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Zhang Y, Liang S, Zhang S, Bai Q, Dai L, Wang J, Yao H, Zhang W, Liu G. Streptococcal arginine deiminase system defences macrophage bactericidal effect mediated by XRE family protein XtrSs. Virulence 2024; 15:2306719. [PMID: 38251714 PMCID: PMC10841013 DOI: 10.1080/21505594.2024.2306719] [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: 07/30/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
The arginine deiminase system (ADS) has been identified in various bacteria and functions to supplement energy production and enhance biological adaptability. The current understanding of the regulatory mechanism of ADS and its effect on bacterial pathogenesis is still limited. Here, we found that the XRE family transcriptional regulator XtrSs negatively affected Streptococcus suis virulence and significantly repressed ADS transcription when the bacteria were incubated in blood. Electrophoretic mobility shift (EMSA) and lacZ fusion assays further showed that XtrSs directly bind to the promoter of ArgR, an acknowledged positive regulator of bacterial ADS, to repress ArgR transcription. Moreover, we provided compelling evidence that S. suis could utilize arginine via ADS to adapt to acid stress, while ΔxtrSs enhanced this acid resistance by upregulating the ADS operon. Moreover, whole ADS-knockout S. suis increased arginine and antimicrobial NO in the infected macrophage cells, decreased intracellular survival, and even caused significant attenuation of bacterial virulence in a mouse infection model, while ΔxtrSs consistently presented the opposite results. Our experiments identified a novel ADS regulatory mechanism in S. suis, whereby XtrSs regulated ADS to modulate NO content in macrophages, promoting S. suis intracellular survival. Meanwhile, our findings provide a new perspective on how Streptococci evade the host's innate immune system.
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Affiliation(s)
- Yumin Zhang
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Song Liang
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shidan Zhang
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Qiankun Bai
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Lei Dai
- Hainan Animal Disease Prevention and Control Center, Haikou, China
| | - Jinxiu Wang
- Hainan Animal Disease Prevention and Control Center, Haikou, China
| | - Huochun Yao
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wei Zhang
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Guangjin Liu
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Hatrongjit R, Fittipaldi N, Gottschalk M, Kerdsin A. Genomic epidemiology in Streptococcus suis: Moving beyond traditional typing techniques. Heliyon 2024; 10:e27818. [PMID: 38509941 PMCID: PMC10951601 DOI: 10.1016/j.heliyon.2024.e27818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/12/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
Streptococcus suis is a bacterial gram-positive pathogen that causes invasive infections in swine and is also a zoonotic disease agent. Traditional molecular typing techniques such as ribotyping, multilocus sequence typing, pulse-field gel electrophoresis, or randomly amplified polymorphic DNA have been used to investigate S. suis population structure, evolution, and genetic relationships and support epidemiological and virulence investigations. However, these traditional typing techniques do not fully reveal the genetically heterogeneous nature of S. suis strains. The high-resolution provided by whole-genome sequencing (WGS), which is now more affordable and more commonly available in research and clinical settings, has unlocked the exploration of S. suis genetics at full resolution, permitting the determination of population structure, genetic diversity, identification of virulent clades, genetic markers, and other bacterial features of interest. This approach will likely become the new gold standard for S. suis strain typing as WGS instruments become more widely available and traditional typing techniques are gradually replaced.
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Affiliation(s)
- Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nahuel Fittipaldi
- GREMIP, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada
| | - Marcelo Gottschalk
- GREMIP, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
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3
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Dechêne-Tempier M, de Boisséson C, Lucas P, Bougeard S, Libante V, Marois-Créhan C, Payot S. Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France. Microb Genom 2024; 10:001224. [PMID: 38536216 PMCID: PMC10995628 DOI: 10.1099/mgen.0.001224] [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: 11/16/2023] [Accepted: 03/08/2024] [Indexed: 04/07/2024] Open
Abstract
Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.
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Affiliation(s)
- Manon Dechêne-Tempier
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
| | - Claire de Boisséson
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Pierrick Lucas
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Génétique Virale et Biosécurité, BP53 22440 Ploufragan, France
| | - Stéphanie Bougeard
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Épidémiologie, santé et bien-être, BP53 22440 Ploufragan, France
| | | | - Corinne Marois-Créhan
- Anses Laboratoire de Ploufragan-Plouzané-Niort, Unité Mycoplasmologie, Bactériologie et Antibiorésistance, BP53 22440 Ploufragan, France
| | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, F-54000 Nancy, France
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Sedano SA, Cantalejo MGCT, Lapitan CGAR, de Guzman AMES, Consignado JT, Tandang NA, Estacio MAC, Kerdsin A, Silva BBI. Epidemiology and genetic diversity of Streptococcus suis in smallhold swine farms in the Philippines. Sci Rep 2023; 13:21178. [PMID: 38040767 PMCID: PMC10692119 DOI: 10.1038/s41598-023-48406-9] [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: 08/29/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023] Open
Abstract
This study aimed to determine the presence and characteristics of locally circulating strains of Streptococcus suis, the most important streptococcal pathogen in swine. Oral swab samples were collected from pigs from 664 representative smallhold farms across nine provinces in the Philippines. Isolates were identified and characterized using PCR assays. The study revealed an isolation rate of 15.8% (105/664, 95% CI: 13.0-18.6) among the sampled farms. Two hundred sixty-nine (269) S. suis isolates were recovered from 119 unique samples. Serotype 31 was the most prevalent (50/269, 95% CI: 13.9-23.2) among the other serotypes identified: 5, 6, 8, 9, 10, 11, 15, 16, 17, 21, 27, 28, and 29. The detection of the three 'classical' S. suis virulence-associated genes showed that 90.7% (244/269, 95% CI: 87.2-94.2) were mrp-/epf-/sly-. Multilocus sequence typing (MLST) analysis further revealed 70 novel sequence types (STs). Notably, several local isolates belonging to these novel STs formed clonal complexes (CC) with S. suis strains recovered from Spain and USA, which are major pork-exporting countries to the Philippines. This study functionally marks the national baseline knowledge of S. suis in Philippines.
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Affiliation(s)
- Susan A Sedano
- Veterinary Vaccines Laboratory, National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines.
| | - Mary Grace Concepcion T Cantalejo
- Veterinary Vaccines Laboratory, National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Christine Grace Angela R Lapitan
- Veterinary Vaccines Laboratory, National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
- Ecosystem Services and Environmental Policy Laboratory, School of Environmental Science and Management, University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Angelo Miguel Elijah S de Guzman
- Veterinary Vaccines Laboratory, National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
- Department of Agrarian Reform, Elliptical Road, Diliman, 1107, Quezon City, Philippines
| | - Jennielyn T Consignado
- Veterinary Vaccines Laboratory, National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Nancy A Tandang
- Institute of Statistics, College of Arts and Sciences, University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Maria Amelita C Estacio
- Department of Basic Veterinary Sciences, College of Veterinary Medicine, University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Benji Brayan Ilagan Silva
- Veterinary Vaccines Laboratory, National Institute of Molecular Biology and Biotechnology (BIOTECH), University of the Philippines Los Baños, 4031, Los Baños, Laguna, Philippines.
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Murray GGR, Hossain ASMM, Miller EL, Bruchmann S, Balmer AJ, Matuszewska M, Herbert J, Hadjirin NF, Mugabi R, Li G, Ferrando ML, Fernandes de Oliveira IM, Nguyen T, Yen PLK, Phuc HD, Zaw Moe A, Su Wai T, Gottschalk M, Aragon V, Valentin-Weigand P, Heegaard PMH, Vrieling M, Thein Maw M, Thidar Myint H, Tun Win Y, Thi Hoa N, Bentley SD, Clavijo MJ, Wells JM, Tucker AW, Weinert LA. The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs. Proc Natl Acad Sci U S A 2023; 120:e2307773120. [PMID: 37963246 PMCID: PMC10666105 DOI: 10.1073/pnas.2307773120] [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: 05/22/2023] [Accepted: 10/02/2023] [Indexed: 11/16/2023] Open
Abstract
The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.
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Affiliation(s)
- Gemma G. R. Murray
- Department of Genetics, Evolution and Environment, University College London, LondonWC1E 6BT, United Kingdom
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | | | - Eric L. Miller
- Department of Biology, Haverford College, Haverford, PA19041
| | - Sebastian Bruchmann
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Andrew J. Balmer
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Marta Matuszewska
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Department of Medicine, University of Cambridge, CambridgeCB2 2QQ, United Kingdom
| | - Josephine Herbert
- Centre for Enzyme Innovation, University of Portsmouth, PortsmouthPO1 2DD, United Kingdom
| | - Nazreen F. Hadjirin
- Nuffield Department of Population Health, University of Oxford, OxfordOX3 7LF, United Kingdom
| | - Robert Mugabi
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Ganwu Li
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Maria Laura Ferrando
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | | | - Thanh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phung L. K. Yen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Aung Zaw Moe
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Thiri Su Wai
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, QuébecJ2S 2M2, Canada
| | - Virginia Aragon
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona, Barcelona08193, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Barcelona08193, Spain
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover30559, Germany
| | - Peter M. H. Heegaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Manouk Vrieling
- Wageningen Bioveterinary Research, 8221 RALelystad, The Netherlands
| | - Min Thein Maw
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | | | - Ye Tun Win
- Livestock Breeding and Veterinary Department, Yangon, Myanmar
| | - Ngo Thi Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7LG, United Kingdom
- Microbiology Department and Center for Tropical Medicine Research, Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, CambridgeCB10 1RQ, United Kingdom
| | - Maria J. Clavijo
- College of Veterinary Medicine, Iowa State University, Ames, IA50011
| | - Jerry M. Wells
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
- Animal Sciences Department, Wageningen University, 6700 AHWageningen, The Netherlands
| | - Alexander W. Tucker
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, CambridgeCB3 0ES, United Kingdom
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Nicholson TL, Kalalah AA, Eppinger M. Population structure and genetic diversity of Streptococcus suis isolates obtained from the United States. Front Microbiol 2023; 14:1250265. [PMID: 37808309 PMCID: PMC10551183 DOI: 10.3389/fmicb.2023.1250265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
Diseases caused by the zoonotic pathogen Streptococcus suis are an extensive economic problem as well as an animal welfare concern for the global swine industry. Previous studies have evaluated the genomic diversity and population structure of S. suis isolates, however, the majority of these studies utilized isolates obtained from countries other than the U.S. This study applied whole genome sequencing and cgMLST-based typing to evaluate the population structure and genetic relatedness among S. suis isolates obtained within the U.S. The established high-resolution phylogenomic framework revealed extensive genomic variation and diversity among the sampled S. suis isolates, with isolates from the U.S. and from countries outside the U.S. found interspersed in the phylogeny. S. suis isolates obtained within the U.S. did not cluster by state or geographic location, however, isolates with similar serotypes, both obtained from within and outside the U.S., generally clustered together. Average nucleotide identity (ANI) values determined for the S. suis genomes were extensively broad, approaching the recommended species demarcation value, and correlated with the phylogenetic group distribution of the cgMLST-based tree. Numerous antimicrobial resistance (AMR) elements were identified among both U.S. and non-U.S. isolates with ble, tetO, and ermB genes identified as the most prevalent. The epf, mrp, and sly genes, historically used as markers for virulence potential, were also observed in the genomes of isolates that grouped together forming a subclade of clonal complex 1 (CC1) isolates. Collectively, the data in this report provides critical information needed to address potential biosurveillance needs and insights into the genetic diversity and population structure of S. suis isolates obtained within the U.S.
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Affiliation(s)
- Tracy L. Nicholson
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Anwar A. Kalalah
- South Texas Center for Emerging Infectious Diseases (STCEID), The University of Texas at San Antonio, San Antonio, TX, United States
- Department of Molecular Microbiology and Immunology (MMI), The University of Texas at San Antonio, San Antonio, TX, United States
| | - Mark Eppinger
- South Texas Center for Emerging Infectious Diseases (STCEID), The University of Texas at San Antonio, San Antonio, TX, United States
- Department of Molecular Microbiology and Immunology (MMI), The University of Texas at San Antonio, San Antonio, TX, United States
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Hatrongjit R, Boueroy P, Jenjaroenpun P, Wongsurawat T, Meekhanon N, Chopjitt P, Zheng H, Fittipaldi N, Chareonsudjai S, Segura M, Gottschalk M, Kerdsin A. Genomic characterization and virulence of Streptococcus suis serotype 4 clonal complex 94 recovered from human and swine samples. PLoS One 2023; 18:e0288840. [PMID: 37498866 PMCID: PMC10374156 DOI: 10.1371/journal.pone.0288840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023] Open
Abstract
Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Herein, we performed genomic analysis of seven S. suis serotype 4 strains belonging to clonal complex (CC) 94 that were recovered from a human patient or from diseased and clinically healthy pigs. Genomic exploration and comparisons, as well as in vitro cytotoxicity tests, indicated that S. suis CC94 serotype 4 strains are potentially virulent. Genomic analysis revealed that all seven strains clustered within minimum core genome group 3 (MCG-3) and had a high number of virulence-associated genes similar to those of virulent serotype 2 strains. Cytotoxicity assays showed that both the human lung adenocarcinoma cell line and HeLa cells rapidly lost viability following incubation for 4 h with the strains at a concentration of 106 bacterial cells. The human serotype 4 strain (ID36054) decreased cell viability profoundly and similarly to the control serotype 2 strain P1/7. In addition, strain ST1689 (ID34572), isolated from a clinically healthy pig, presented similar behaviour in an adenocarcinoma cell line and HeLa cells. The antimicrobial resistance genes tet(O) and ermB that confer resistance to tetracyclines, macrolides, and lincosamides were commonly found in the strains. However, aminoglycoside and streptothricin resistance genes were found only in certain strains in this study. Our results indicate that S. suis CC94 serotype 4 strains are potentially pathogenic and virulent and should be monitored.
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Affiliation(s)
- Rujirat Hatrongjit
- Faculty of Science and Engineering, Department of General Sciences, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Piroon Jenjaroenpun
- Faculty of Medicine Siriraj Hospital, Department of Research and Development, Division of Bioinformatics and Data Management for Research, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Faculty of Medicine Siriraj Hospital, Department of Research and Development, Division of Bioinformatics and Data Management for Research, Mahidol University, Bangkok, Thailand
| | - Nattakan Meekhanon
- Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Han Zheng
- National Institute for Communicable Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Nahuel Fittipaldi
- Faculty of Veterinary Medicine, Research Group on Infectious Diseases in Production Animals (GREMIP), University of Montreal, Quebec, Canada
| | - Sorujsiri Chareonsudjai
- Faculty of Medicine, Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Mariela Segura
- Faculty of Veterinary Medicine, Research Group on Infectious Diseases in Production Animals (GREMIP), University of Montreal, Quebec, Canada
| | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, Research Group on Infectious Diseases in Production Animals (GREMIP), University of Montreal, Quebec, Canada
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
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Kerdsin A, Bamphensin N, Sittichottumrong K, Ungcharoen R, Boueroy P, Chopjitt P, Hatrongjit R, Gottschalk M, Sunthamala N. Evaluation of pathotype marker genes in Streptococcus suis isolated from human and clinically healthy swine in Thailand. BMC Microbiol 2023; 23:133. [PMID: 37193946 DOI: 10.1186/s12866-023-02888-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Streptococcus suis is a zoonotic pathogen that causes substantial economic losses in the pig industry and contributes to human infections worldwide, especially in Southeast Asia. Recently, a multiplex polymerase chain reaction (PCR) process was developed to distinguish disease-associated and non-disease-associated pathotypes of S. suis European strains. Herein, we evaluated the ability of this multiplex PCR approach to distinguish pathotypes of S. suis in Thailand. RESULTS This study was conducted on 278 human S. suis isolates and 173 clinically healthy pig S. suis isolates. PCR identified 99.3% of disease-associated strains in the human isolates and 11.6% of non-disease-associated strains in the clinically healthy pig isolates. Of the clinically healthy pig S. suis isolates, 71.1% were classified as disease-associated. We also detected undetermined pathotype forms in humans (0.7%) and pigs (17.3%). The PCR assay classified the disease-associated isolates into four types. Statistical analysis revealed that human S. suis clonal complex (CC) 1 isolates were significantly associated with the disease-associated type I, whereas CC104 and CC25 were significantly associated with the disease-associated type IV. CONCLUSION Multiplex PCR cannot differentiate non-disease-associated from disease-associated isolates in Thai clinically healthy pig S. suis strains, although the method works well for human S. suis strains. This assay should be applied to pig S. suis strains with caution. It is highly important that multiplex PCR be validated using more diverse S. suis strains from different geographic areas and origins of isolation.
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Nichari Bamphensin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Kulsatri Sittichottumrong
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Ratchadaporn Ungcharoen
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon, Province Campus, Sakon Nakhon, 47000, Thailand
| | - Marcelo Gottschalk
- Groupe de recherche sur les maladies infectieuses en production animale (GREMIP), The Swine and Poultry Infectious Diseases Research Centre (CRIPA), Faculty of Veterinary Medicine, University of Montreal, Québec, Canada
| | - Nuchsupha Sunthamala
- Department of Biology, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand.
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9
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Hatrongjit R, Fittipaldi N, Jenjaroenpun P, Wongsurawat T, Visetnan S, Zheng H, Gottschalk M, Kerdsin A. Genomic comparison of two Streptococcus suis serotype 1 strains recovered from porcine and human disease cases. Sci Rep 2023; 13:5380. [PMID: 37009816 PMCID: PMC10068604 DOI: 10.1038/s41598-023-32724-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 03/31/2023] [Indexed: 04/04/2023] Open
Abstract
Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 strains are most prevalent worldwide, other serotypes are also occasionally detected. Herein, we investigated the genomes of two S. suis serotype 1 strains belonging to the clonal complex 1, which were recovered from a human patient and an asymptomatic pig, respectively. The genomes differed in pathotype, virulence-associated gene (VAG) profile, minimum core genome (MCG) typing, and antimicrobial resistance gene content. The porcine serotype 1 strain was sequence type (ST) 237 and MCG1, whereas the human serotype 1 strain was ST105 and MCG ungroupable. Both strains were susceptible to several antibiotics consisting of β-lactams, fluoroquinolones, and chloramphenicol. Resistance to tetracycline, macrolides, and clindamycin was observed, which was attributed to the genes tet(O) and erm(B). Analysis of 99 VAG revealed Hhly3, NisK, NisR, salK/salR, srtG, virB4, and virD4 were absent in both serotype 1. However, the porcine strain lacked sadP (Streptococcal adhesin P), whereas the human strain harbored sadP1. Phylogenetic analysis revealed that human S. suis ST105 strains from Vietnam were genetically the closest to the human serotype 1 strain, whereas porcine S. suis ST11 strains from China and Thailand were genetically the closest to the porcine strain.
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Affiliation(s)
- Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand.
| | - Nahuel Fittipaldi
- GREMIP, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Suwattana Visetnan
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping, Beijing, China
| | - Marcelo Gottschalk
- GREMIP, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, 47000, Thailand.
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10
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Nicholson TL, Bayles DO. Comparative virulence and antimicrobial resistance distribution of Streptococcus suis isolates obtained from the United States. Front Microbiol 2022; 13:1043529. [PMID: 36439859 PMCID: PMC9687383 DOI: 10.3389/fmicb.2022.1043529] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/25/2022] [Indexed: 09/29/2023] Open
Abstract
Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry worldwide. Most S. suis genome sequences available in public databases are from isolates obtained outside the United States. We sequenced the genomes of 106 S. suis isolates from the U.S. and analyzed them to identify their potential to function as zoonotic agents and/or reservoirs for antimicrobial resistance (AMR) dissemination. The objective of this study was to evaluate the genetic diversity of S. suis isolates obtained within the U.S., for the purpose of screening for genomic elements encoding AMR and any factors that could increase or contribute to the capacity of S. suis to transmit, colonize, and/or cause disease in humans. Forty-six sequence types (STs) were identified with ST28 observed as the most prevalent, followed by ST87. Of the 23 different serotypes identified, serotype 2 was the most prevalent, followed by serotype 8 and 3. Of the virulence genes analyzed, the highest nucleotide diversity was observed in sadP, mrp, and ofs. Tetracycline resistance was the most prevalent phenotypic antimicrobial resistance observed followed by macrolide-lincosamide-streptogramin B (MLSB) resistance. Numerous AMR elements were identified, many located within MGE sequences, with the highest frequency observed for ble, tetO and ermB. No genes encoding factors known to contribute to the transmission, colonization, and/or causation of disease in humans were identified in any of the S. suis genomes in this study. This includes the 89 K pathogenicity island carried by the virulent S. suis isolates responsible for human infections. Collectively, the data reported here provide a comprehensive evaluation of the genetic diversity among U.S. S. suis isolates. This study also serves as a baseline for determining any potential risks associated with occupational exposure to these bacteria, while also providing data needed to address public health concerns.
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Affiliation(s)
- Tracy L. Nicholson
- National Animal Disease Center, Agricultural Research Service (USDA), Ames, IA, United States
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11
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K V V, Gangwar P, Chaturji Thakor J, Dinesh M, Sahoo M, Singh R, Mahajan S, Qureshi S, Laddika L, Ranjan Sahoo N, K De U. Carrier status of Streptococcus suis in the palatine tonsils of apparently healthy slaughtered pigs of India. J Immunoassay Immunochem 2022; 43:557-578. [PMID: 35354365 DOI: 10.1080/15321819.2022.2048011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Streptococcus suis is an emerging bacterial pathogen of huge economic impact to the swine industry worldwide. The information regarding the carrier status of S. suis in the slaughtered pigs along with its genetic characterization is not available in Indian pig population, which needs to be addressed for the therapeutic and preventive measures. In the present study, 563 palatine tonsils of apparently healthy slaughtered pigs were probed for the prevalence, and genetic characterization of S. suis and prevalence were found to be 15.45% and 32.68% by bacteriological and molecular methods, respectively. In 87 isolates recovered, 6 cps-types were detected showing the predominance of serotype 7 (24.13%) and 5 (18.39%), whereas 11 cps-types were detected in tonsillar DNA involving cps-types 9 (28.26%) and 7 (14.13%) as the major serotypes with arcA+/sly+/epf+/mrp- being the prevalent genotype. The histopathological changes with the immunodetection of S. suis antigen confirmed its persistence in asymptomatic carriers. Of 87 bacterial isolates, 7 isolates (serotypes 7 & 2) were pathogenic to Swiss albino mice showing the classical lesions of meningitis and septicemia. The presence of virulent serotypes of S. suis in healthy slaughtered pigs suggests a great health risk to the people engaged in piggery operations and in-contact pigs.
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Affiliation(s)
- Vishva K V
- Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Pradeep Gangwar
- Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | | | - Murali Dinesh
- Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Monalisa Sahoo
- Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India.,International Center for Foot and Mouth Disease, ICAR-DFMD, Arugul, Khordha, India
| | - Rajendra Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Sonalika Mahajan
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Salauddin Qureshi
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Lahari Laddika
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
| | - Nihar Ranjan Sahoo
- International Center for Foot and Mouth Disease, ICAR-DFMD, Arugul, Khordha, India
| | - Ujjawal K De
- Division of Medicine, ICAR-Indian Veterinary Research Institute (IVRI), Izatnagar, India
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12
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Estrada AA, Gottschalk M, Gebhart CJ, Marthaler DG. Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates. Vet Res 2022; 53:23. [PMID: 35303917 PMCID: PMC8932342 DOI: 10.1186/s13567-022-01039-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/17/2022] [Indexed: 11/10/2022] Open
Abstract
Streptococcus suis is a significant economic and welfare concern in the swine industry. Pan-genome analysis provides an in-silico approach for the discovery of genes involved in pathogenesis in bacterial pathogens. In this study, we performed pan-genome analysis of 208 S. suis isolates classified into the pathogenic, possibly opportunistic, and commensal pathotypes to identify novel candidate virulence-associated genes (VAGs) of S. suis. Using chi-square tests and LASSO regression models, three accessory pan-genes corresponding to S. suis strain P1/7 markers SSU_RS09525, SSU_RS09155, and SSU_RS03100 (>95% identity) were identified as having a significant association with the pathogenic pathotype. The proposed novel SSU_RS09525 + /SSU_RS09155 + /SSU_RS03100 + genotype identified 96% of the pathogenic pathotype strains, suggesting a novel genotyping scheme for predicting the pathogenicity of S. suis isolates in North America. In addition, mobile genetic elements carrying antimicrobial resistance genes (ARGs) and VAGs were identified but did not appear to play a major role in the spread of ARGs and VAGs.
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Affiliation(s)
- April A Estrada
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA.
| | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Connie J Gebhart
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
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13
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Kerdsin A, Hatrongjit R, Wongsurawat T, Jenjaroenpun P, Chopjitt P, Boueroy P, Fittipaldi N, Zheng H, Gottschalk M. Genomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients. Front Microbiol 2022; 12:812436. [PMID: 35003043 PMCID: PMC8733411 DOI: 10.3389/fmicb.2021.812436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 is prevalent among patient and swine infections, other serotypes are occasionally detected in humans. Of these, serotype 24 clonal complex (CC) 221/234 are recognized as emerging clones of human infection. Genomic exploration of three S. suis serotype 24 CC221/234 strains revealed antimicrobial resistance genes, pathotyping, virulence-associated gene (VAG) profiles, minimum core genome (MCG) typing, and comparison of the genomes. Based on these analyzes, all three serotype 24 strains were MCG7-3 and should be classified in the intermediate/weakly virulent (I/WV) group. All selected serotype 24 strains were susceptible to several antibiotics including β-lactam, fluoroquinolone, and chloramphenicol. Resistance to tetracycline, macrolide, and clindamycin was observed and attributed to the genes tet(O) and erm(B). Genomic comparison revealed the strains S12X, LSS66, LS0L, LS0E, 92–4,172, and IMT40201 that had phylogenetic affinity with serotype 24 CC221/234. Analysis of 80 virulence-associated genes (VAG) showed that all three serotype 24 strains lacked 24 genes consisting of adhesin P, epf, hyl, ihk, irr, mrp, nadR, neuB, NisK/R, ofs, permease (SSU0835), rgg, revS, salK/R, sao, sly, spyM3_0908, srtBCD, srtF, srtG, SSU05_0473, virA, virB4, and virD4. Eleven specific sequences were identified in the 3 serotype 24 genomes that differed from the genomes of the representative strains of epidemic (E; SC84), highly virulent (HV; P1/7), I/WV (89–1,591), and avirulent (T15 and 05HAS68).
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nahuel Fittipaldi
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Marcelo Gottschalk
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
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14
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Cucco L, Paniccià M, Massacci FR, Morelli A, Ancora M, Mangone I, Di Pasquale A, Luppi A, Vio D, Cammà C, Magistrali CF. New Sequence Types and Antimicrobial Drug-Resistant Strains of Streptococcus suis in Diseased Pigs, Italy, 2017-2019. Emerg Infect Dis 2022; 28:139-147. [PMID: 34932464 PMCID: PMC8714200 DOI: 10.3201/eid2801.210816] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Streptococcus suis is a pathogen associated with severe diseases in pigs and humans. Human infections have a zoonotic origin in pigs. To assess circulating strains, we characterized the serotypes, sequence types, and antimicrobial susceptibility of 78 S. suis isolates from diseased farmed pigs in Italy during 2017-2019. Almost 60% of infections were caused by serotypes 1/2 and 9. All but 1 of the serotype 2 and 1/2 isolates were confined to a single cluster, and serotype 9 isolates were distributed along the phylogenetic tree. Besides sequence type (ST) 1, the serotype 2 cluster included ST7, which caused severe human infections in China in 1998 and 2005. A large proportion of serotype 9 isolates, assigned to ST123, were resistant to penicillin. The emergence of this clone threatens the successful treatment of S. suis infection. Characterizing S. suis isolates from pigs will promote earlier detection of emerging clones.
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15
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Aradanas M, Poljak Z, Fittipaldi N, Ricker N, Farzan A. Serotypes, Virulence-Associated Factors, and Antimicrobial Resistance of Streptococcus suis Isolates Recovered From Sick and Healthy Pigs Determined by Whole-Genome Sequencing. Front Vet Sci 2021; 8:742345. [PMID: 34796225 PMCID: PMC8593187 DOI: 10.3389/fvets.2021.742345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/23/2021] [Indexed: 11/20/2022] Open
Abstract
Streptococcus suis is ubiquitous in swine, and yet, only a small percentage of pigs become clinically ill. The objective of this study was to describe the distribution of serotypes, virulence-associated factor (VAF), and antimicrobial resistance (AMR) genes in S. suis isolates recovered from systemic (blood, meninges, spleen, and lymph node) and non-systemic (tonsil, nasal cavities, ileum, and rectum) sites of sick and healthy pigs using whole-genome sequencing. In total, 273 S. suis isolates recovered from 112 pigs (47 isolates from systemic and 136 from non-systemic sites of 65 sick pigs; 90 isolates from non-systemic sites of 47 healthy pigs) on 17 Ontario farms were subjected to whole-genome sequencing. Using in silico typing, 21 serotypes were identified with serotypes 9 (13.9%) and 2 (8.4%) as the most frequent serotypes, whereas 53 (19.4%) isolates remained untypable. The relative frequency of VAF genes in isolates from systemic (Kruskal–Wallis, p < 0.001) and non-systemic (Kruskal–Wallis, p < 0.001) sites in sick pigs was higher compared with isolates from non-systemic sites in healthy pigs. Although many VAF genes were abundant in all isolates, three genes, including dltA [Fisher's test (FT), p < 0.001], luxS (FT, p = 0.01), and troA (FT, p = 0.02), were more prevalent in isolates recovered from systemic sites compared with non-systemic sites of pigs. Among the isolates, 98% had at least one AMR gene, and 79% had genes associated with at least four drug classes. The most frequently detected AMR genes were tetO conferring resistance to tetracycline and ermB conferring resistance to macrolide, lincosamide, and streptogramin. The wide distribution of VAFs genes in S. suis isolates in this study suggests that other host and environmental factors may contribute to S. suis disease development.
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Affiliation(s)
- Maverick Aradanas
- Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Zvonimir Poljak
- Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Nahuel Fittipaldi
- Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Nicole Ricker
- Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Abdolvahab Farzan
- Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.,Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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16
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Hadjirin NF, Miller EL, Murray GGR, Yen PLK, Phuc HD, Wileman TM, Hernandez-Garcia J, Williamson SM, Parkhill J, Maskell DJ, Zhou R, Fittipaldi N, Gottschalk M, Tucker AW(D, Hoa NT, Welch JJ, Weinert LA. Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis. BMC Biol 2021; 19:191. [PMID: 34493269 PMCID: PMC8422772 DOI: 10.1186/s12915-021-01094-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/13/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans. RESULTS We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order. CONCLUSIONS We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.
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Affiliation(s)
- Nazreen F. Hadjirin
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Eric L. Miller
- grid.256868.70000 0001 2215 7365Microbial Ecology and Evolution Laboratory, Haverford College, Haverford, USA
| | - Gemma G. R. Murray
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Phung L. K. Yen
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho D. Phuc
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thomas M. Wileman
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Juan Hernandez-Garcia
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Susanna M. Williamson
- grid.13689.350000 0004 0426 1697Department for Environment, Food and Rural Affairs (Defra), London, UK
| | - Julian Parkhill
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Duncan J. Maskell
- grid.1008.90000 0001 2179 088XChancellery, University of Melbourne, Melbourne, Australia
| | - Rui Zhou
- grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Nahuel Fittipaldi
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - Marcelo Gottschalk
- grid.14848.310000 0001 2292 3357Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Canada
| | - A. W. ( Dan) Tucker
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ngo Thi Hoa
- grid.412433.30000 0004 0429 6814Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - John J. Welch
- grid.5335.00000000121885934Department of Genetics, University of Cambridge, Cambridge, UK
| | - Lucy A. Weinert
- grid.5335.00000000121885934Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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17
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Weiße C, Dittmar D, Jakóbczak B, Florian V, Schütze N, Alber G, Klose K, Michalik S, Valentin-Weigand P, Völker U, Baums CG. Immunogenicity and protective efficacy of a Streptococcus suis vaccine composed of six conserved immunogens. Vet Res 2021; 52:112. [PMID: 34433500 PMCID: PMC8390293 DOI: 10.1186/s13567-021-00981-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/20/2021] [Indexed: 01/12/2023] Open
Abstract
A vaccine protecting against different Streptococcus suis serotypes is highly needed in porcine practice to improve animal welfare and reduce the use of antibiotics. We hypothesized that immunogens prominently recognized by convalescence sera but significantly less so by sera of susceptible piglets are putative protective antigens. Accordingly, we investigated immunogenicity and protective efficacy of a multicomponent vaccine including six main conserved immunogens, namely SSU0934, SSU1869, SSU0757, SSU1950, SSU1664 and SSU0187. Flow cytometry confirmed surface expression of all six immunogens in S. suis serotypes 2, 9 and 14. Although prime-booster vaccination after weaning resulted in significantly higher specific IgG levels against all six immunogens compared to the placebo-treated group, no significant differences between bacterial survival in blood from either vaccinated or control animals were recorded for serotype 2, 9 and 14 strains. Furthermore, vaccinated piglets were not protected against morbidity elicited through intranasal challenge with S. suis serotype 14. As ~50% of animals in both groups did not develop disease, we investigated putative other correlates of protection. Induction of reactive oxygen species (ROS) in blood granulocytes was not associated with vaccination but correlated with protection as all piglets with >5% ROS survived the challenge. Based on these findings we discuss that the main immunogens of S. suis might actually not be a priori good candidates for protective antigens. On the contrary, expression of immunogens that evoke antibodies that do not mediate killing of this pathogen might constitute an evolutionary advantage conserved in many different S. suis strains.
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Affiliation(s)
- Christine Weiße
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Denise Dittmar
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Nicole Schütze
- Institute of Immunology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Gottfried Alber
- Institute of Immunology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Kristin Klose
- Institute of Pathology, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - Stephan Michalik
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter Valentin-Weigand
- Department of Infectious Diseases, Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Christoph Georg Baums
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany.
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18
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Application of the MISTEACHING(S) disease susceptibility framework to Actinobacillus pleuropneumoniae to identify research gaps: an exemplar of a veterinary pathogen. Anim Health Res Rev 2021; 22:120-135. [PMID: 34275511 DOI: 10.1017/s1466252321000074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Historically, the MISTEACHING (microbiome, immunity, sex, temperature, environment, age, chance, history, inoculum, nutrition, genetics) framework to describe the outcome of host-pathogen interaction, has been applied to human pathogens. Here, we show, using Actinobacillus pleuropneumoniae as an exemplar, that the MISTEACHING framework can be applied to a strict veterinary pathogen, enabling the identification of major research gaps, the formulation of hypotheses whose study will lead to a greater understanding of pathogenic mechanisms, and/or improved prevention/therapeutic measures. We also suggest that the MISTEACHING framework should be extended with the inclusion of a 'strain' category, to become MISTEACHINGS. We conclude that the MISTEACHINGS framework can be applied to veterinary pathogens, whether they be bacteria, fungi, viruses, or parasites, and hope to stimulate others to use it to identify research gaps and to formulate hypotheses worthy of study with their own pathogens.
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19
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Mayer L, Bornemann N, Lehnert S, de Greeff A, Strutzberg-Minder K, Rieckmann K, Baums CG. Survival patterns of Streptococcus suis serotypes 1 and 14 in porcine blood indicate cross-reactive bactericidal antibodies in naturally infected pigs. Vet Microbiol 2021; 260:109183. [PMID: 34304027 DOI: 10.1016/j.vetmic.2021.109183] [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] [Received: 04/28/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Streptococcus suis serotype (cps) 1 and cps14 have been detected in association with severe diseases such as meningitis and polyarthritis in pigs. Though these two cps are very similar, only cps14 is an important zoonotic agent in Asia and only cps1 is described to be associated with diseases in suckling piglets rather than weaning piglets. The main objective of this study was to assess restriction of survival of cps14 and cps1 in porcine blood by IgG and IgM putatively cross-reacting with these two cps. Furthermore, we differentiate recent European cps1/14 strains by agglutination, cpsK sequencing, MLST and virulence-associated gene profiling. Our data confirmed cps1 of clonal complex 1 as an important pathotype causing polyarthritis in suckling piglets in Europe. The experimental design included also bactericidal assays with blood samples drawn at different ages of piglets naturally infected with different S. suis cps types including cps1 but not cps14. We report survival of a cps1 and a cps14 strain (both of sequence type 1) in blood of suckling piglets with high levels of maternal IgG binding to the bacterial surface. In contrast, killing of cps1 and cps14 was recorded in older piglets due to an increase of IgM as demonstrated by specific cleavage of IgM. Heterologous absorption of antibodies with cps1 or cps14 is sufficient to significantly increase the survival of the other cps. In conclusion, IgM elicited by natural S. suis infection is crucial for killing of S. suis cps1 and cps14 in older weaning piglets and has most likely the potential to cross-react between cps1 and cps14.
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Affiliation(s)
- L Mayer
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - N Bornemann
- IVD Innovative Veterinary Diagnostics (IVD GmbH), Albert-Einstein-Str. 5, 30926, Seelze, Germany
| | - S Lehnert
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - A de Greeff
- Wageningen Bioveterinary Research, part of Wageningen University and Research, Lelystad, the Netherlands
| | - K Strutzberg-Minder
- IVD Innovative Veterinary Diagnostics (IVD GmbH), Albert-Einstein-Str. 5, 30926, Seelze, Germany
| | - K Rieckmann
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany
| | - C G Baums
- Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, Leipzig University, Leipzig, Germany.
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20
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Murray GGR, Charlesworth J, Miller EL, Casey MJ, Lloyd CT, Gottschalk M, Tucker AW(D, Welch JJ, Weinert LA. Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence. Mol Biol Evol 2021; 38:1570-1579. [PMID: 33313861 PMCID: PMC8042751 DOI: 10.1093/molbev/msaa323] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). Although genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, that is, host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of nonfunctional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a consistent correlate of pathogenicity in bacteria.
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Affiliation(s)
- Gemma G R Murray
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jane Charlesworth
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Eric L Miller
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Haverford College, Haverford, PA, USA
| | - Michael J Casey
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- School of Mathematical Sciences, University of Southampton, Southampton, United Kingdom
| | - Catrin T Lloyd
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Marcelo Gottschalk
- Département de Pathologie et Microbiologie, Université de Montréal, Montréal, QC, Canada
| | | | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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21
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Obradovic MR, Segura M, Segalés J, Gottschalk M. Review of the speculative role of co-infections in Streptococcus suis-associated diseases in pigs. Vet Res 2021; 52:49. [PMID: 33743838 PMCID: PMC7980725 DOI: 10.1186/s13567-021-00918-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022] Open
Abstract
Streptococcus suis is one of the most important bacterial swine pathogens affecting post-weaned piglets, causing mainly meningitis, arthritis and sudden death. It not only results in severe economic losses but also raises concerns over animal welfare and antimicrobial resistance and remains an important zoonotic agent in some countries. The definition and diagnosis of S. suis-associated diseases can be complex. Should S. suis be considered a primary or secondary pathogen? The situation is further complicated when referring to respiratory disease, since the pathogen has historically been considered as a secondary pathogen within the porcine respiratory disease complex (PRDC). Is S. suis a respiratory or strictly systemic pathogen? S. suis is a normal inhabitant of the upper respiratory tract, and the presence of potentially virulent strains alone does not guarantee the appearance of clinical signs. Within this unclear context, it has been largely proposed that co-infection with some viral and bacterial pathogens can significantly influence the severity of S. suis-associated diseases and may be the key to understanding how the infection behaves in the field. In this review, we critically addressed studies reporting an epidemiological link (mixed infections or presence of more than one pathogen at the same time), as well as in vitro and in vivo studies of co-infection of S. suis with other pathogens and discussed their limitations and possibilities for improvement and proposed recommendations for future studies.
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Affiliation(s)
- Milan R Obradovic
- Groupe de Recherche Sur Les Maladies Infectieuses en Production Animale (GREMIP), Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA), Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte, Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - Mariela Segura
- Groupe de Recherche Sur Les Maladies Infectieuses en Production Animale (GREMIP), Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA), Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte, Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - Joaquim Segalés
- UAB, CReSA (IRTA-UAB), Campus de la UAB, 08193, Bellaterra (Cerdanyola del Vallès), Spain.,Departament de Sanitat I Anatomia Animals, Facultat de Veterinària, UAB, 08193, Bellaterra (Cerdanyola del Vallès), Spain.,OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193, Bellaterra, Barcelona, Spain
| | - Marcelo Gottschalk
- Groupe de Recherche Sur Les Maladies Infectieuses en Production Animale (GREMIP), Centre de Recherche en Infectiologie Porcine et Aviaire (CRIPA), Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte, Saint-Hyacinthe, QC, J2S 2M2, Canada.
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22
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Estrada AA, Gottschalk M, Rendahl A, Rossow S, Marshall-Lund L, Marthaler DG, Gebhart CJ. Proposed virulence-associated genes of Streptococcus suis isolates from the United States serve as predictors of pathogenicity. Porcine Health Manag 2021; 7:22. [PMID: 33648592 PMCID: PMC7917538 DOI: 10.1186/s40813-021-00201-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/16/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND There is limited information on the distribution of virulence-associated genes (VAGs) in U.S. Streptococcus suis isolates, resulting in little understanding of the pathogenic potential of these isolates. This lack also reduces our understanding of the epidemiology associated with S. suis in the United States and thus affects the efficiency of control and prevention strategies. In this study we applied whole genome sequencing (WGS)-based approaches for the characterization of S. suis and identification of VAGs. RESULTS Of 208 S. suis isolates classified as pathogenic, possibly opportunistic, and commensal pathotypes, the genotype based on the classical VAGs (epf, mrp, and sly encoding the extracellular protein factor, muramidase-release protein, and suilysin, respectively) was identified in 9% (epf+/mrp+/sly+) of the pathogenic pathotype. Using the chi-square test and LASSO regression model, the VAGs ofs (encoding the serum opacity factor) and srtF (encoding sortase F) were selected out of 71 published VAGs as having a significant association with pathotype, and both genes were found in 95% of the pathogenic pathotype. The ofs+/srtF+ genotype was also present in 74% of 'pathogenic' isolates from a separate validation set of isolates. Pan-genome clustering resulted in the differentiation of a group of isolates from five swine production companies into clusters corresponding to clonal complex (CC) and virulence-associated (VA) genotypes. The same CC-VA genotype patterns were identified in multiple production companies, suggesting a lack of association between production company, CC, or VA genotype. CONCLUSIONS The proposed ofs and srtF genes were stronger predictors for differentiating pathogenic and commensal S. suis isolates compared to the classical VAGs in two sets of U.S. isolates. Pan-genome analysis in combination with metadata (serotype, ST/CC, VA genotype) was illustrated to be a valuable subtyping tool to describe the genetic diversity of S. suis.
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Affiliation(s)
- April A Estrada
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA.
| | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada
| | - Aaron Rendahl
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Stephanie Rossow
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Lacey Marshall-Lund
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Connie J Gebhart
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, USA
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23
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Nicholson TL, Waack U, Anderson TK, Bayles DO, Zaia SR, Goertz I, Eppinger M, Hau SJ, Brockmeier SL, Shore SM. Comparative Virulence and Genomic Analysis of Streptococcus suis Isolates. Front Microbiol 2021; 11:620843. [PMID: 33574803 PMCID: PMC7870872 DOI: 10.3389/fmicb.2020.620843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Streptococcus suis is a zoonotic bacterial swine pathogen causing substantial economic and health burdens to the pork industry. Mechanisms used by S. suis to colonize and cause disease remain unknown and vaccines and/or intervention strategies currently do not exist. Studies addressing virulence mechanisms used by S. suis have been complicated because different isolates can cause a spectrum of disease outcomes ranging from lethal systemic disease to asymptomatic carriage. The objectives of this study were to evaluate the virulence capacity of nine United States S. suis isolates following intranasal challenge in swine and then perform comparative genomic analyses to identify genomic attributes associated with swine-virulent phenotypes. No correlation was found between the capacity to cause disease in swine and the functional characteristics of genome size, serotype, sequence type (ST), or in vitro virulence-associated phenotypes. A search for orthologs found in highly virulent isolates and not found in non-virulent isolates revealed numerous predicted protein coding sequences specific to each category. While none of these predicted protein coding sequences have been previously characterized as potential virulence factors, this analysis does provide a reliable one-to-one assignment of specific genes of interest that could prove useful in future allelic replacement and/or functional genomic studies. Collectively, this report provides a framework for future allelic replacement and/or functional genomic studies investigating genetic characteristics underlying the spectrum of disease outcomes caused by S. suis isolates.
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Affiliation(s)
- Tracy L Nicholson
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Ursula Waack
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States.,Oak Ridge Institute for Science and Education, United States Department of Energy, Oak Ridge, TN, United States
| | - Tavis K Anderson
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Darrell O Bayles
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Sam R Zaia
- South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Isaiah Goertz
- South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Mark Eppinger
- South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, United States.,Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Samantha J Hau
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States.,Oak Ridge Institute for Science and Education, United States Department of Energy, Oak Ridge, TN, United States
| | - Susan L Brockmeier
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Sarah M Shore
- National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
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24
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Scherrer S, Rosato G, Spoerry Serrano N, Stevens MJA, Rademacher F, Schrenzel J, Gottschalk M, Stephan R, Peterhans S. Population structure, genetic diversity and pathotypes of Streptococcus suis isolated during the last 13 years from diseased pigs in Switzerland. Vet Res 2020; 51:85. [PMID: 32641158 PMCID: PMC7346511 DOI: 10.1186/s13567-020-00813-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Streptococcus (S.) suis is a globally important swine pathogen, which comprises certain zoonotic serotypes. In this study, a detailed characterization of 88 porcine S. suis isolates was performed by analyzing capsular (cps) types, multilocus sequence typing (MLST) and investigation of the minimum core genome (MCG). In order to focus on the virulence potential of presumable invasive disease-associated S. suis isolates, virulence-associated gene profiles were assessed followed by screening a chosen subset of S. suis strains with a molecular pathotyping tool. Results showed a high genetic variability within this strain collection. In total, seventeen cps types were identified with a predominance of cps type 9 (15.9%) and 6 (14.8%). MLST revealed 48 sequence types (STs) including 41 novel ones. The population structure of S. suis was heterogenous and isolates belonged to eight different clonal complexes (CCs) including CC28 (9.1%), CC1109 (8%), CC13/149 (6.8%), CC1237 (5.7%), CC1 (3.4%), CC17 (3.4%), CC87 (2.3%), and CC1112 (1.1%), whereas a significant portion of isolates (60.2%) could not be assigned to any described CCs. Virulence-associated markers, namely extracellular protein factor (epf), muramidase-released protein (mrp), and suilysin (sly), showed a link with STs rather than with cps types. With this study an expanded knowledge about the population structure and the genetic diversity of S. suis could be achieved, which helps to contribute to an optimal public health surveillance system by promoting a focus on strains with an increased virulence and zoonotic potential.
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Affiliation(s)
- Simone Scherrer
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.
| | - Giuliana Rosato
- Institute for Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nathalie Spoerry Serrano
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marc J A Stevens
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Fenja Rademacher
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Jacques Schrenzel
- Bacteriology Laboratory, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Marcelo Gottschalk
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Groupe de recherche sur les maladies infectieuses des animaux de production (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Roger Stephan
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Sophie Peterhans
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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25
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Rieckmann K, Pendzialek SM, Vahlenkamp T, Baums CG. A critical review speculating on the protective efficacies of autogenous Streptococcus suis bacterins as used in Europe. Porcine Health Manag 2020; 6:12. [PMID: 32391166 PMCID: PMC7201539 DOI: 10.1186/s40813-020-00150-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/20/2020] [Indexed: 11/10/2022] Open
Abstract
Background Streptococcus (S.) suis is a major porcine pathogen causing high morbidity worldwide. This includes well-managed herds with high hygiene standards. In Europe, no licensed vaccine is available. As practitioners are obliged to reduce the use of antibiotics, autogenous S. suis vaccines have become very popular in Europe. Main body Autogenous vaccines (AV) are generally neither tested for safety, immunogenicity nor protective efficacy, which leads to substantial uncertainties regarding control of disease and return on investment. Here, S. suis publications are reviewed that include important data on epidemiology, pathologies and bacterin vaccination relevant for the use of AV in the field. Differences between herds such as the porcine reproductive and respiratory syndrome virus infection status and the impact of specific S. suis pathotypes are probably highly relevant for the outcome of immunoprophylaxis using autogenous S. suis bacterins. Thus, a profound diagnosis of the herd status is crucial for management of expectations and successful implementation of AV as a tool to control S. suis disease. Induction of opsonizing antibodies is an in vitro correlate of protective immunity elicited by S. suis bacterins. However, opsonophagocytosis assays are difficult to include in the portfolio of diagnostic services. Conclusion Autogenous S. suis bacterins are associated with limitations and risks of failure, which can partly be managed through improvement of diagnostics.
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Affiliation(s)
- Karoline Rieckmann
- 1Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, University Leipzig, An den Tierkliniken 29, 04103 Leipzig, Germany
| | - Sophia-Mareike Pendzialek
- 1Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, University Leipzig, An den Tierkliniken 29, 04103 Leipzig, Germany
| | - Thomas Vahlenkamp
- 2Institute of Virology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, University Leipzig, Leipzig, Germany
| | - Christoph G Baums
- 1Institute of Bacteriology and Mycology, Centre for Infectious Diseases, Faculty of Veterinary Medicine, University Leipzig, An den Tierkliniken 29, 04103 Leipzig, Germany
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26
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Tools for Molecular Epidemiology of Streptococcus suis. Pathogens 2020; 9:pathogens9020081. [PMID: 32012668 PMCID: PMC7168656 DOI: 10.3390/pathogens9020081] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/04/2022] Open
Abstract
Diseases caused by Streptococcus suis are a significant economic and welfare concern in pigs as well as in humans. Several molecular methods have been applied to investigate S. suis strain diversity and identify phylogenetic groups. Multilocus sequence typing (MLST), commonly used to differentiate between S. suis strains, has been instrumental in identifying that the species is genetically highly diverse. Recent advances in whole-genome analysis have resulted in schemes permitting the classification of S. suis populations as pathogenic or non-pathogenic, or disease-associated or non-disease associated. Here, we review these and other molecular approaches that can be used for surveillance, outbreak tracking, preventative health management, effective treatment and control, as well as vaccine development, including PCR based-assays that are easy to apply in modest diagnostic settings and which allow for the rapid screening of a large number of isolates at relatively low cost, granting the identification of several major clonal complexes of the S. suis population.
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