1
|
Zhu J, Wang J, Kang W, Zhang X, Kerdsin A, Yao H, Zheng H, Wu Z. Streptococcus suis serotype 4: a population with the potential pathogenicity in humans and pigs. Emerg Microbes Infect 2024; 13:2352435. [PMID: 38703011 PMCID: PMC11097711 DOI: 10.1080/22221751.2024.2352435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024]
Abstract
Streptococcus suis is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Different S. suis serotypes exhibit diverse characteristics in population structure and pathogenicity. Surveillance data highlight the significance of S. suis serotype 4 (SS4) in swine streptococcusis, a pathotype causing human infections. However, except for a few epidemiologic studies, the information on SS4 remains limited. In this study, we investigated the population structure, pathogenicity, and antimicrobial characteristics of SS4 based on 126 isolates, including one from a patient with septicemia. We discovered significant diversities within this population, clustering into six minimum core genome (MCG) groups (1, 2, 3, 4, 7-2, and 7-3) and five lineages. Two main clonal complexes (CCs), CC17 and CC94, belong to MCG groups 1 and 3, respectively. Numerous important putative virulence-associated genes are present in these two MCG groups, and 35.00% (7/20) of pig isolates from CC17, CC94, and CC839 (also belonging to MCG group 3) were highly virulent (mortality rate ≥ 80%) in zebrafish and mice, similar to the human isolate ID36054. Cytotoxicity assays showed that the human and pig isolates of SS4 strains exhibit significant cytotoxicity to human cells. Antimicrobial susceptibility testing showed that 95.83% of strains isolated from our labs were classified as multidrug-resistant. Prophages were identified as the primary vehicle for antibiotic resistance genes. Our study demonstrates the public health threat posed by SS4, expanding the understanding of SS4 population structure and pathogenicity characteristics and providing valuable information for its surveillance and prevention.
Collapse
Affiliation(s)
- Jinlu Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
| | - Jianping Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Weiming Kang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xiyan Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
| | - Han Zheng
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Shanxi Key Laboratory of Birth Defect and Cell Regeneration, MOE Key Laboratory of Coal Environmental Pathogenicity and Prevention, Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, People’s Republic of China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, People’s Republic of China
- WOAH Reference Lab for Swine Streptococcosis, Nanjing, People’s Republic of China
- Guangdong Provincial Key Laboratory of Research on the Technology of Pig-breeding and Pig-disease Prevention, Guangzhou, People’s Republic of China
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Massacci FR, Cucco L, Panicciá M, Luppi A, Albini E, Peruzzo A, Ferroni L, Ustulin M, Orsini M, Magistrali CF. Streptococcus suis serotype 9 in Italy: genomic insights into high-risk clones with emerging resistance to penicillin. J Antimicrob Chemother 2024; 79:403-411. [PMID: 38153239 PMCID: PMC10832592 DOI: 10.1093/jac/dkad395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Streptococcus suis is an important pig pathogen and an emerging zoonotic agent. In a previous study, we described a high proportion of penicillin-resistant serotype 9 S. suis (SS9) isolates on pig farms in Italy. OBJECTIVES We hypothesized that resistance to penicillin emerged in some SS9 lineages characterized by substitutions at the PBPs, contributing to the successful spread of these lineages in the last 20 years. METHODS Sixty-six SS9 isolates from cases of streptococcosis in pigs were investigated for susceptibility to penicillin, ceftiofur and ampicillin. The isolates were characterized for ST, virulence profile, and antimicrobial resistance genes through WGS. Multiple linear regression models were employed to investigate the associations between STs, year of isolation, substitutions at the PBPs and an increase in MIC values to β-lactams. RESULTS MIC values to penicillin increased by 4% each year in the study period. Higher MIC values for penicillin were also positively associated with ST123, ST1540 and ST1953 compared with ST16. The PBP sequences presented a mosaic organization of blocks. Within the same ST, substitutions at the PBPs were generally more frequent in recent isolates. Resistance to penicillin was driven by substitutions at PBP2b, including K479T, D512E and K513E, and PBP2x, including T551S, while reduced susceptibility to ceftiofur and ampicillin were largely dependent on substitutions at PBP2x. CONCLUSIONS Here, we identify the STs and substitutions at the PBPs responsible for increased resistance of SS9 to penicillin on Italian pig farms. Our data highlight the need for monitoring the evolution of S. suis in the coming years.
Collapse
Affiliation(s)
| | - Lucilla Cucco
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Marta Panicciá
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Andrea Luppi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Parma, Italy
| | - Elisa Albini
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Arianna Peruzzo
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | - Laura Ferroni
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche ‘Togo Rosati’, Perugia, Italy
| | - Martina Ustulin
- Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy
| | | | | |
Collapse
|
4
|
Uruén C, Gimeno J, Sanz M, Fraile L, Marín CM, Arenas J. Invasive Streptococcus suis isolated in Spain contain a highly promiscuous and dynamic resistome. Front Cell Infect Microbiol 2024; 13:1329632. [PMID: 38317790 PMCID: PMC10839070 DOI: 10.3389/fcimb.2023.1329632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/26/2023] [Indexed: 02/07/2024] Open
Abstract
Introduction Streptococcus suis is a major pathogen for swine and human. Here we aimed to know the rates of antimicrobial resistance (AMR) in invasive S. suis isolates recovered along Spain between 2016 - 2021 and elucidate their genetic origin. Methods Antibiotic susceptibility testing was performed for 116 isolates of different genetic backgrounds and geographic origins against 18 antibiotics of 9 families. The association between AMR and genotypes and the origin of the isolates were statistically analyzed using Pearson´s chi-square test and the likelihood ratio. The antimicrobial resistant genes were identified by whole genome sequencing analysis and PCR screenings. Results High AMR rates (>80%) were detected for tetracyclines, spectinomycin, lincosamides, and marbofloxacin, medium (20-40%) for sulphonamides/trimethoprim, tiamulin, penicillin G, and enrofloxacin, and low (< 20%) for florfenicol, and four additional β-lactams. The occurrence of multidrug resistance was observed in 90% of isolates. For certain antibiotics (penicillin G, enrofloxacin, marbofloxacin, tilmicosin, and erythromycin), AMR was significantly associated with particular sequence types (STs), geographic regions, age of pigs, and time course. Whole genome sequencing comparisons and PCR screenings identified 23 AMR genes, of which 19 were previously reported in S. suis (aph(3')-IIIa, sat4, aadE, spw, aac(6')-Ie-aph(2'')-Ia, fexA, optrA, erm(B), mef(A/E), mrs(D), mph(C), lnu(B), lsa(E), vga(F), tet(M), tet(O), tet(O/W/32/O), tet(W)), and 4 were novel (aph(2'')-IIIa, apmA, erm(47), tet(T)). These AMR genes explained the AMR to spectinomycin, macrolides, lincosamides, tiamulin, and tetracyclines. Several genes were located on mobile genetic elements which showed a variable organization and composition. As AMR gene homologs were identified in many human and animal pathogens, the resistome of S. suis has a different phylogenetic origin. Moreover, AMR to penicillin G, fluoroquinolones, and trimethoprim related to mutations in genes coding for target enzymes (pbp1a, pbp2b, pbp2x, mraY, gyrA, parC, and dhfr). Bioinformatic analysis estimated traits of recombination on target genes, also indicative of gene transfer events. Conclusions Our work evidences that S. suis is a major contributor to AMR dissemination across veterinary and human pathogens. Therefore, control of AMR in S. suis should be considered from a One Health approach in regions with high pig production to properly tackle the issue of antimicrobial drug resistance.
Collapse
Affiliation(s)
- Cristina Uruén
- Unit of Microbiology and Immunology, Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
- Institute Agrofood of Aragón-IA2, University of Zaragoza-CITA, Zaragoza, Spain
| | - Jorge Gimeno
- Unit of Microbiology and Immunology, Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
- Institute Agrofood of Aragón-IA2, University of Zaragoza-CITA, Zaragoza, Spain
| | - Marina Sanz
- Unit of Microbiology and Immunology, Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
- Institute Agrofood of Aragón-IA2, University of Zaragoza-CITA, Zaragoza, Spain
| | - Lorenzo Fraile
- Department of Animal Science, ETSEA, University of Lleida-Agrotecno, Lleida, Spain
| | - Clara M. Marín
- Institute Agrofood of Aragón-IA2, University of Zaragoza-CITA, Zaragoza, Spain
- Department of Animal Production and Health, CITA, Zaragoza, Spain
| | - Jesús Arenas
- Unit of Microbiology and Immunology, Faculty of Veterinary, University of Zaragoza, Zaragoza, Spain
- Institute Agrofood of Aragón-IA2, University of Zaragoza-CITA, Zaragoza, Spain
| |
Collapse
|
5
|
Breyer GM, Rocha Jacques da Silva ME, Slaviero M, Albuquerque de Almeida B, Machado Sousa da Silva E, de Queiroz Schmidt VR, Alievi M, Maboni G, Petinatti Pavarini S, Maboni Siqueira F. Genotypic characterization of Streptococcus didelphis causative of fatal infection in white-eared opossums. Lett Appl Microbiol 2023; 76:ovad131. [PMID: 37968138 DOI: 10.1093/lambio/ovad131] [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: 08/16/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023]
Abstract
Streptococcus didelphis was once reported as related to severe infections in opossums. Thus, we present the first comprehensive whole-genome characterization of clinical S. didelphis strains isolated from white-eared opossums (Didelphis albiventris). Long-read whole-genome sequencing was performed using the MinION platform, which allowed the prediction of several genomic features. We observed that S. didelphis genomes harbor a cluster for streptolysin biosynthesis and a conserved genomic island with genes involved in transcriptional regulation (arlR) and transmembrane transport (bcrA). Antimicrobial resistance genes for several drug classes were found, including beta-lactam, which is the main antimicrobial class used in Streptococcus spp. infections; however, no phenotypical resistance was observed. In addition, we predicted the presence of 33 virulence factors in the analyzed genomes. High phylogenetic similarity was observed between clinical and reference strains, yet no clonality was suggested. We also proposed dnaN, gki, pros, and xpt as housekeeping candidates to be used in S. didelphis sequence typing. This is the first whole-genome characterization of S. didelphis, whose data provide important insights into its pathogenicity.
Collapse
Affiliation(s)
- Gabriela Merker Breyer
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Maria Eduarda Rocha Jacques da Silva
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Mônica Slaviero
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Bruno Albuquerque de Almeida
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Emanoelly Machado Sousa da Silva
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Victória Regina de Queiroz Schmidt
- Preservas-Núcleo de Conservação e Reabilitação de Animais Silvestres, Hospital de Clínicas Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Marcelo Alievi
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Preservas-Núcleo de Conservação e Reabilitação de Animais Silvestres, Hospital de Clínicas Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Grazieli Maboni
- Department of Pathobiology, University of Guelph, 50 Stone Road East, NIG 2W1 - Guelph/ON, Canada
| | - Saulo Petinatti Pavarini
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Laboratório de Patologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| | - Franciele Maboni Siqueira
- Laboratório de Bacteriologia Veterinária, Departamento de Patologia Veterinária, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Federal do Rio Grande do Sul, 9090 Bento Gonçalves Avenue, 91540-000 - Porto Alegre/RS, Brazil
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Dechêne-Tempier M, Jouy E, Bayon-Auboyer MH, Bougeard S, Chauvin C, Libante V, Payot S, Marois-Créhan C. Antimicrobial resistance profiles of Streptococcus suis isolated from pigs, wild boars, and humans in France between 1994 and 2020. J Clin Microbiol 2023; 61:e0016423. [PMID: 37655935 PMCID: PMC10512786 DOI: 10.1128/jcm.00164-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/02/2023] [Indexed: 09/02/2023] Open
Abstract
Streptococcus suis, an emerging zoonotic pathogen, causes invasive infections and substantial economic losses in the pig industry worldwide. Antimicrobial resistance against 22 antibiotics was studied for 200 S. suis strains collected in different geographical regions of France. Most of the strains (86%) showed resistance to at least one antibiotic with a low rate of resistance to fluoroquinolones, penicillins, pleuromutilin, and diaminopyrimidine-sulfonamides, and a higher rate to macrolides-lincosamides and tetracycline. Multi-resistance patterns were observed in 138 strains; three of them being resistant to six antibiotic families. Statistical analyses highlighted a decrease in the resistance to trimethoprim-sulfamethoxazole, in our collection, between the two periods studied-before 2010 and after 2015-as well as an impact of the geographical origin with a higher rate of resistance to macrolides-lincosamides and penicillin in Brittany than in the other French regions. Furthermore, macrolides-lincosamides and tetracycline resistance patterns were more likely to be found in pig isolates than in human and wild boar isolates. A difference in resistance was also observed between serotypes. Most of the penicillin-resistant strains belong to serotypes 1, 5, 9, 11, 12, 15, 27, and 29. Finally, penicillin and pleuromutilin resistances were mostly found in "non-clinical" isolates. The empirical treatment of human and porcine infections due to S. suis in France can therefore still be carried out with beta-lactams. However, this study emphasizes the need to monitor antimicrobial resistance in this zoonotic pathogen.
Collapse
Affiliation(s)
- Manon Dechêne-Tempier
- ANSES, Mycoplasmology, Bacteriology and Antimicrobial Resistance Unit, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
- Université de Lorraine, INRAE, DynAMic, Nancy, France
| | - Eric Jouy
- ANSES, Mycoplasmology, Bacteriology and Antimicrobial Resistance Unit, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | - Stéphanie Bougeard
- ANSES, Epidemiology, Health and Welfare Unit, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Claire Chauvin
- ANSES, Epidemiology, Health and Welfare Unit, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | | | - Sophie Payot
- Université de Lorraine, INRAE, DynAMic, Nancy, France
| | - Corinne Marois-Créhan
- ANSES, Mycoplasmology, Bacteriology and Antimicrobial Resistance Unit, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Fredriksen S, de Warle S, van Baarlen P, Boekhorst J, Wells JM. Resistome expansion in disease-associated human gut microbiomes. MICROBIOME 2023; 11:166. [PMID: 37507809 PMCID: PMC10386251 DOI: 10.1186/s40168-023-01610-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome. RESULTS The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer. CONCLUSIONS Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.
Collapse
Affiliation(s)
- Simen Fredriksen
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands.
| | - Stef de Warle
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands
| | - Jos Boekhorst
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands
| | - Jerry M Wells
- Host-Microbe Interactomics Group, Animal Sciences Department, Wageningen University & Research, Wageningen, The Netherlands.
| |
Collapse
|
10
|
Dolbec D, Lehoux M, Okura M, Takamatsu D, Gottschalk M, Segura M. Streptococcus suis surface-antigen recognition by antibodies and bacterial elimination is influenced by capsular polysaccharide structure. Front Cell Infect Microbiol 2023; 13:1228496. [PMID: 37545852 PMCID: PMC10401424 DOI: 10.3389/fcimb.2023.1228496] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023] Open
Abstract
Streptococcus suis is an encapsulated bacterium causing severe diseases in swine. Here, we compared the protective properties of the capsular polysaccharide (CPS) of different S. suis serotypes by using serotype-switched mutants in a mouse model of infection. CPS structure influenced bacterial survival in mice, antibody binding, and antibody-mediated bacterial killing. The CPS of serotypes 3, 4 and 14 allowed more antibody binding and bacterial elimination than the CPS of serotypes 2, 7 and 9. Results suggest that the different CPS structures of S. suis provide varying levels of protection by influencing antigen availability and elimination by the host immune system.
Collapse
Affiliation(s)
- Dominic Dolbec
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Diseases Research Center (CRIPA), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Mélanie Lehoux
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Diseases Research Center (CRIPA), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Masatoshi Okura
- Division of Transboundary Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Kagoshima, Japan
| | - Daisuke Takamatsu
- Division of Infectious Animal Disease Research, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
- The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
- Joint Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Marcelo Gottschalk
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Diseases Research Center (CRIPA), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| | - Mariela Segura
- Research Group on Infectious Diseases in Production Animals (GREMIP) and Swine and Poultry Infectious Diseases Research Center (CRIPA), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, QC, Canada
| |
Collapse
|
11
|
Brizuela J, Kajeekul R, Roodsant TJ, Riwload A, Boueroy P, Pattanapongpaibool A, Thaipadungpanit J, Jenjaroenpun P, Wongsurawat T, Batty EM, van der Putten BCL, Schultsz C, Kerdsin A. Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand. Microb Genom 2023; 9:mgen000952. [PMID: 36790403 PMCID: PMC9997742 DOI: 10.1099/mgen.0.000952] [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: 02/16/2023] Open
Abstract
Streptococcus suis is an emerging zoonotic swine pathogen which can cause severe infections in humans. In March 2021, an outbreak of S. suis infections with 19 confirmed cases of septicemia and meningitis leading to two deaths, occurred in Nakhon Ratchasima province, Thailand. We characterized the outbreak through an epidemiological investigation combined with Illumina and Nanopore whole genome sequencing (WGS). The source of the outbreak was traced back to a raw pork dish prepared from a single pig during a Buddhist ceremony attended by 241 people. WGS analysis revealed that a single S. suis serotype 2 strain belonging to a novel sequence type (ST) of the emergent Thai zoonotic clade CC233/379, was responsible for the infections. The outbreak clone grouped together with other Thai zoonotic strains from CC233/379 and CC104 in a global S. suis phylogeny and capsule switching events between serotype 2 zoonotic strains and serotype 7 porcine strains were identified. The outbreak strain showed reduced susceptibility to penicillin corresponding with mutations in key residues in the penicillin binding proteins (PBPs). Furthermore, the outbreak strain was resistant to tetracycline, erythromycin, clindamycin, linezolid and chloramphenicol, having acquired an integrative and conjugative element (ICE) carrying resistance genes tetO and ermB, as well as a transposon from the IS1216 family carrying optrA and ermA. This investigation demonstrates that multi-drug resistant zoonotic lineages of S. suis which pose a threat to human health continue to emerge.
Collapse
Affiliation(s)
- Jaime Brizuela
- Amsterdam UMC location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Paasheuvelweg 25, Amsterdam, The Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Rattagan Kajeekul
- Department of Medicine, Maharat Nakhon Ratchasima Hospital, Nakhon Ratchasima, Thailand
| | - Thomas J Roodsant
- Amsterdam UMC location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Paasheuvelweg 25, Amsterdam, The Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Athita Riwload
- Clinical Microbiology Laboratory, Department of Medical Technology, Maharat Nakhon Ratchasima Hospital, Nakhon Ratchasima, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | | | - Janjira Thaipadungpanit
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, 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
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Elizabeth M Batty
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Boas C L van der Putten
- Amsterdam UMC location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Paasheuvelweg 25, Amsterdam, The Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Constance Schultsz
- Amsterdam UMC location University of Amsterdam, Department of Global Health, Amsterdam Institute for Global Health and Development, Paasheuvelweg 25, Amsterdam, The Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| |
Collapse
|
12
|
Relationship between Penicillin-Binding Proteins Alterations and β-Lactams Non-Susceptibility of Diseased Pig-Isolated Streptococcus suis. Antibiotics (Basel) 2023; 12:antibiotics12010158. [PMID: 36671359 PMCID: PMC9854507 DOI: 10.3390/antibiotics12010158] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Streptococcus suis is a zoonotic pathogen causing disease in both animals and humans, and the emergence of increasingly resistant bacteria to antimicrobial agents has become a significant challenge globally. The objective of this study was to investigate the genetic basis for declining susceptibility to penicillin and other β-lactams among S. suis. Antimicrobial susceptibility testing and penicillin-binding proteins (PBP1a, PBP2a, PBP2b, and PBP2x) sequence analysis were performed on 225 S. suis isolated from diseased pigs. This study found that a growing trend of isolates displayed reduced susceptibility to β-lactams including penicillin, ampicillin, amoxicillin/clavulanic acid, and cephalosporins. A total of 342 substitutions within the transpeptidase domain of four PBPs were identified, of which 18 substitutions were most statistically associated with reduced β-lactams susceptibility. Almost all the S. suis isolates which exhibited penicillin-non-susceptible phenotype (71.9%) had single nucleotide polymorphisms, leading to alterations of PBP1a (P409T) and PBP2a (T584A and H588Y). The isolates may manifest a higher level of penicillin resistance by additional mutation of M341I in the 339STMK active site motif of PBP2x. The ampicillin-non-susceptible isolates shared the mutations in PBP1a (P409T) and PBP2a (T584A and H588Y) with additional alterations of PBP2b (T625R) and PBP2x (T467S). The substitutions, including PBP1a (M587S/T), PBP2a (M433T), PBP2b (I428L), and PBP2x (Q405E/K/L), appeared to play significant roles in mediating the reduction in amoxicillin/clavulanic acid susceptibility. Among the cephalosporins, specific mutations strongly associated with the decrease in cephalosporins susceptibility were observed for ceftiofur: PBP1a (S477D/G), PBP2a (E549Q and A568S), PBP2b (T625R), and PBP2x (Q453H). It is concluded that there was genetically widespread presence of PBPs substitutions associated with reduced susceptibility to β-lactam antibiotics.
Collapse
|
13
|
Uruén C, García C, Fraile L, Tommassen J, Arenas J. How Streptococcus suis escapes antibiotic treatments. Vet Res 2022; 53:91. [DOI: 10.1186/s13567-022-01111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
AbstractStreptococcus suis is a zoonotic agent that causes sepsis and meningitis in pigs and humans. S. suis infections are responsible for large economic losses in pig production. The lack of effective vaccines to prevent the disease has promoted the extensive use of antibiotics worldwide. This has been followed by the emergence of resistance against different classes of antibiotics. The rates of resistance to tetracyclines, lincosamides, and macrolides are extremely high, and resistance has spread worldwide. The genetic origin of S. suis resistance is multiple and includes the production of target-modifying and antibiotic-inactivating enzymes and mutations in antibiotic targets. S. suis genomes contain traits of horizontal gene transfer. Many mobile genetic elements carry a variety of genes that confer resistance to antibiotics as well as genes for autonomous DNA transfer and, thus, S. suis can rapidly acquire multiresistance. In addition, S. suis forms microcolonies on host tissues, which are associations of microorganisms that generate tolerance to antibiotics through a variety of mechanisms and favor the exchange of genetic material. Thus, alternatives to currently used antibiotics are highly demanded. A deep understanding of the mechanisms by which S. suis becomes resistant or tolerant to antibiotics may help to develop novel molecules or combinations of antimicrobials to fight these infections. Meanwhile, phage therapy and vaccination are promising alternative strategies, which could alleviate disease pressure and, thereby, antibiotic use.
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Tracy L. Nicholson
- National Animal Disease Center, Agricultural Research Service (USDA), Ames, IA, United States
| | | |
Collapse
|
15
|
Kittiwan N, Calland JK, Mourkas E, Hitchings MD, Murray S, Tadee P, Tadee P, Duangsonk K, Meric G, Sheppard SK, Patchanee P, Pascoe B. Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs. Microb Genom 2022; 8:mgen000882. [PMID: 36326658 PMCID: PMC9836093 DOI: 10.1099/mgen.0.000882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact.
Collapse
Affiliation(s)
- Nattinee Kittiwan
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang 52190, Thailand
| | - Jessica K. Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK
| | - Matthew D. Hitchings
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK
| | - Susan Murray
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK,Present address: Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Pakpoom Tadee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai 50290, Thailand
| | - Kwanjit Duangsonk
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guillaume Meric
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Present address: Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Faculty of Allied Medical Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Prapas Patchanee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,*Correspondence: Prapas Patchanee,
| | - Ben Pascoe
- Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK,*Correspondence: Ben Pascoe,
| |
Collapse
|
16
|
Tetracycline, Macrolide and Lincosamide Resistance in Streptococcus canis Strains from Companion Animals and Its Genetic Determinants. Antibiotics (Basel) 2022; 11:antibiotics11081034. [PMID: 36009903 PMCID: PMC9405182 DOI: 10.3390/antibiotics11081034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022] Open
Abstract
Growing antimicrobial resistance (AMR) in companion-animal pathogens, including Streptococcus canis (S. canis), is a significant concern for pet treatment as well for public health. Despite the importance of S. canis in veterinary and human medicine, studies concerning the AMR of this bacterium are still scarce. A total of 65 S. canis strains, isolated from dogs and cats, were assessed to test for susceptibility to six clinically relevant antimicrobials via a microdilution method. The prevalence of the selected acquired-resistance genes was also investigated via PCR. High MIC50 and MIC90 values (≥128 μg/mL) were noted for tetracycline, erythromycin and clindamycin. Only a few strains were resistant to the tested beta-lactams (6.2%). Tetracycline resistance was found in 66.2% of the strains. Resistance to erythromycin and clindamycin (ML resistance) was found in 55.4% of the strains. Strains with a phenotype showing concurrent resistance to tetracycline and ML were predominant (53.8%). AMR in the tested S. canis strains was associated with a variety of acquired and potentially transferable genes. Tetracycline resistance was conferred by tet(O) (40.0%), tet(M) (9.2%), and tet(T) (1.5%), which is reported for the first time in S. canis. In most cases, the tet(M) gene was detected in relation to the conjugative transposon Tn916. The MLSB phenotype was confirmed in the strains harboring erm(B) (43.1%) and erm(TR) (7.7%). To conclude, a high rate of S. canis strains occurring in dogs and cats displayed resistance to antimicrobials important for treatment; moreover, they are a potential reservoirs of various resistance determinants. Therefore, AMR in these pathogens should be continuously monitored, especially regarding the One Health concept.
Collapse
|
17
|
Antimicrobial Susceptibility Testing of Porcine Bacterial Pathogens: Investigating the Prospect of Testing a Representative Drug for Each Antimicrobial Family. Antibiotics (Basel) 2022; 11:antibiotics11050638. [PMID: 35625283 PMCID: PMC9137606 DOI: 10.3390/antibiotics11050638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022] Open
Abstract
Antimicrobial susceptibility testing is necessary to carry out antimicrobial stewardship but a limited number of drugs belonging to each antimicrobial family has to be tested for technical limitations and economic resources. In this study, we have determined the minimal inhibitory concentration, using microdilution following international standards (CLSI), for 490 Actinobacillus pleuropneumoniae, 285 Pasteurella multocida, 73 Bordetella bronchiseptica, 398 Streptococcus suis and 1571 Escherichia coli strains from clinical cases collected in Spain between 2018 and 2020. The antimicrobial susceptibility pattern was deciphered using a principal component analysis for each bacterium and a matrix correlation (high > 0.8, medium 0.5−0.8 and low < 0.5) was obtained for each pair of antimicrobials. No significant associations were observed between MIC patterns for different antimicrobial families, suggesting that co-selection mechanisms are not generally present in these porcine pathogens. However, a high correlation was observed between the fluroquinolones (marbofloxacin and enrofloxacin) for all mentioned pathogens and for ceftiofur and cefquinome for E. coli and S. suis. Moreover, a significant association was also observed for tetracyclines (doxycycline and oxytetracycline) and B. bronchiseptica and tildipirosin/tulathromycin for P. multocida. These results suggest that generally, a representative drug per antimicrobial class cannot be selected, however, for some drug−bug combinations, MIC values from one representative drug could be extrapolated to the whole antimicrobial family.
Collapse
|
18
|
Effect of Dextranase and Dextranase-and-Nisin-Containing Mouthwashes on Oral Microbial Community of Healthy Adults—A Pilot Study. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study analyzed the alteration of oral microbial composition in healthy subjects after using dextranase-containing mouthwash (DMW; Mouthwash formulation I) and dextranase-and-nisin-containing mouthwash (DNMW; Mouthwash formulation II). Eighteen participants were recruited and were randomly allocated to two groups: G1 (DMW user; n = 8) and G2 (DNMW user; n = 10). The subjects were instructed to use the provided mouthwash regularly twice a day for 30 days. The bleeding on probing (BOP), plaque index (PI), probing depth (PBD), and gingival index (GI) were analyzed, and saliva samples were collected before (day 0) and after (day 30) the use of mouthwashes. The saliva metagenomic DNA was extracted and sequenced (next-generation sequencing, Miseq paired-end Illumina 2 × 250 bp platform). The oral microbial community in the pre-and post-treated samples were annotated using QIIME 2™. The results showed the PI and PBD values were significantly reduced in G2 samples. The BOP and GI values of both groups were not significantly altered. The post-treated samples of both groups yielded a reduced amount of microbial DNA. The computed phylogenetic diversity, species richness, and evenness were reduced significantly in the post-treated samples of G2 compared to the post-treated G1 samples. The mouthwash formulations also supported some pathogens’ growth, which indicated that formulations required further improvement. The study needs further experiments to conclude the results. The study suggested that the improved DNMW could be an adjuvant product to improve oral hygiene.
Collapse
|