genetic variation, but substantial geographical clustering. When inferring the relatedness of the three international APP8 collections, the topology highlighted the existence of two distinct monophyletic branches characterized by the Norwegian and UK isolates, respectively. Three Danish isolates were scattered across the UK branch, whereas the remaining 19 Danish isolates clustered in two monophyletic groups nested in the Norwegian branch. Coalescence analysis, performed to estimate the divergences from a common ancestor, indicated a last common ancestor several centuries ago. The phylogenetic analyses also revealed striking differences in occurrence of AMR genes, as these were 23-times more prevalent among the UK isolates than among the Norwegian isolates. An increased understanding of the effects of population strategies is helpful in surveillance and control of infectious diseases.
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Affiliation(s)
- Liza Miriam Cohen
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Janine T Bossé
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Yanwen Li
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Camilla Kielland
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | | | | | - Birgit Ranheim
- Department of Production Animal Clinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | | | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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15
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Abstract
Neonatal sepsis (NS) kills 750,000 infants every year. Effectively treating NS requires timely diagnosis and antimicrobial therapy matched to the causative pathogens, but most blood cultures for suspected NS do not recover a causative pathogen. We refer to these suspected but unidentified pathogens as microbial dark matter. Given these low culture recovery rates, many non–culture-based technologies are being explored to diagnose NS, including PCR, 16S amplicon sequencing, and whole metagenomic sequencing. However, few of these newer technologies are scalable or sustainable globally. To reduce worldwide deaths from NS, one possibility may be performing population-wide pathogen discovery. Because pathogen transmission patterns can vary across space and time, computational models can be built to predict the pathogens responsible for NS by region and season. This approach could help to optimally treat patients, decreasing deaths from NS and increasing antimicrobial stewardship until effective diagnostics that are scalable become available globally.
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16
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Stringer OW, Bossé JT, Lacouture S, Gottschalk M, Fodor L, Angen Ø, Velazquez E, Penny P, Lei L, Langford PR, Li Y. Proposal of Actinobacillus pleuropneumoniae serovar 19, and reformulation of previous multiplex PCRs for capsule-specific typing of all known serovars. Vet Microbiol 2021; 255:109021. [PMID: 33667982 DOI: 10.1016/j.vetmic.2021.109021] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/22/2021] [Indexed: 02/01/2023]
Abstract
Two serologically and molecularly non-typeable isolates of the porcine lung pathogen Actinobacillus pleuropneumoniae have been identified from diseased swine in two different continents. Genome sequencing was carried out to identify their diagnostically relevant genotypes. Both isolates are biovar 1 and encode genes for production of ApxIV and ApxII (apxIICA structural genes, and apxIBD export genes). They both possess the same novel type II capsule locus (most similar to serovar 1, but with two capsule genes not previously found in A. pleuropneumoniae) but differ in their O-Ag loci. Strain 7213384-1 from Denmark, which we propose as the reference strain for serovar 19, has a serogroup 3/6/8/15 O-Ag locus; the Canadian isolate A08-013 has a serogroup 4/7 O-Ag locus. We have expanded the second of our two previously described A. pleuropneumoniae mPCRs to include capsule gene-specific primers for definitive detection of serovars 13-14 and 16-19.
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Affiliation(s)
- Oliver W Stringer
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, UK
| | - Janine T Bossé
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, UK.
| | - Sonia Lacouture
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - Øystein Angen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Liancheng Lei
- College of Veterinary Medicine, Jilin University, Changchun, PR China
| | - Paul R Langford
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, UK.
| | - Yanwen Li
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, UK
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17
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Guo F, Guo J, Cui Y, Cao X, Zhou H, Su X, Yang B, Blackall PJ, Xu F. Exposure to Sublethal Ciprofloxacin Induces Resistance to Ciprofloxacin and Cross-Antibiotics, and Reduction of Fitness, Biofilm Formation, and Apx Toxin Secretion in Actinobacillus pleuropneumoniae. Microb Drug Resist 2021; 27:1290-1300. [PMID: 33739878 DOI: 10.1089/mdr.2020.0348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Actinobacillus pleuropneumoniae, the etiological agent of porcine pleuropneumonia, is increasingly resistant to antibiotics. However, little is known about the mechanisms of antibiotic resistance in this pathogen. In this study, we experimentally evolved the reference strain of both A. pleuropneumoniae serovar 1 and serovar 7, the most prevalent serovars worldwide, to quinolone resistance by sequential exposure to subinhibitory concentrations of ciprofloxacin. The adaptive ciprofloxacin-resistant mutants of A. pleuropneumoniae serovar 1 and serovar 7 had a minimum inhibitory concentration (MIC) increment from 0.004 to 1 or 2 μg/mL, respectively. Adaptation to ciprofloxacin was shown to confer quinolone resistance with a 32- to 512-fold increase (serovars 1 and 7, respectively) as well as cross-resistance to ampicillin with an increased MIC by 16,384- and 64-fold (serovars 1 and 7, respectively). The genetic analysis of quinolone resistance-determining region mutations showed that substitutions occurred in gyrA (S83A) and parC (D84N) of serovar 1, and gyrA (D87N) of serovar 7. The ciprofloxacin-resistant mutants showed significantly reduced bacterial fitness. The mutants also showed changes in efflux ability and biofilm formation. Notably, the transcription and secretion levels of Apx toxins were dramatically reduced in ciprofloxacin-resistant mutants compared with their wild-type strains. Altogether, these results demonstrated marked phenotypic changes in ciprofloxacin-resistant mutants of A. pleuropneumoniae. The results stress the need for further studies on the impact of both the genotypic and phenotypic characteristics of A. pleuropneumoniae following exposure to subinhibitory concentrations of antibiotics.
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Affiliation(s)
- Fangfang Guo
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jie Guo
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yifang Cui
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaoya Cao
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hongzhuan Zhou
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xia Su
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Bing Yang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Patrick J Blackall
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Australia
| | - Fuzhou Xu
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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18
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Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res 2021; 10:80. [DOI: 10.12688/f1000research.39214.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 01/12/2023] Open
Abstract
Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges remain in demonstrating sufficient trust to act upon the meaningful information produced from raw data, partly because of the reliance on bioinformatics pipelines, which can produce different results and therefore lead to different interpretations. With the constant evolution of the field, it is difficult to identify, harmonise and recommend specific methods for large-scale implementations over time. In this article, we propose to address this challenge through establishing a transparent, performance-based, evaluation approach to provide flexibility in the bioinformatics tools of choice, while demonstrating proficiency in meeting common performance standards. The approach is two-fold: first, a community-driven effort to establish and maintain “live” (dynamic) benchmarking platforms to provide relevant performance metrics, based on different use-cases, that would evolve together with the AMR field; second, agreed and defined datasets to allow the pipelines’ implementation, validation, and quality-control over time. Following previous discussions on the main challenges linked to this approach, we provide concrete recommendations and future steps, related to different aspects of the design of benchmarks, such as the selection and the characteristics of the datasets (quality, choice of pathogens and resistances, etc.), the evaluation criteria of the pipelines, and the way these resources should be deployed in the community.
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19
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Gale C, Velazquez E. Actinobacillus pleuropneumoniae: a review of an economically important pathogen. ACTA ACUST UNITED AC 2020. [DOI: 10.12968/live.2020.25.6.308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Actinobacillus pleuropneumoniae is one of the causative agents of porcine pleuropneumonia, which is an economically important respiratory disease of pig production. Clinical signs vary based on the severity of disease and lung lesions present, but include fever and severe respiratory signs including coughing and laboured breathing. Numerous serotypes exist which vary in their virulence, and virulence of serotypes has also been shown to be vary between countries. It is important to establish which serotypes are present and active on a farm as well as carrying out seroprofiling to determine the correct time for implementation of control measures such as vaccination. Understanding of transmission routes is vital, including the role of carrier animals on the farm which are persistently infected and can shed the bacteria, therefore infecting other animals. Therefore, as with all infectious diseases, good standards of internal and external biosecurity are important in controlling the disease on farm. Vaccination has been shown to be effective on affected farms in preventing outbreaks, reducing clinical signs if they occur, and most important to the farmer, preventing losses in mortality, feed conversion ratio and growth. Therefore, vaccines are often a good choice for controlling pleuropneumonia on farm and reducing the need for treatment using antimicrobials.
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20
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Cao Y, Gao L, Zhang L, Zhou L, Yang J, Deng L, Zhao J, Qi C, Liu J. Genome-wide screening of lipoproteins in Actinobacillus pleuropneumoniae identifies three antigens that confer protection against virulent challenge. Sci Rep 2020; 10:2343. [PMID: 32047221 PMCID: PMC7012816 DOI: 10.1038/s41598-020-58968-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 01/23/2020] [Indexed: 11/24/2022] Open
Abstract
Actinobacillus pleuropneumoniae is an important veterinary pathogen that causes porcine pleuropneumonia. Lipoproteins of bacterial pathogens play pleiotropic roles in the infection process. In addition, many bacterial lipoproteins are antigenic and immunoprotective. Therefore, characterization of lipoproteins is a promising strategy for identification of novel vaccine candidates or diagnostic markers. We cloned 58 lipoproteins from A. pleuropneumoniae JL03 (serovar 3) and expressed them in Escherichia coli. Five proteins with strong positive signals in western blotting analysis were used to immunize mice. These proteins elicited significant antibody responses, and three of them (APJL_0922, APJL_1380 and APJL_1976) generated efficient immunoprotection in mice against lethal heterologous challenge with A. pleuropneumoniae 4074 (serovar 1), both in the active and passive immunization assays. Then immunogenicity of these three lipoproteins (APJL_0922, APJL_1380 and APJL_1976) were further tested in pigs. Results showed that these proteins elicited considerable humoral immune responses and effective protective immunity against virulent A. pleuropneumoniae challenge. Our findings suggest that these three novel lipoproteins could be potential subunit vaccine candidates.
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Affiliation(s)
- Yurou Cao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Lulu Gao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Li Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Lixiang Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Jihong Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Lingfu Deng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Jin Zhao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Chao Qi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
| | - Jinlin Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China.
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21
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Liu Z, Deng D, Lu H, Sun J, Lv L, Li S, Peng G, Ma X, Li J, Li Z, Rong T, Wang G. Evaluation of Machine Learning Models for Predicting Antimicrobial Resistance of Actinobacillus pleuropneumoniae From Whole Genome Sequences. Front Microbiol 2020; 11:48. [PMID: 32117101 PMCID: PMC7016212 DOI: 10.3389/fmicb.2020.00048] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/10/2020] [Indexed: 01/05/2023] Open
Abstract
Antimicrobial resistance (AMR) is becoming a huge problem in countries all over the world, and new approaches to identifying strains resistant or susceptible to certain antibiotics are essential in fighting against antibiotic-resistant pathogens. Genotype-based machine learning methods showed great promise as a diagnostic tool, due to the increasing availability of genomic datasets and AST phenotypes. In this article, Support Vector Machine (SVM) and Set Covering Machine (SCM) models were used to learn and predict the resistance of the five drugs (Tetracycline, Ampicillin, Sulfisoxazole, Trimethoprim, and Enrofloxacin). The SVM model used the number of co-occurring k-mers between the genome of the isolates and the reference genes to learn and predict the phenotypes of the bacteria to a specific antimicrobial, while the SCM model uses a greedy approach to construct conjunction or disjunction of Boolean functions to find the most concise set of k-mers that allows for accurate prediction of the phenotype. Five-fold cross-validation was performed on the training set of the SVM and SCM model to select the best hyperparameter values to avoid model overfitting. The training accuracy (mean cross-validation score) and the testing accuracy of SVM and SCM models of five drugs were above 90% regardless of the resistant mechanism of which were acquired resistant or point mutation in the chromosome. The results of correlation between the phenotype and the model predictions of the five drugs indicated that both SVM and SCM models could significantly classify the resistant isolates from the sensitive isolates of the bacteria (p < 0.01), and would be used as potential tools in antimicrobial resistance surveillance and clinical diagnosis in veterinary medicine.
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Affiliation(s)
- Zhichang Liu
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Dun Deng
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Huijie Lu
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Jian Sun
- National Veterinary Microbiological Drug Resistance Risk Assessment Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Luchao Lv
- National Veterinary Microbiological Drug Resistance Risk Assessment Laboratory, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shuhong Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Guanghui Peng
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Xianyong Ma
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Jiazhou Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Zhenming Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Ting Rong
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
| | - Gang Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science of Ministry of Agriculture (South China), Guangzhou, China.,Guangdong Engineering Technology Research Center of Animal Meat Quality and Safety Control and Evaluation, Guangzhou, China
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22
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Holmer I, Salomonsen CM, Jorsal SE, Astrup LB, Jensen VF, Høg BB, Pedersen K. Antibiotic resistance in porcine pathogenic bacteria and relation to antibiotic usage. BMC Vet Res 2019; 15:449. [PMID: 31829171 PMCID: PMC6907208 DOI: 10.1186/s12917-019-2162-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/29/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Optimal treatment and prudent use of antimicrobials for pigs is imperative to secure animal health and prevent development of critical resistance. An important step in this one-health context is to monitor resistance patterns of important animal pathogens. The aim of this study was to investigate the antimicrobial resistance patterns of five major pathogens in Danish pigs during a period from 2004 to 2017 and elucidate any developments or associations between resistance and usage of antibiotics. RESULTS The minimum inhibitory concentration (MIC) for Escherichia coli, Actinobacillus pleuropneumoniae, Streptococcus suis, Bordetella bronchiseptica, and Staphylococcus hyicus was determined to representatives of antibiotic classes relevant for treatment or surveillance. Escherichia coli isolates were mostly sensitive to fluoroquinolones and colistin, whereas high levels of resistance were observed to ampicillin, spectinomycin, streptomycin, sulfonamides and tetracycline. While resistance levels to most compounds remained relatively stable during the period, resistance to florfenicol increased from 2.1% in 2004 to 18.1% in 2017, likely in response to a concurrent increase in usage. A temporal association between resistance and usage was also observed for neomycin. E. coli serovars O138 and O149 were generally more resistant than O139. For A. pleuropneumoniae, the resistance pattern was homogenous and predictable throughout the study period, displaying high MIC values only to erythromycin whereas almost all isolates were susceptible to all other compounds. Most S. suis isolates were sensitive to penicillin whereas high resistance levels to erythromycin and tetracycline were recorded, and resistance to erythromycin and trimethoprim increasing over time. For S. hyicus, sensitivity to the majority of the antimicrobials tested was observed. However, penicillin resistance was recorded in 69.4-88.9% of the isolates. All B. bronchiseptica isolates were resistant to ampicillin, whereas all but two isolates were sensitive to florfenicol. The data obtained have served as background for a recent formulation of evidence-based treatment guidelines for pigs. CONCLUSIONS Antibiotic resistance varied for some pathogens over time and in response to usage. Resistance to critically important compounds was low. The results emphasize the need for continuous surveillance of resistance patterns also in pig pathogenic bacteria.
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Affiliation(s)
- I Holmer
- Technical University of Denmark, Kemitorvet Building 202, Anker Engelunds Vej 1, DK-2800, Kgs. Lyngby, Denmark
| | | | - S E Jorsal
- Technical University of Denmark, Kemitorvet Building 202, Anker Engelunds Vej 1, DK-2800, Kgs. Lyngby, Denmark
| | - L B Astrup
- Technical University of Denmark, Kemitorvet Building 202, Anker Engelunds Vej 1, DK-2800, Kgs. Lyngby, Denmark
| | - V F Jensen
- Technical University of Denmark, Kemitorvet Building 202, Anker Engelunds Vej 1, DK-2800, Kgs. Lyngby, Denmark
| | - B Borck Høg
- Technical University of Denmark, Kemitorvet Building 202, Anker Engelunds Vej 1, DK-2800, Kgs. Lyngby, Denmark
| | - K Pedersen
- National Veterinary Institute, Ulls väg 2B, 751 89, Uppsala, Sweden.
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23
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Naidenov B, Lim A, Willyerd K, Torres NJ, Johnson WL, Hwang HJ, Hoyt P, Gustafson JE, Chen C. Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia. Front Microbiol 2019; 10:1446. [PMID: 31333599 PMCID: PMC6622151 DOI: 10.3389/fmicb.2019.01446] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 06/07/2019] [Indexed: 01/21/2023] Open
Abstract
The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and E. meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations (MICs) for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies (ONT) and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning (ML) algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84, respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75, and 0.54, respectively. By producing two sets of quality biological predictors, pan-genome genes and core-genome SNPs, from long-read sequence data and applying an ensemble of ML techniques, our results demonstrated that accurate phenotypic inference, at multiple AMR resolutions, can be achieved.
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Affiliation(s)
- Bryan Naidenov
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Alexander Lim
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Karyn Willyerd
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Nathanial J. Torres
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, United States
| | - William L. Johnson
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Hong Jin Hwang
- 110F Henry Bellmon Research Center, Bioinformatics Graduate Certificate Program and Genomics Core Facility, Oklahoma State University, Stillwater, OK, United States
| | - Peter Hoyt
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
- 110F Henry Bellmon Research Center, Bioinformatics Graduate Certificate Program and Genomics Core Facility, Oklahoma State University, Stillwater, OK, United States
| | - John E. Gustafson
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
| | - Charles Chen
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK, United States
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24
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Jiang F, Wu Z, Zheng Y, Frana TS, Sahin O, Zhang Q, Li G. Genotypes and Antimicrobial Susceptibility Profiles of Hemolytic Escherichia coli from Diarrheic Piglets. Foodborne Pathog Dis 2019; 16:94-103. [PMID: 30688527 DOI: 10.1089/fpd.2018.2480] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hemolytic Escherichia coli are important pathogens in neonatal and weaned pigs. In this study, we analyzed 95 hemolytic E. coli isolated from intestinal contents or fecal samples of diarrheic piglets in 15 states of the United States between November 2013 and December 2014. Phenotypic antimicrobial susceptibility was determined through Sensititre BOFO6F plates for all the strains. They were all resistant to clindamycin, penicillin, tiamulin, tilmicosin, and highly resistant to oxytetracycline (91.6%), chlortetracycline (78.9%), ampicillin (75.8%), and sulfadimethoxine (68.4%). 86.2% of them were multidrug resistant. Whole genome sequencing (WGS) showed that 55 strains were enterotoxigenic E. coli (ETEC) and 40 strains were non-ETEC, and the strains belonged to 22 known and 2 novel sequence types (STs). ST100 and ST10 were the main and predominant STs in ETEC strains, whereas the non-ETEC strains were diverse with ST23 and ST761 as the main STs. Antibiotic resistance gene/mutation profiling of the genomes confirmed the results of antimicrobial susceptibility test. Notably, significant differences were found in the susceptibility to enrofloxacin between ETEC and non-ETEC (58.2% vs. 5.0%) and gentamicin (32.7% vs. 7.5%). ampH, ampC2, and ampC1 were the most common beta-lactamase genes in all E. coli strains, and extended-spectrum beta-lactamase (ESBL) genes were rare in these isolates. This study provides new insights into antibiotic resistance and genotypes of intestinal pathogenic E. coli associated with swine disease in the United States, and support the utility of WGS in accurate prediction of resistance to most antibiotics.
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Affiliation(s)
- Fengwei Jiang
- 1 Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Zuowei Wu
- 3 Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Ying Zheng
- 2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Timothy S Frana
- 2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Orhan Sahin
- 2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Qijing Zhang
- 3 Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa
| | - Ganwu Li
- 1 Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,2 Department of Veterinary Diagnostic and Production Animal Medicine and College of Veterinary Medicine, Iowa State University, Ames, Iowa
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25
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Abstract
Members of the highly heterogeneous family Pasteurellaceae cause a wide variety of diseases in humans and animals. Antimicrobial agents are the most powerful tools to control such infections. However, the acquisition of resistance genes, as well as the development of resistance-mediating mutations, significantly reduces the efficacy of the antimicrobial agents. This article gives a brief description of the role of selected members of the family Pasteurellaceae in animal infections and of the most recent data on the susceptibility status of such members. Moreover, a review of the current knowledge of the genetic basis of resistance to antimicrobial agents is included, with particular reference to resistance to tetracyclines, β-lactam antibiotics, aminoglycosides/aminocyclitols, folate pathway inhibitors, macrolides, lincosamides, phenicols, and quinolones. This article focusses on the genera of veterinary importance for which sufficient data on antimicrobial susceptibility and the detection of resistance genes are currently available (Pasteurella, Mannheimia, Actinobacillus, Haemophilus, and Histophilus). Additionally, the role of plasmids, transposons, and integrative and conjugative elements in the spread of the resistance genes within and beyond the aforementioned genera is highlighted to provide insight into horizontal dissemination, coselection, and persistence of antimicrobial resistance genes. The article discusses the acquisition of diverse resistance genes by the selected Pasteurellaceae members from other Gram-negative or maybe even Gram-positive bacteria. Although the susceptibility status of these members still looks rather favorable, monitoring of their antimicrobial susceptibility is required for early detection of changes in the susceptibility status and the newly acquired/developed resistance mechanisms.
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26
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Passmore IJ, Andrejeva A, Wren BW, Cuccui J. Cytoplasmic glycoengineering of Apx toxin fragments in the development of Actinobacillus pleuropneumoniae glycoconjugate vaccines. BMC Vet Res 2019; 15:6. [PMID: 30606265 PMCID: PMC6318927 DOI: 10.1186/s12917-018-1751-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Actinobacillus pleuropneumoniae is the causative agent of porcine pleuropneumonia and represents a major burden to the livestock industry. Virulence can largely be attributed to the secretion of a series of haemolytic toxins, which are highly immunogenic. A. pleuropneumoniae also encodes a cytoplasmic N-glycosylation system, which involves the modification of high molecular weight adhesins with glucose residues. Central to this process is the soluble N-glycosyl transferase, ngt, which is encoded in an operon with a subsequent glycosyl transferase, agt. Plasmid-borne recombinant expression of these genes in E. coli results in the production of a glucose polymer on peptides containing the appropriate acceptor sequon, NX(S/T). However to date, there is little evidence to suggest that such a glucose polymer is formed on its target peptides in A. pleuropneumoniae. Both the toxins and glycosylation system represent potential targets for the basis of a vaccine against A. pleuropneumoniae infection. RESULTS In this study, we developed cytoplasmic glycoengineering to construct glycoconjugate vaccine candidates composed of soluble toxin fragments modified by glucose. We transferred ngt and agt to the chromosome of Escherichia coli in order to generate a native-like operon for glycoengineering. A single chromosomal copy of ngt and agt resulted in the glucosylation of toxin fragments by a short glycan, rather than a polymer. CONCLUSIONS A vaccine candidate that combines toxin fragment with a conserved glycan offers a novel approach to generating epitopes important for both colonisation and disease progression.
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Affiliation(s)
- Ian J Passmore
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Anna Andrejeva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jon Cuccui
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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27
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Li Y, da Silva GC, Li Y, Rossi CC, Fernandez Crespo R, Williamson SM, Langford PR, Bazzolli DMS, Bossé JT. Evidence of Illegitimate Recombination Between Two Pasteurellaceae Plasmids Resulting in a Novel Multi-Resistance Replicon, pM3362MDR, in Actinobacillus pleuropneumoniae. Front Microbiol 2018; 9:2489. [PMID: 30405558 PMCID: PMC6206304 DOI: 10.3389/fmicb.2018.02489] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022] Open
Abstract
Evidence of plasmids carrying the tetracycline resistance gene, tet(B), was found in the previously reported whole genome sequences of 14 United Kingdom, and 4 Brazilian, isolates of Actinobacillus pleuropneumoniae. Isolation and sequencing of selected plasmids, combined with comparative sequence analysis, indicated that the four Brazilian isolates all harbor plasmids that are nearly identical to pB1001, a plasmid previously found in Pasteurella multocida isolates from Spain. Of the United Kingdom isolates, 13/14 harbor plasmids that are (almost) identical to pTetHS016 from Haemophilus parasuis. The remaining United Kingdom isolate, MIDG3362, harbors a 12666 bp plasmid that shares extensive regions of similarity with pOV from P. multocida (which carries blaROB-1 , sul2, and strAB genes), as well as with pTetHS016. The newly identified multi-resistance plasmid, pM3362MDR, appears to have arisen through illegitimate recombination of pTetHS016 into the stop codon of the truncated strB gene in a pOV-like plasmid. All of the tet(B)-carrying plasmids studied were capable of replicating in Escherichia coli, and predicted origins of replication were identified. A putative origin of transfer (oriT) sequence with similar secondary structure and a nic-site almost identical to that of RP4 was also identified in these plasmids, however, attempts to mobilize them from an RP4-encoding E. coli donor strain were not successful, indicating that specific conjugation machinery may be required.
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Affiliation(s)
- Yinghui Li
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom.,Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Giarlã Cunha da Silva
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Ciro C Rossi
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
| | - Denise Mara Soares Bazzolli
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, London, United Kingdom
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28
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Li Y, Li Y, Fernandez Crespo R, Leanse LG, Langford PR, Bossé JT. Characterization of the Actinobacillus pleuropneumoniae SXT-related integrative and conjugative element ICEApl2 and analysis of the encoded FloR protein: hydrophobic residues in transmembrane domains contribute dynamically to florfenicol and chloramphenicol efflux. J Antimicrob Chemother 2018; 73:57-65. [PMID: 29029160 PMCID: PMC5890775 DOI: 10.1093/jac/dkx342] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/23/2017] [Indexed: 11/29/2022] Open
Abstract
Objectives To characterize ICEApl2, an SXT-related integrative and conjugative element (ICE) found in a clinical isolate of the porcine pathogen Actinobacillus pleuropneumoniae, and analyse the functional nature of the encoded FloR. Methods ICEApl2 was identified in the genome of A. pleuropneumoniae MIDG3553. Functional analysis was done using conjugal transfer experiments. MIDG3553 was tested for susceptibility to the antimicrobials for which resistance genes are present in ICEApl2. Lack of florfenicol/chloramphenicol resistance conferred by the encoded FloR protein was investigated by cloning and site-directed mutagenesis experiments in Escherichia coli. Results ICEApl2 is 92660 bp and contains 89 genes. Comparative sequence analysis indicated that ICEApl2 is a member of the SXT/R391 ICE family. Conjugation experiments showed that, although ICEApl2 is capable of excision from the chromosome, it is not self-transmissible. ICEApl2 encodes the antimicrobial resistance genes floR, strAB, sul2 and dfrA1, and MIDG3553 is resistant to streptomycin, sulfisoxazole and trimethoprim, but not florfenicol or chloramphenicol. Cloning and site-directed mutagenesis of the floR gene revealed the importance of the nature of the hydrophobic amino acid residues at positions 160 and 228 in FloR for determining resistance to florfenicol and chloramphenicol. Conclusions Our results indicate that the nature of hydrophobic residues at positions 160 and 228 of FloR contribute dynamically to specific efflux of florfenicol and chloramphenicol, although some differences in resistance levels may depend on the bacterial host species. This is also, to our knowledge, the first description of an SXT/R391 ICE in A. pleuropneumoniae or any member of the Pasteurellaceae.
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Affiliation(s)
- Yinghui Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK.,Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Roberto Fernandez Crespo
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Leon G Leanse
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
| | - Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, St Mary's Campus, London, UK
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29
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Hoeltig D, Rohde J, Brunner B, Hellmann K, Grandemange E, Waldmann KH. Efficacy of a one-shot marbofloxacin treatment on acute pleuropneumonia after experimental aerosol inoculation of nursery pigs. Porcine Health Manag 2018; 4:13. [PMID: 29977591 PMCID: PMC6013868 DOI: 10.1186/s40813-018-0089-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/29/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Porcine pleuropneumonia, caused by Actinobacillus pleuropneumoniae, is a bacterial respiratory disease of swine. Acute outbreaks of the disease are often accompanied by high mortality and economic losses. As severe cases of the disease frequently require parenteral antibiotic treatment of the animals, the efficacy of a single, high dose of marbofloxacin was compared to a three-time application of a dose of enrofloxacin under experimental conditions. METHODS A blinded, controlled, randomized and blocked dose confirmation study was conducted to test the efficacy and safety of a single dose of 8 mg/kg marbofloxacin (160 mg/ml, Forcyl® Swine, Vetoquinol SA, France) to treat acute porcine pleuropneumonia after experimental aerosol inoculation of pigs with A. pleuropneumoniae serotype 2. The results were compared to a three consecutive day treatment of 2.5 mg/kg enrofloxacin and a mock (saline) treatment. Criteria for the assessment of efficacy were severity of lung lesions, bacteriological cure and the course of clinical disease after treatment. RESULTS Thirty six nursery pigs were divided into three treatment groups: marbofloxacin (T1), enrofloxacin (T2) and mock (T3). Statistically significant superiority (p < 0.05) of marbofloxacin and enrofloxacin compared to the mock-treated group was demonstrated for all efficacy criteria. The need of rescue euthanasia due to severity of symptoms was significantly reduced in both treatment groups (T1: 1 pig; T2: 0 pigs; vs. T3: 8 pigs). On day 6 after treatment initiation, clinical cure was observed in 10 (T1), 10 (T2) but only 1 of the piglets in T3. Extent of lung lesions (mean of lung lesion score T1: 3.9, T2: 6.0, T3: 21.1) and bacteriological isolation from lung tissue (on day 6 after treatment initiation: T1 = 0 pigs; T2 = 1 pig; T3 = all pigs) were also significantly reduced within both treatment groups. There were no adverse events linked to the drug administration and no injection site reactions were observed. CONCLUSIONS Both applied antimicrobial treatments were proven safe and efficacious for the treatment of acute porcine pleuropneumonia. No statistically significant differences were detected between the antibiotic treatments.
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Affiliation(s)
- Doris Hoeltig
- Clinic for Swine, Small Ruminants, forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany
| | - Judith Rohde
- Institute for Microbiology, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany
| | - Birgit Brunner
- Klifovet AG, Geyerspergerstr. 27, D-80689 Munich, Germany
| | - Klaus Hellmann
- Klifovet AG, Geyerspergerstr. 27, D-80689 Munich, Germany
| | - Erik Grandemange
- Vetoquinol SA, Research and Development Centre, B.P. 189, Cedex 70204 Lure, France
| | - Karl-Heinz Waldmann
- Clinic for Swine, Small Ruminants, forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Foundation, Bischofsholer Damm 15, D-30173 Hannover, Germany
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Oniciuc EA, Likotrafiti E, Alvarez-Molina A, Prieto M, Santos JA, Alvarez-Ordóñez A. The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain. Genes (Basel) 2018; 9:E268. [PMID: 29789467 PMCID: PMC5977208 DOI: 10.3390/genes9050268] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 05/14/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.
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Affiliation(s)
- Elena A Oniciuc
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati 800008, Romania.
| | - Eleni Likotrafiti
- Laboratory of Food Microbiology, Department of Food Technology, Alexander Technological Educational Institute of Thessaloniki, Thessaloniki T.K. 57400, Greece.
| | - Adrián Alvarez-Molina
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Miguel Prieto
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Jesús A Santos
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain.
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Activation of Porcine Alveolar Macrophages by Actinobacillus pleuropneumoniae Lipopolysaccharide via the Toll-Like Receptor 4/NF-κB-Mediated Pathway. Infect Immun 2018; 86:IAI.00642-17. [PMID: 29229731 DOI: 10.1128/iai.00642-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/01/2017] [Indexed: 12/17/2022] Open
Abstract
Actinobacillus pleuropneumoniae is the causative agent of porcine contagious pleuropneumonia. Overproduction of proinflammatory cytokines, like interleukin-1β (IL-1β), IL-6, tumor necrosis factor alpha, and resistin, in the lung is an important feature of A. pleuropneumoniae infection. These proinflammatory cytokines enhance inflammatory and immunological responses. However, the mechanism that leads to cytokine production remains unclear. As a major virulence factor of A. pleuropneumoniae, lipopolysaccharide (LPS) may act as a potent stimulator of Toll-like receptor 4 (TLR4), triggering a number of intracellular signaling pathways that lead to the synthesis of proinflammatory cytokines. Porcine alveolar macrophages (PAMs) are the first line of defense against pathogenic microbes during pathogen invasion. The results of the present study demonstrate that A. pleuropneumoniae LPS induces PAMs to produce inflammatory cytokines in time- and dose-dependent manners. Moreover, PAMs were activated by A. pleuropneumoniae LPS, resulting in upregulation of signaling molecules, including TLR4, MyD88, TRIF-related adaptor molecule, and NF-κB. In contrast, the activation effects of A. pleuropneumoniae LPS on PAMs could be suppressed by specific inhibitors, like small interfering RNA and Bay11-7082. Taken together, our data indicate that A. pleuropneumoniae LPS can induce PAMs to produce proinflammatory cytokines via the TLR4/NF-κB-mediated pathway. These findings partially reveal the mechanism of the overproduction of proinflammatory cytokines in the lungs of swine with A. pleuropneumoniae infection and may provide targets for the prevention of A. pleuropneumoniae-induced pneumonia. All the data could be used as a reference for the pathogenesis of respiratory infection.
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Bossé JT, Li Y, Sárközi R, Fodor L, Lacouture S, Gottschalk M, Casas Amoribieta M, Angen Ø, Nedbalcova K, Holden MTG, Maskell DJ, Tucker AW, Wren BW, Rycroft AN, Langford PR. Proposal of serovars 17 and 18 of Actinobacillus pleuropneumoniae based on serological and genotypic analysis. Vet Microbiol 2018; 217:1-6. [PMID: 29615241 PMCID: PMC5901230 DOI: 10.1016/j.vetmic.2018.02.019] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/15/2018] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
Identification of two new serovars of Actinobacillus pleuropneumoniae. Serological confirmation of specific reactivity with homologous antisera. Characterization of the capsule loci of serovars 17 and 18. Development of PCRs for molecular diagnostics.
The aim of this study was to investigate isolates of Actinobacillus pleuropneumoniae previously designated serologically either as non-typable (NT) or as ‘K2:07’, which did not produce serovar-specific amplicons in PCR assays. We used whole genome sequencing to identify the capsule (CPS) loci of six previously designated biovar 1 NT and two biovar 1 ‘K2:O7’ isolates of A. pleuropneumoniae from Denmark, as well as a recent biovar 2 NT isolate from Canada. All of the NT isolates have the same six-gene type I CPS locus, sharing common cpsABC genes with serovars 2, 3, 6, 7, 8, 9, 11 and 13. The two ‘K2:O7’ isolates contain a unique three-gene type II CPS locus, having a cpsA gene similar to that of serovars 1, 4, 12, 14 and 15. The previously NT isolates share the same O-antigen genes, found between erpA and rpsU, as serovars 3, 6, 8, and 15. Whereas the ‘K2:O7’ isolates, have the same O-antigen genes as serovar 7, which likely contributed to their previous mis-identification. All of the NT and ‘K2:O7’ isolates have only the genes required for production of ApxII (apxIICA structural genes, and apxIBD export genes). Rabbit polyclonal antisera raised against representative isolates with these new CPS loci demonstrated distinct reactivity compared to the 16 known serovars. The serological and genomic results indicate that the isolates constitute new serovars 17 (previously NT) and 18 (previously ‘K2:O7’). Primers designed for amplification of specific serovar 17 and 18 sequences for molecular diagnostics will facilitate epidemiological tracking of these two new serovars of A. pleuropneumoniae.
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Affiliation(s)
- Janine T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, UK.
| | - Yanwen Li
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, UK
| | - Rita Sárközi
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
| | - Sonia Lacouture
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, Québec, Canada
| | | | - Øystein Angen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Alexander W Tucker
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Brendan W Wren
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrew N Rycroft
- Department of Pathology and Pathogen Biology, The Royal Veterinary College, Hawkshead Campus, UK
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, St. Mary's Campus, London, UK
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Yee S, Blackall PJ, Turni C. Genetic diversity and toxin gene distribution among serovars ofActinobacillus pleuropneumoniaefrom Australian pigs. Aust Vet J 2018; 96:17-23. [DOI: 10.1111/avj.12660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 11/29/2022]
Affiliation(s)
- S Yee
- EcoSciences Precinct, Queensland Alliance for Agriculture and Food Innovation; The University of Queensland; Boggo Road Dutton Park Queensland 4102 Australia
| | - PJ Blackall
- EcoSciences Precinct, Queensland Alliance for Agriculture and Food Innovation; The University of Queensland; Boggo Road Dutton Park Queensland 4102 Australia
| | - C Turni
- EcoSciences Precinct, Queensland Alliance for Agriculture and Food Innovation; The University of Queensland; Boggo Road Dutton Park Queensland 4102 Australia
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Bujold AR, Shure AE, Liu R, Kropinski AM, MacInnes JI. Investigation of putative invasion determinants of Actinobacillus species using comparative genomics. Genomics 2018; 111:59-66. [PMID: 29317305 DOI: 10.1016/j.ygeno.2018.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/13/2017] [Accepted: 01/02/2018] [Indexed: 11/24/2022]
Abstract
Actinobacillus spp. are Gram-negative bacteria associated with mucosal membranes. While some are commensals, others can cause important human and animal diseases. A. pleuropneumoniae causes severe fibrinous hemorrhagic pneumonia in swine but not systemic disease whereas other species invade resulting in septicemia and death. To understand the invasive phenotype of Actinobacillus spp., complete genomes of eight isolates were obtained and pseudogenomes of five isolates were assembled and annotated. Phylogenetically, A. suis isolates clustered by surface antigen type and were more closely related to the invasive A. ureae, A. equuli equuli, and A. capsulatus than to the other swine pathogen, A. pleuropneumoniae. Using the LS-BSR pipeline, 251 putative virulence genes associated with serum resistance and invasion were detected. To our knowledge, this is the first genome-wide study of the genus Actinobacillus and should contribute to a better understanding of host tropism and mechanisms of invasion of pathogenic Actinobacillus and related genera.
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Affiliation(s)
- Adina R Bujold
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada.
| | - Andrew E Shure
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada
| | - Rui Liu
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada
| | - Janet I MacInnes
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, 50 Stone Road East, Guelph N1G 2W1, Ontario, Canada.
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35
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Sassu EL, Bossé JT, Tobias TJ, Gottschalk M, Langford PR, Hennig-Pauka I. Update on Actinobacillus pleuropneumoniae-knowledge, gaps and challenges. Transbound Emerg Dis 2017; 65 Suppl 1:72-90. [PMID: 29083117 DOI: 10.1111/tbed.12739] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 12/15/2022]
Abstract
Porcine pleuropneumonia, caused by the bacterial porcine respiratory tract pathogen Actinobacillus pleuropneumoniae, leads to high economic losses in affected swine herds in most countries of the world. Pigs affected by peracute and acute disease suffer from severe respiratory distress with high lethality. The agent was first described in 1957 and, since then, knowledge about the pathogen itself, and its interactions with the host, has increased continuously. This is, in part, due to the fact that experimental infections can be studied in the natural host. However, the fact that most commercial pigs are colonized by this pathogen has hampered the applicability of knowledge gained under experimental conditions. In addition, several factors are involved in development of disease, and these have often been studied individually. In a DISCONTOOLS initiative, members from science, industry and clinics exchanged their expertise and empirical observations and identified the major gaps in knowledge. This review sums up published results and expert opinions, within the fields of pathogenesis, epidemiology, transmission, immune response to infection, as well as the main means of prevention, detection and control. The gaps that still remain to be filled are highlighted, and present as well as future challenges in the control of this disease are addressed.
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Affiliation(s)
- E L Sassu
- Department of Pathobiology, Institute of Immunology, University of Veterinary Medicine, Vienna, Austria
| | - J T Bossé
- Section of Paediatrics, Department of Medicine, Imperial College London, London, UK
| | - T J Tobias
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M Gottschalk
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - P R Langford
- Section of Paediatrics, Department of Medicine, Imperial College London, London, UK
| | - I Hennig-Pauka
- Field Station for Epidemiology, University of Veterinary Medicine Hannover, Foundation, Bakum, Germany
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Xie F, Wang Y, Li G, Liu S, Cui N, Liu S, Langford PR, Wang C. The SapA Protein Is Involved in Resistance to Antimicrobial Peptide PR-39 and Virulence of Actinobacillus pleuropneumoniae. Front Microbiol 2017; 8:811. [PMID: 28539918 PMCID: PMC5423912 DOI: 10.3389/fmicb.2017.00811] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/20/2017] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial peptides are essential to the innate immune defense of the mammal against bacterial infection. However, pathogenic bacteria have evolved multiple strategies to resist and evade antimicrobial peptides, which is vital to bacterial survival and colonization in hosts. PR-39 is a linear porcine antimicrobial peptide containing 39 amino acid residues with a high proline content. Resistance to antimicrobial peptide PR-39 has been observed in Actinobacillus pleuropneumoniae. However, little is known about the factors required for this resistance. In the present study, PR-39 exposure increased the expression of the sapA gene in A. pleuropneumoniae. The sapA gene, which encodes a putative peptide transport periplasmic protein, was deleted from this bacterium. The ΔsapA mutant showed increased sensitivity to PR-39 compared to the wild-type MD12 and complemented PΔsapA strains. However, the ΔsapA mutant did not exhibit any alterations in outer membrane integrity. Scanning electron microscopy showed that the ΔsapA mutant displayed morphological defects, as indicated by a deformed and sunken shape after PR-39 treatment. In addition, disruption of the SapA protein led to reduced colonization and attenuated virulence of A. pleuropneumoniae in the BALB/c mouse model. Collectively, these data suggest that SapA acts as one mechanism for A. pleuropneumoniae to counteract PR-39-mediated killing. To the best of our knowledge, this is the first study to show a mechanism underlying antimicrobial peptide resistance in A. pleuropneumoniae.
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Affiliation(s)
- Fang Xie
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesHarbin, China
| | - Yalei Wang
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesHarbin, China.,Shanghai Veterinary Research Institute, Chinese Academy of Agricultural SciencesShanghai, China
| | - Gang Li
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesHarbin, China
| | - Shuanghong Liu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesHarbin, China
| | - Ning Cui
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesHarbin, China
| | - Siguo Liu
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesHarbin, China
| | - Paul R Langford
- Section of Paediatrics, Department of Medicine, Imperial College LondonLondon, UK
| | - Chunlai Wang
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural SciencesHarbin, China
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