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Dong Z, Li C, Tian X, Guo X, Li X, Ren W, Chi J, Zhang L, Li F, Zhu Y, Zhang W, Yan M. Characterization Studies on the sugC Gene of Streptococcus suis Serotype 2 in Adhesion, Invasion, and Virulence in Mice. Vet Sci 2024; 11:447. [PMID: 39330826 PMCID: PMC11435659 DOI: 10.3390/vetsci11090447] [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: 08/03/2024] [Revised: 09/08/2024] [Accepted: 09/20/2024] [Indexed: 09/28/2024] Open
Abstract
The sugC gene of Streptococcus suis (S. suis) is a coding gene for the ATP-binding transporter-associated protein with strong pathogenicity. In order to reveal the effect of the sugC gene on the virulence of S. suis serotype 2, a wild-type strain of TJS75, isolated from fattening pigs' brain tissue samples, was used as a parent strain, and a knockout sugC gene (ΔsugC) and complementary strain (CΔsugC) were successfully constructed via homologous recombination technology. The biological characteristics of TJS75, ΔsugC and CΔsugC were compared and analyzed through growth curves, biochemical characteristics, hemolysis characteristics, cell infection tests and pathogenicity tests on BALB/c mice. The results of the growth characteristic experiments in vitro showed that the plateau stage growth period of ΔsugC was delayed compared to the TJS75 strain, but there was no difference in the total number of bacteria. The biochemical characteristics and hemolysis ability of ΔsugC in sheep blood had no difference compared with TJS75, but its adhesion and invasion abilities in PK-15 cells were decreased. Knockout of the sugC gene had no impact on the expression levels of adhesion-related genes in TJS75 in real-time PCR analysis. In addition, the LD50 of ΔsugC in BALB/c mice was 1.47 × 108 CFU, seven times higher than that of TJS75 (LD50 = 2.15 × 107 CFU). These results illustrate that the deletion of sugC reduced the virulence of TJS75 to BALB/c mice, but its role in the adhesion and invasion of PK-15 cells in this strain needs to be further explored. In summary, this study provides evidence that the sugC gene is a virulence-related gene in the S. suis serotype 2 strain and plays a crucial role in the adhesion and invasion of S. suis. This study lays a foundation for the further exploration of the potential virulence factors and pathogenesis of S. suis.
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Affiliation(s)
- Zhimin Dong
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Cheng Li
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Xiangxue Tian
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Xiaoran Guo
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Xiuli Li
- Institute of Agro-Product Safety and Nutrition, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China;
| | - Weike Ren
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Jingjing Chi
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Li Zhang
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Fuqiang Li
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
| | - Yao Zhu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.Z.); (W.Z.)
| | - Wanjiang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China; (Y.Z.); (W.Z.)
| | - Minghua Yan
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Tianjin Engineering Research Center of Animal Healthy Farming, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China; (Z.D.); (C.L.); (X.T.); (X.G.); (W.R.); (J.C.); (L.Z.); (F.L.)
- National Data Center of Animal Health, Tianjin 300381, China
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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.
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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
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Wang Z, Zhou Y, Guo G, Li Q, Yu Y, Zhang W. Promising potential of machine learning-assisted MALDI-TOF MS as an effective detector for Streptococcus suis serotype 2 and virulence thereof. Appl Environ Microbiol 2023; 89:e0128423. [PMID: 37861326 PMCID: PMC10686076 DOI: 10.1128/aem.01284-23] [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: 07/26/2023] [Accepted: 09/01/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE To the best of our knowledge, this study reveals a strong correlation between mass spectra pattern and virulence phenotype among S. suis for the first time. In order to make the findings applicable and to excavate the intrinsic information in the spectra, the classifiers based on the machine learning algorithms were established, and RF (Random Forest)-based models have achieved an accuracy of over 90%. Overall, this study will pave the way for virulent SS2 (Streptococcus suis serotype 2) rapid detection, and the important findings on the association between genotype and mass spectrum may provide a new idea for the genotype-dependent detection of specific pathogens.
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Affiliation(s)
- Zhuohao Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Yu Zhou
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Genglin Guo
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yanfei Yu
- Key Laboratory of Veterinary Biological Engineering and Technology of Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing, China
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing, China
- The Sanya Institute of Nanjing Agriculture University, Sanya, China
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Werinder A, Aspán A, Jacobson M, Backhans A, Sjölund M, Guss B, Söderlund R. Genome characteristics related to the virulence of Streptococcus suis in Swedish pigs. Vet Microbiol 2023; 284:109839. [PMID: 37531841 DOI: 10.1016/j.vetmic.2023.109839] [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: 03/24/2023] [Revised: 06/12/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023]
Abstract
The impact of S. suis on Swedish pig production has increased in recent years, and characterization of the strains present in the pig population is needed to aid in surveillance and prevention. Therefore, the aim of this study was to identify and characterize differences in the genomes between Swedish S. suis isolates associated with disease and isolates from healthy animals. Isolates categorized as being pathogenic (n = 100) or non-pathogenic (n = 117) were whole-genome sequenced, serotyped in silico, and sequence-typed using traditional MLST and core-genome MLST, and a genome-wide association study was performed to identify virulence-associated genes. In decreasing order, serotypes 2, 1, and 7 were the most common in the pathogenic group, and serotypes 15 and 12 were the most common in the non-pathogenic group. Among the commonly disease-associated sequence types, ST28 and ST25 were identified, whereas ST1 was scarcely found. The majority of isolates belonged to novel sequence types, revealing differences between Swedish isolates and those reported from other countries. The genomes of the pathogenic isolates were on average smaller and less heterogenic as compared to those of the non-pathogenic isolates. Although a majority of the previously published virulence-associated genes included in the study were found in the genomes of both pathogenic and non-pathogenic isolates, several new, significantly virulence-associated genes were identified.
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Affiliation(s)
- Anna Werinder
- Swedish University of Agricultural Sciences (SLU), Department of Clinical Sciences, Box 7054, 750 07 Uppsala, Sweden.
| | - Anna Aspán
- National Veterinary Institute (SVA), Department of Microbiology, 751 89 Uppsala, Sweden
| | - Magdalena Jacobson
- Swedish University of Agricultural Sciences (SLU), Department of Clinical Sciences, Box 7054, 750 07 Uppsala, Sweden
| | - Annette Backhans
- National Veterinary Institute (SVA), Department of Animal Health and Antimicrobial Strategies, 751 89 Uppsala, Sweden
| | - Marie Sjölund
- Swedish University of Agricultural Sciences (SLU), Department of Clinical Sciences, Box 7054, 750 07 Uppsala, Sweden; National Veterinary Institute (SVA), Department of Animal Health and Antimicrobial Strategies, 751 89 Uppsala, Sweden
| | - Bengt Guss
- Swedish University of Agricultural Sciences (SLU), Department of Biomedical Science and Veterinary Public Health, Box 7036, 750 07 Uppsala, Sweden
| | - Robert Söderlund
- National Veterinary Institute (SVA), Department of Microbiology, 751 89 Uppsala, Sweden
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Yang P, Yang L, Cao K, Hu Q, Hu Y, Shi J, Zhao D, Yu X. Novel virulence factor Cba induces antibody-dependent enhancement (ADE) of Streptococcus suis Serotype 9 infection in a mouse model. Front Cell Infect Microbiol 2023; 13:1027419. [PMID: 36896190 PMCID: PMC9989217 DOI: 10.3389/fcimb.2023.1027419] [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: 08/25/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023] Open
Abstract
Streptococcus suis (SS) is a zoonotic pathogen that affects the health of humans and the development of the pig industry. The SS Cba protein is a collagen adhesin, and a few of its homologs are related to the enhancement of bacterial adhesion. We compared the phenotypes of SS9-P10, SS9-P10 cba knockout strains and its complementary strains in vitro and in vivo and found that knocking out the cba gene did not affect the growth characteristics of the strain, but it significantly reduced the ability of SS to form biofilms, adhesion to host cells, phagocytic resistance to macrophages and attenuated virulence in a mouse infection model. These results indicated that Cba was a virulence related factor of SS9. In addition, Mice immunized with the Cba protein had higher mortality and more serious organ lesions after challenge, and the same was observed in passive immunization experiments. This phenomenon is similar to the antibody-dependent enhancement of infection by bacteria such as Acinetobacter baumannii and Streptococcus pneumoniae. To our knowledge, this is the first demonstration of antibody-dependent enhancement of SS, and these observations highlight the complexity of antibody-based therapy for SS infection.
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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.
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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,
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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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Kamble S, Barale S, Dhanavade M, Sonawane K. Structural significance of Neprylysin from Streptococcus suis GZ1 in the degradation of Aβ peptides, a causative agent in Alzheimer's disease. Comput Biol Med 2021; 136:104691. [PMID: 34343891 DOI: 10.1016/j.compbiomed.2021.104691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/24/2021] [Accepted: 07/25/2021] [Indexed: 11/17/2022]
Abstract
Alzheimer's disease (AD) is a progressive brain disorder. The accumulation of amyloid beta (Aβ) peptides in the human brain leads to AD. The cleavage of Aβ peptides by several enzymes is being considered as an essential aspect in the treatment of AD. Neprilysin (NEP) is an important enzyme that clears the Aβ plaques in the human brain. The human NEP activity has been found reduced due to mutations in NEP and the presence of inhibitors. However, the role of NEP in the degradation of Aβ peptides in detail at the molecular level is not yet clear. Hence, in the present study, we have investigated the structural significance of NEP from the bacterial source Streptococcus suis GZ1 using various bioinformatics approaches. The homology modelling technique was used to predict the three-dimensional structure of NEP. Further, molecular dynamic (MD) simulated model of NEP was docked with Aβ peptide. Analysis of MD simulated docked complex showed that the wild-type NEP-Aβ-peptide complex is more stable as compared to mutant complex. Hydrogen bonding interactions between NEP with Zn2+and Aβ peptide confirm the degradation of the Aβ peptide. The molecular docking and MD simulation results revealed that the active site residue Glu-538 of bacterial NEP along with Zn2+ interact with His-13 of Aβ peptide. This stable interaction confirms the involvement of NEP with Glu-538 in the degradation of the Aβ peptide. The other residues such as Glu203, Ser537, Gly140, Val587, and Val536 could also play an important role in the cleavage of Aβ peptide in between Asp1-Ala2, Arg5-His6, Val18-Phe19, Gly9-Tyr10, and Arg5-His6. Hence, the predicted model of the NEP enzyme of Streptococcus suis GZ1could be useful to understand the Aβ peptide degradation in detail at the molecular level. The information obtained from this study would be helpful in designing new lead molecules for the effective treatment of AD.
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Affiliation(s)
- Subodh Kamble
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416004, M.S., India
| | - Sagar Barale
- Department of Microbiology, Shivaji University, Kolhapur, 416004, M.S., India
| | - Maruti Dhanavade
- Department of Microbiology, Bharati Vidyapeeth's Dr. Patangrao Kadam Mahavidyalaya Sangli, Pin-416416, India
| | - Kailas Sonawane
- Structural Bioinformatics Unit, Department of Biochemistry, Shivaji University, Kolhapur, 416004, M.S., India; Department of Microbiology, Shivaji University, Kolhapur, 416004, M.S., India.
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Xu L, Lin L, Lu X, Xiao P, Liu R, Wu M, Jin M, Zhang A. Acquiring high expression of suilysin enable non-epidemic Streptococccus suis to cause streptococcal toxic shock-like syndrome (STSLS) through NLRP3 inflammasome hyperactivation. Emerg Microbes Infect 2021; 10:1309-1319. [PMID: 33792531 PMCID: PMC8253218 DOI: 10.1080/22221751.2021.1908098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The epidemic Streptococcus suis (S. suis) strain [Sequence type (ST) 7] was gradually evolving from the non-epidemic ST1 strain and got the ability for high expressing of suilysin (SLY). And the high expression of SLY was required for the epidemic strain to cause NLRP3 hyperactivation, which is essential for the induction of cytokines storm, dysfunction of multiple organs, and a high incidence of mortality, the characters of streptococcal toxic shock-like syndrome (STSLS). However, it remains to be elucidated whether acquiring high SLY expression due to genome evolution was sufficient for the non-epidemic strain to cause STSLS. Here, we found that the overexpression of SLY in ST1 strain (P1/7-SLY) could obviously increase the inflammasome activation, which was dependent on NLRP3 signalling. In contrast, the strain (P1/7-mSLY) overexpressing the mutant SLY (protein without hemolytic activity) could not significantly increase the inflammasome activation. Furthermore, similar to the epidemic strain, P1/7-SLY could cause STSLS in nlrp3+/+ mice but not in nlrp3−/− mice. In contrast, P1/7-mSLY could not cause STSLS in both nlrp3+/+ mice and nlrp3−/− mice. In summary, we demonstrate that genetic evolution enabling S. suis strain to express high level of SLY may be an essential and sufficient condition for NLRP3 inflammasome hyperactivation, which could further cause cytokines storm and STSLS.
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Affiliation(s)
- Lei Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Lan Lin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China.,Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xi Lu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Peng Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Ran Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Meizhou Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, People's Republic of China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, People's Republic of China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, People's Republic of China.,Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture of the People's Republic of China, Wuhan, People's Republic of China.,International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, People's Republic of China
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10
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Chen L, Huang J, Huang X, He Y, Sun J, Dai X, Wang X, Shafiq M, Wang L. Horizontal Transfer of Different erm(B)-Carrying Mobile Elements Among Streptococcus suis Strains With Different Serotypes. Front Microbiol 2021; 12:628740. [PMID: 33841355 PMCID: PMC8032901 DOI: 10.3389/fmicb.2021.628740] [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: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 11/24/2022] Open
Abstract
Macrolide-resistant Streptococcus suis is highly prevalent worldwide. The acquisition of the erm(B) gene mediated by mobile genetic elements (MGEs) in particular integrative and conjugative elements (ICEs) is recognized as the main reason for the rapid spread of macrolide-resistant streptococcal strains. However, knowledge about different erm(B)-carrying elements responsible for the widespread of macrolide resistance and their transferability in S. suis remains poorly understood. In the present study, two erm(B)- and tet(O)-harboring putative ICEs, designated as ICESsuYSB17_rplL and ICESsuYSJ15_rplL, and a novel erm(B)- and aadE-spw-like-carrying genomic island (GI), named GISsuJHJ17_rpsI, were identified to be excised from the chromosome and transferred among S. suis strains with different serotypes. ICESsuYSB17_rplL and ICESsuYSJ15_rplL were integrated downstream the rplL gene, a conserve locus of the ICESa2603 family. GISsuJHJ17_rpsI, with no genes belonging to the conjugation module, was integrated into the site of rpsI. All transconjugants did not exhibit obvious fitness cost by growth curve and competition assays when compared with the recipient. The results demonstrate that different erm(B)-carrying elements were presented and highlight the role of these elements in the dissemination of macrolide resistance in S. suis.
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Affiliation(s)
- Li Chen
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jinhu Huang
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xinxin Huang
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Yuping He
- Technical Center for Animal, Plant and Food Inspection and Quarantine of Shanghai Customs, Shanghai, China
| | - Junjie Sun
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xingyang Dai
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaoming Wang
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Shafiq
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Liping Wang
- Ministry of Education (MOE) Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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11
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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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12
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Yi S, Huang J, Hu X, Chen L, Dai X, Sun J, Liu P, Wang X, Wen J, Wang L. Nonconservative integration and diversity of a new family of integrative and conjugative elements associated with antibiotic resistance in zoonotic pathogen Streptococcus suis. Vet Microbiol 2021; 254:109009. [PMID: 33640677 DOI: 10.1016/j.vetmic.2021.109009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/02/2021] [Indexed: 11/24/2022]
Abstract
Macrolide and tetracycline resistance in streptococci is mainly caused by acquisition of integrative and conjugative elements (ICEs) of the ICESa2603 family carrying erm(B) and tet(O). But the characteristics about the transferability and physiological consequences of ICEs with triplet serine integrases are still rare. This study tested the transferability of ICESsuYZDH1_SSU0877, a novel erm(B)- and tet(O)-carrying ICESa2603 family-like ICE with triplet serine integrases, and evaluated the physiological consequences after ICE transferred and integrated into recipient. The prevalence of ICESsuYZDH1-like ICEs in S. suis was analyzed based on 1334 genomic sequences available in GenBank and examined in 330 clinical isolates in China. Nonconservative transfer was observed by integrating of ICESsuYZDH1 into SSU1797 gene besides the primary SSU0877 site. Imperfect direct repeats of 2-/4-nt (5'-TC-3'/5'-TCCC-3') and (5'-GC-3'/5'-TCCC-3') were observed at SSU0877 and SSU1797 sites, respectively. The transconjugant suffered a weak fitness cost with stunted growth and less competition with recipient strain. Successive passages indicate the ICESsuYZDH1 could be persist and endued stable resistant phenotype. Comprehensive analysis of the ICESsuYZDH1-like ICEs from both public genome database and our clinical isolates revealed the widespread and diversity of the ICEs by integration at the sites of SSU0877, SSU0468, SSU1262, and SSU1797. The ICESsuYZDH1-like ICEs could stably co-exist within the host chromosome at more than one attachment sites, which is probably mediated by the triplet serine integrases. Nonconservative integration and diversity of the ICESsuYZDH1 family of ICEs might have contributed to the evolution of ICEs and the dissemination of macrolide and tetracycline resistance in S. suis.
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Affiliation(s)
- Sida Yi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Hu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
| | - Li Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingyang Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Junjie Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiyu Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Wen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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13
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Zondervan NA, Martins Dos Santos VAP, Suarez-Diez M, Saccenti E. Phenotype and multi-omics comparison of Staphylococcus and Streptococcus uncovers pathogenic traits and predicts zoonotic potential. BMC Genomics 2021; 22:102. [PMID: 33541265 PMCID: PMC7860044 DOI: 10.1186/s12864-021-07388-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 01/13/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Staphylococcus and Streptococcus species can cause many different diseases, ranging from mild skin infections to life-threatening necrotizing fasciitis. Both genera consist of commensal species that colonize the skin and nose of humans and animals, and of which some can display a pathogenic phenotype. RESULTS We compared 235 Staphylococcus and 315 Streptococcus genomes based on their protein domain content. We show the relationships between protein persistence and essentiality by integrating essentiality predictions from two metabolic models and essentiality measurements from six large-scale transposon mutagenesis experiments. We identified clusters of strains within species based on proteins associated to similar biological processes. We built Random Forest classifiers that predicted the zoonotic potential. Furthermore, we identified shared attributes between of Staphylococcus aureus and Streptococcus pyogenes that allow them to cause necrotizing fasciitis. CONCLUSIONS Differences observed in clustering of strains based on functional groups of proteins correlate with phenotypes such as host tropism, capability to infect multiple hosts and drug resistance. Our method provides a solid basis towards large-scale prediction of phenotypes based on genomic information.
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Affiliation(s)
- Niels A Zondervan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands
- LifeGlimmer GmBH, Markelstraße 38, 12163, Berlin, Germany
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708WE, Wageningen, Netherlands.
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14
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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: 11] [Impact Index Per Article: 3.7] [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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15
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Zoledowska S, Motyka-Pomagruk A, Misztak A, Lojkowska E. Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. Methods Mol Biol 2021; 2242:91-112. [PMID: 33961220 DOI: 10.1007/978-1-0716-1099-2_7] [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] [Indexed: 06/12/2023]
Abstract
High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. All of them were applied in the studies focused on revealing inter- and intraspecies variation in pectinolytic plant pathogenic bacteria classified to Dickeya solani and Pectobacterium parmentieri. As the described software performed well on the species within the Pectobacteriaceae family, it presumably may be readily utilized on some closely related taxa from the Enterobacteriaceae family. First of all, implementation of various annotation software is discussed and compared. Then, tools computing whole genome comparisons including generation of circular juxtapositions of multiple sequences, revealing the order of synteny blocks or calculation of ANI or Tetra values are presented. Besides, web servers intended either for functional annotation of the genes of interest or for detection of genomic islands, plasmids, prophages, CRISPR/Cas are described. Last but not least, utilization of the software designed for pangenome studies and the further downstream analyses is explained. The presented work not only summarizes broad possibilities assured by the comparative genomic approach but also provides a user-friendly guide that might be easily followed by nonbioinformaticians interested in undertaking similar studies.
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Affiliation(s)
- Sabina Zoledowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
- Institute of Biotechnology and Molecular Medicine, Gdansk, 3 Trzy Lipy, Poland
| | - Agata Motyka-Pomagruk
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
| | - Agnieszka Misztak
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland
| | - Ewa Lojkowska
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland.
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16
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Zou Y, Sun Y, Qi H, Liu D, Tian H, Wang N, Li X. Streptococcus xiaochunlingii sp. nov. E24 Isolated From the Oropharynx of Healthy Chinese Children. Front Microbiol 2020; 11:563213. [PMID: 33133039 PMCID: PMC7550633 DOI: 10.3389/fmicb.2020.563213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
A Gram-positive, α-hemolytic, catalase-negative, facultative anaerobic and non-motile coccus was isolated form throat swabs taken from the oropharynx of healthy children. The genome was shown to be 1.950,659 bp long and contained 42.03 mol% G + C bases with 1,942 protein-coding and 53 RNA coding genes. The results of 16S rRNA gene sequencing strongly suggested that the strain is a member of the Streptococcus genus, with 98.04, 98.11, and 97.34% similarities to Streptococcus australis ATCC 700641T, Streptococcus rubneri LMG 27207T and Streptococcus parasanguinis ATCC 15912T, respectively. A sodA gene comparison exhibited a sequence identity of 92.6% with the closest strain Streptococcus australis ATCC 700641T. In silico DNA-DNA hybridization showed a highest DNA similarity value of 52% with Streptococcus australis ATCC 700641T. Comparing 18 biochemical traits, the similarities of the Streptococcus strain E24 were 72% with Streptococcus rubneri LMG 27207T, 78% with Streptococcus australis ATCC 700641T and 44% with Streptococcus parasanguinis ATCC 15912T. We suggest that based on the genotypic and phenotypic results that the strain E24 is a novel species of the Streptococcus genus and propose the name Streptococcus xiaochunlingii sp. nov. E24.
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Affiliation(s)
- Yang Zou
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Ye Sun
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - He Qi
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Defeng Liu
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Han Tian
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Nan Wang
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
| | - Xinming Li
- Key Laboratory of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, Shenyang, China
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17
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Yun BR, Malik A, Kim SB. Genome based characterization of Kitasatospora sp. MMS16-BH015, a multiple heavy metal resistant soil actinobacterium with high antimicrobial potential. Gene 2020; 733:144379. [PMID: 31972312 DOI: 10.1016/j.gene.2020.144379] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/26/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022]
Abstract
An actinobacterial strain designated Kitasatospora sp. MMS16-BH015, exhibiting high level of heavy metal resistance, was isolated from soil of an abandoned metal mining site, and its potential for metal resistance and secondary metabolite production was studied. The strain was resistant to multiple heavy metals including zinc (up to 100 mM), nickel (up to 2 mM) and copper (up to 0.8 mM), and also showed antimicrobial potential against a broad group of microorganisms, in particular filamentous fungi. The genome of strain MMS16-BH015 was 8.96 Mbp in size with a G + C content of 72.7%, and contained 7270 protein-coding genes and 107 tRNA/rRNA genes. The genome analysis revealed presence of at least 121 metal resistance related genes, which was prominently higher in strain MMS16-BH015 compared to other genomes of Kitasatospora. The genes included those for proteins representing various families involved in the transport of heavy metals, for example dipeptide transport ATP-binding proteins, high-affinity nickel transport proteins, and P-type heavy metal-transporting ATPases. Additionally, 43 biosynthetic gene clusters (BGCs) for secondary metabolites, enriched with those for non-ribosomal peptides, were detected in this multiple heavy metal resistant actinobacterium, which was again the highest among the compared genomes of Kitasatospora. The pan-genome analysis also identified higher numbers of unique genes related to secondary metabolite production and metal resistance mechanism in strain MMS16-BH015. A high level of correlation between the biosynthetic potential and heavy metal resistance could be observed, thus indicating that heavy metal resistant actinobacteria can be a promising source of bioactive compounds.
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Affiliation(s)
- Bo-Ram Yun
- Department of Microbiology and Molecular Biology, 99 Daehak-Ro, Yuseong, Daejeon 34134, Chungnam National University, Daejeon, Republic of Korea; Bacterial Disease Division, Animal and Plant Quarantine Agency, 177, Hyeoksin 8-Ro, Gimcheon, Gyeongsangbuk-Do 39660, Republic of Korea
| | - Adeel Malik
- Department of Microbiology and Molecular Biology, 99 Daehak-Ro, Yuseong, Daejeon 34134, Chungnam National University, Daejeon, Republic of Korea
| | - Seung Bum Kim
- Department of Microbiology and Molecular Biology, 99 Daehak-Ro, Yuseong, Daejeon 34134, Chungnam National University, Daejeon, Republic of Korea.
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18
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Zhao Y, Li G, Yao XY, Lu SG, Wang J, Shen XD, Li M. The Impact of SsPI-1 Deletion on Streptococcus suis Virulence. Pathogens 2019; 8:pathogens8040287. [PMID: 31817637 PMCID: PMC6963714 DOI: 10.3390/pathogens8040287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/26/2023] Open
Abstract
(1) Background: Streptococcus suis is an important zoonotic pathogen that infects pigs and can occasionally cause life-threatening systemic infections in humans. Two large-scale outbreaks of streptococcal toxic shock-like syndrome in China suggest that the pathogenicity of S. suis has been changing in recent years. Genetic analysis revealed the presence of a chromosomal pathogenicity island (PAI) designated SsPI-1 in Chinese epidemic S. suis strains. The purpose of this study is to define the role of SsPI-1 in the virulence of S. suis. (2) Methods: A SsPI-1 deletion mutant was compared to the wild-type strain regarding the ability to attach to epithelial cells, to cause host disease and mortality, and to stimulate host immune response in experimental infection of piglets. (3) Results: Deletion of SsPI-1 significantly reduces adherence of S. suis to epithelial cells and abolishes the lethality of the wild-type strain in piglets. The SsPI-1 mutant causes no significant pathological lesions and exhibits an impaired ability to induce proinflammatory cytokine production. (4) Conclusions: Deletion of the SsPI-1 PAI attenuates the virulence of this pathogen. We conclude that SsPI-1 is a critical contributor to the evolution of virulence in epidemic S. suis.
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Affiliation(s)
- Yan Zhao
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Key Laboratory of Microbial Engineering under the Educational Committee in Chongqing, Chongqing 400038, China; (Y.Z.); (G.L.); (S.-G.L.); (J.W.)
| | - Gang Li
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Key Laboratory of Microbial Engineering under the Educational Committee in Chongqing, Chongqing 400038, China; (Y.Z.); (G.L.); (S.-G.L.); (J.W.)
| | - Xin-Yue Yao
- Jinling Hospital Research Institute of Clinical Laboratory Medicine, Nanjing University, School of Medicine, Nanjing 210002, China;
| | - Shu-Guang Lu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Key Laboratory of Microbial Engineering under the Educational Committee in Chongqing, Chongqing 400038, China; (Y.Z.); (G.L.); (S.-G.L.); (J.W.)
| | - Jing Wang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Key Laboratory of Microbial Engineering under the Educational Committee in Chongqing, Chongqing 400038, China; (Y.Z.); (G.L.); (S.-G.L.); (J.W.)
| | - Xiao-Dong Shen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Chongqing 400038, China
- Correspondence: (M.L.); (X.-D.S.); Tel.: +86-23-68772241 (M.L.)
| | - Ming Li
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University (Third Military Medical University), Key Laboratory of Microbial Engineering under the Educational Committee in Chongqing, Chongqing 400038, China; (Y.Z.); (G.L.); (S.-G.L.); (J.W.)
- Correspondence: (M.L.); (X.-D.S.); Tel.: +86-23-68772241 (M.L.)
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19
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Ma J, Liu J, Zhang Y, Wang D, Liu R, Liu G, Yao H, Pan Z. Bacitracin resistance and enhanced virulence of Streptococcus suis via a novel efflux pump. BMC Vet Res 2019; 15:377. [PMID: 31660968 PMCID: PMC6819616 DOI: 10.1186/s12917-019-2115-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/26/2019] [Indexed: 02/08/2023] Open
Abstract
Background Streptococcus suis is a prominent pathogen causing septicemia and meningitis in swine and humans. Bacitracin is used widely as a growth promoter in animal feed and to control the spread of necrotic enteritis in most developing countries. This study aimed to characterize a novel membrane transporter module Sst comprising SstE, SstF, and SstG for bacitracin resistance. Results Comparative genomics and protein homology analysis found a potential efflux pump SstFEG encoded upstream of well-known bacitracin-resistance genes bceAB and bceRS. A four-fold decrease in bacitracin susceptibility was observed in sstFEG deletion mutant comparing with S. suis wildtype strain CZ130302. Further studies indicated that the bacitracin tolerance mediated by SstFEG is not only independent of the BceAB transporter, but also regulated by the two-component system BceSR. Given that SstFEG are harbored by almost all virulent strains, but not in the avirulent strains, we managed to explore its potential role in bacterial pathogencity. Indeed, our results showed that SstFEG is involved in S. suis colonization and virulence in animal infection model by its potential competitive survival advantage against host bactericidal effect. Conclusion To our knowledge, this is the first study to functionally characterize the bacitracin efflux pump in S. suis to provide evidence regarding the important roles of the novel ABC transporter system SstFEG with respect to drug resistance and virulence.
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Affiliation(s)
- Jiale Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, 210095, China
| | - Jin Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yue Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, 210095, China
| | - Dan Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, 210095, China
| | - Runxia Liu
- South Dakota State University, Brookings, SD, 57007, USA
| | - Guangjin Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, 210095, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, 210095, China.,MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China
| | - Zihao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China. .,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, 210095, China. .,MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing, China.
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20
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Shelyakin PV, Bochkareva OO, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow. BMC Evol Biol 2019; 19:83. [PMID: 30917781 PMCID: PMC6437910 DOI: 10.1186/s12862-019-1403-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae. Results Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism. Conclusions Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines. Electronic supplementary material The online version of this article (10.1186/s12862-019-1403-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pavel V Shelyakin
- Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina str. 3, Moscow, 119991, Russia. .,Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia. .,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
| | - Olga O Bochkareva
- Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna A Karan
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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21
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Wirojsirasak W, Kalapanulak S, Saithong T. Pan- and core- gene association networks: Integrative approaches to understanding biological regulation. PLoS One 2019; 14:e0210481. [PMID: 30625202 PMCID: PMC6326509 DOI: 10.1371/journal.pone.0210481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/25/2018] [Indexed: 02/06/2023] Open
Abstract
The rapid increase in transcriptome data provides an opportunity to access the complex regulatory mechanisms in cellular systems through gene association network (GAN). Nonetheless, GANs derived from single datasets generally allow us to envisage only one side of the regulatory network, even under the particular condition of study. The circumstance is well demonstrated by inconsistent GANs of individual datasets proposed for similar experimental conditions, which always leads to ambiguous interpretation. Here, pan- and core-gene association networks (pan- and core-GANs), analogous to the pan- and core-genome concepts, are proposed to increase the power of inference through the integration of multiple, diverse datasets. The core-GAN represents the consensus associations of genes that were inferred from all individual networks. On the other hand, the pan-GAN represents the extensive gene-gene associations that occurred in each individual network. The pan- and core-GANs prospects were demonstrated based on three time series microarray datasets in leaves of Arabidopsis thaliana grown under diurnal conditions. We showed the overall performance of pan- and core-GANs was more robust to the number of data points in gene expression data compared to the GANs inferred from individual datasets. In addition, the incorporation of multiple data broadened our understanding of the biological regulatory system. While the pan-GAN enabled us to observe the landscape of gene association system, core-GAN highlighted the basic gene-associations in essence of the regulation regulating starch metabolism in leaves of Arabidopsis.
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Affiliation(s)
- Warodom Wirojsirasak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Saowalak Kalapanulak
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Treenut Saithong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- * E-mail:
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22
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Chen X, Zhang Y, Zhang Z, Zhao Y, Sun C, Yang M, Wang J, Liu Q, Zhang B, Chen M, Yu J, Wu J, Jin Z, Xiao J. PGAweb: A Web Server for Bacterial Pan-Genome Analysis. Front Microbiol 2018; 9:1910. [PMID: 30186253 PMCID: PMC6110895 DOI: 10.3389/fmicb.2018.01910] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 01/22/2023] Open
Abstract
An astronomical increase in microbial genome data in recent years has led to strong demand for bioinformatic tools for pan-genome analysis within and across species. Here, we present PGAweb, a user-friendly, web-based tool for bacterial pan-genome analysis, which is composed of two main pan-genome analysis modules, PGAP and PGAP-X. PGAweb provides key interactive and customizable functions that include orthologous clustering, pan-genome profiling, sequence variation and evolution analysis, and functional classification. PGAweb presents features of genomic structural dynamics and sequence diversity with different visualization methods that are helpful for intuitively understanding the dynamics and evolution of bacterial genomes. PGAweb has an intuitive interface with one-click setting of parameters and is freely available at http://PGAweb.vlcc.cn/.
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Affiliation(s)
- Xinyu Chen
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
| | - Yadong Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhewen Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yongbing Zhao
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chen Sun
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Ming Yang
- Office of General Affairs, Chinese Academy of Sciences, Beijing, China
| | - Jinyue Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qian Liu
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
| | - Baohua Zhang
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
| | - Meili Chen
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.,Center of Scientific Computing Applications and Research, Chinese Academy of Sciences, Beijing, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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23
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Abstract
Streptococcus suis is an important swine pathogen that can also cause severe diseases in humans. Herein, we describe the genome sequence of Streptococcus suis serotype 2 virulent strain SS2-1, which was isolated from a diseased dead pig amid the 1998 Streptococcus suis outbreak in Jiangsu Province in China.
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24
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Zheng H, Du P, Qiu X, Kerdsin A, Roy D, Bai X, Xu J, Vela AI, Gottschalk M. Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada. Vet Res 2018; 49:1. [PMID: 29316972 PMCID: PMC5759227 DOI: 10.1186/s13567-017-0498-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 12/07/2017] [Indexed: 11/21/2022] Open
Abstract
Streptococcus suis is one of the most important bacterial pathogens in the porcine industry and also a zoonotic agent. Serotype 9 is becoming one of the most prevalent serotypes within the S. suis population in certain European countries. In the present study, serotype 9 strains isolated from a country where infection due to this serotype is endemic (Spain), were compared to those recovered from Canada, where this serotype is rarely isolated from diseased pigs. For comparison purposes, strains from Brazil and the only strain isolated from a human case, in Thailand, were also incorporated. Firstly, sequence types (STs) were obtained followed by detection of putative virulence factors. Phylogenetic trees were constructed using the non-recombinant single nucleotide polymorphisms from core genomes of tested strains. Most Spanish strains were either ST123 or ST125, whereas Canadian strains were highly heterogeneous. However, the distribution of putative virulence factors was similar in both groups of strains. The fact that ST16 strains harbored more putative virulence genes and shared greater similarity with the genome of human serotype 2 strains suggests that they present a higher zoonotic and virulence potential than those from Canada and Spain. More than 80% of the strains included in this study carried genes associated with resistance to tetracycline, lincosamides and macrolides. Serotype 9 strains may be nearly 400 years old and have evolved in parallel into 2 lineages. The rapid population expansion of dominant lineage 1 occurred within the last 40 years probably due to the rapid development of the porcine industry.
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Affiliation(s)
- Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Pengchen Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaotong Qiu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Bangkok, Sakon Nakhon, Thailand
| | - David Roy
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC, Canada
| | - Xuemei Bai
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| | - Ana I Vela
- Departamento de Sanidad Animal, Facultad de Veterinaria and Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense de Madrid, Madrid, Spain
| | - Marcelo Gottschalk
- Swine and Poultry Infectious Diseases Research Center, Faculty of Veterinary Medicine, University of Montreal, Montreal, QC, Canada.
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25
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Chuzeville S, Auger JP, Dumesnil A, Roy D, Lacouture S, Fittipaldi N, Grenier D, Gottschalk M. Serotype-specific role of antigen I/II in the initial steps of the pathogenesis of the infection caused by Streptococcus suis. Vet Res 2017; 48:39. [PMID: 28705175 PMCID: PMC5513104 DOI: 10.1186/s13567-017-0443-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/19/2017] [Indexed: 01/15/2023] Open
Abstract
Streptococcus suis is one of the most important post-weaning porcine bacterial pathogens worldwide. The serotypes 2 and 9 are often considered the most virulent and prevalent serotypes involved in swine infections, especially in Europe. However, knowledge of the bacterial factors involved in the first steps of the pathogenesis of the infection remains scarce. In several pathogenic streptococci, expression of multimodal adhesion proteins known as antigen I/II (AgI/II) have been linked with persistence in the upper respiratory tract and the oral cavity, as well as with bacterial dissemination. Herein, we report expression of these immunostimulatory factors by S. suis serotype 2 and 9 strains and that AgI/II-encoding genes are carried by integrative and conjugative elements. Using mutagenesis and different in vitro assays, we demonstrate that the contribution of AgI/II to the virulence of the serotype 2 strain used herein appears to be modest. In contrast, data demonstrate that the serotype 9 AgI/II participates in self-aggregation, induces salivary glycoprotein 340-related aggregation, contributes to biofilm formation and increased strain resistance to low pH, as well as in bacterial adhesion to extracellular matrix proteins and epithelial cells. Moreover, the use of a porcine infection model revealed that AgI/II contributes to colonization of the upper respiratory tract of pigs. Taken together, these findings suggest that surface exposed AgI/II likely play a key role in the first steps of the pathogenesis of the S. suis serotype 9 infection.
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Affiliation(s)
- Sarah Chuzeville
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Saint-Hyacinthe, QC, Canada.,Groupe de recherche sur les maladies infectieuses en production animale (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - Jean-Philippe Auger
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Saint-Hyacinthe, QC, Canada.,Groupe de recherche sur les maladies infectieuses en production animale (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - Audrey Dumesnil
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Saint-Hyacinthe, QC, Canada.,Groupe de recherche sur les maladies infectieuses en production animale (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - David Roy
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Saint-Hyacinthe, QC, Canada.,Groupe de recherche sur les maladies infectieuses en production animale (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - Sonia Lacouture
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Saint-Hyacinthe, QC, Canada.,Groupe de recherche sur les maladies infectieuses en production animale (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., Saint-Hyacinthe, QC, J2S 2M2, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario Laboratory Toronto and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Daniel Grenier
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Saint-Hyacinthe, QC, Canada.,Oral Ecology Research Group, Faculty of Dentistry, Laval University, Quebec City, QC, Canada
| | - Marcelo Gottschalk
- Swine and Poultry Infectious Diseases Research Center (CRIPA), Saint-Hyacinthe, QC, Canada. .,Groupe de recherche sur les maladies infectieuses en production animale (GREMIP), Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte St., Saint-Hyacinthe, QC, J2S 2M2, Canada.
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26
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Draft Genome Sequence of Clinical Strain TANI1 of Streptococcus suis Serotype 5 Isolated from a Bacteremia Patient in Japan. GENOME ANNOUNCEMENTS 2017; 5:5/18/e00260-17. [PMID: 28473377 PMCID: PMC5477185 DOI: 10.1128/genomea.00260-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Streptococcus suis is a swine pathogen that causes severe economic damage to the porcine industry. It occasionally evokes zoonotic infection in humans. Here, we report a draft genome sequence of a S. suis serotype 5 strain isolated from a bacteremia patient that was reported by Taniyama et al. (D. Taniyama, M. Sakurai, T. Sakai, T. Kikuchi, and T. Takahashi, IDCases 6:36–38, 2016, https://doi.org/10.1016/j.idcr.2016.09.011).
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27
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Okura M, Nozawa T, Watanabe T, Murase K, Nakagawa I, Takamatsu D, Osaki M, Sekizaki T, Gottschalk M, Hamada S, Maruyama F. A Locus Encoding Variable Defense Systems against Invading DNA Identified in Streptococcus suis. Genome Biol Evol 2017; 9:1000-1012. [PMID: 28379509 PMCID: PMC5398294 DOI: 10.1093/gbe/evx062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
Streptococcus suis, an important zoonotic pathogen, is known to have an open pan-genome and to develop a competent state. In S. suis, limited genetic lineages are suggested to be associated with zoonosis. However, little is known about the evolution of diversified lineages and their respective phenotypic or ecological characteristics. In this study, we performed comparative genome analyses of S. suis, with a focus on the competence genes, mobile genetic elements, and genetic elements related to various defense systems against exogenous DNAs (defense elements) that are associated with gene gain/loss/exchange mediated by horizontal DNA movements and their restrictions. Our genome analyses revealed a conserved competence-inducing peptide type (pherotype) of the competence system and large-scale genome rearrangements in certain clusters based on the genome phylogeny of 58 S. suis strains. Moreover, the profiles of the defense elements were similar or identical to each other among the strains belonging to the same genomic clusters. Our findings suggest that these genetic characteristics of each cluster might exert specific effects on the phenotypic or ecological differences between the clusters. We also found certain loci that shift several types of defense elements in S. suis. Of note, one of these loci is a previously unrecognized variable region in bacteria, at which strains of distinct clusters code for different and various defense elements. This locus might represent a novel defense mechanism that has evolved through an arms race between bacteria and invading DNAs, mediated by mobile genetic elements and genetic competence.
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Affiliation(s)
- Masatoshi Okura
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takashi Nozawa
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
| | - Takayasu Watanabe
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Kazunori Murase
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
| | - Daisuke Takamatsu
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, Japan
| | - Makoto Osaki
- Division of Bacterial and Parasitic Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Tsutomu Sekizaki
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal, St-Hyacinthe, Quebec, Canada
| | - Shigeyuki Hamada
- Research Institute for Microbial Diseases, Thailand-Japan Collaboration Center for Emerging and Re-emerging Infections, Osaka University, Suita-Osaka, Japan
| | - Fumito Maruyama
- Department of Microbiology, Kyoto University Graduate School of Medicine, Japan
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28
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Li Q, Fu Y, Ma C, He Y, Yu Y, Du D, Yao H, Lu C, Zhang W. The non-conserved region of MRP is involved in the virulence of Streptococcus suis serotype 2. Virulence 2017; 8:1274-1289. [PMID: 28362221 DOI: 10.1080/21505594.2017.1313373] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Muramidase-released protein (MRP) of Streptococcus suis serotype 2 (SS2) is an important epidemic virulence marker with an unclear role in bacterial infection. To investigate the biologic functions of MRP, 3 mutants named Δmrp, Δmrp domain 1 (Δmrp-d1), and Δmrp domain 2 (Δmrp-d2) were constructed to assess the phenotypic changes between the parental strain and the mutant strains. The results indicated that MRP domain 1 (MRP-D1, the non-conserved region of MRP from a virulent strain, a.a. 242-596) played a critical role in adherence of SS2 to host cells, compared with MRP domain 1* (MRP-D1*, the non-conserved region of MRP from a low virulent strain, a.a. 239-598) or MRP domain 2 (MRP-D2, the conserved region of MRP, a.a. 848-1222). We found that MRP-D1 but not MRP-D2, could bind specifically to fibronectin (FN), factor H (FH), fibrinogen (FG), and immunoglobulin G (IgG). Additionally, we confirmed that mrp-d1 mutation significantly inhibited bacteremia and brain invasion in a mouse infection model. The mrp-d1 mutation also attenuated the intracellular survival of SS2 in RAW246.7 macrophages, shortened the growth ability in pig blood and decreased the virulence of SS2 in BALB/c mice. Furthermore, antiserum against MRP-D1 was found to dramatically impede SS2 survival in pig blood. Finally, immunization with recombinant MRP-D1 efficiently enhanced murine viability after SS2 challenge, indicating its potential use in vaccination strategies. Collectively, these results indicated that MRP-D1 is involved in SS2 virulence and eloquently demonstrate the function of MRP in pathogenesis of infection.
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Affiliation(s)
- Quan Li
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Yang Fu
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Caifeng Ma
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Yanan He
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Yanfei Yu
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Dechao Du
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Huochun Yao
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Chengping Lu
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
| | - Wei Zhang
- a Key Lab of Animal Bacteriology, OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Ministry of Agriculture , Nanjing Agricultural University , Nanjing , China
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Yuan L, Yu Y, Zhu Y, Li Y, Li C, Li R, Ma Q, Siu GKH, Yu J, Jiang T, Xiao J, Kang Y. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes. BMC Genomics 2017; 18:952. [PMID: 28198678 PMCID: PMC5310280 DOI: 10.1186/s12864-016-3267-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. RESULTS Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. CONCLUSIONS GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.
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Affiliation(s)
- Lina Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Yang Yu
- School of Life Sciences, Liaoning University, Shenyang, 110036, China
| | - Yanmin Zhu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yulai Li
- Beijing SpeedyCloud Technologies Co., Ltd., Beijing, 110036, China
| | - Changqing Li
- Department of Otolaryngology, Beijing Geriatric Hospital, Beijing, 100095, China
| | - Rujiao Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qin Ma
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taijiao Jiang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.,Suzhou Institute of Systems Medicine, Suzhou, 215123, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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Characterization of Spectinomycin Resistance in Streptococcus suis Leads to Two Novel Insights into Drug Resistance Formation and Dissemination Mechanism. Antimicrob Agents Chemother 2016; 60:6390-2. [PMID: 27458226 DOI: 10.1128/aac.01157-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022] Open
Abstract
Spectinomycin is an aminocyclitol antibiotic used clinically to treat a variety of infections in animals. Here, we characterized drug resistance prevalence in clinical Streptococcus suis isolates and discovered a novel resistance mechanism in which the s5 mutation (Gly26Asp) results in high spectinomycin resistance. Additionally, a novel integrative and conjugative element encompassing a multidrug resistance spw_like-aadE-lnu(B)-lsa(E) cluster and a cadmium resistance operon were identified, suggesting a possible cause for the wide dissemination of spectinomycin resistance in S. suis.
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31
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Huang K, Song Y, Zhang Q, Zhang A, Jin M. Characterisation of a novel integrative and conjugative element ICESsD9 carrying erm(B) and tet(O) resistance determinants in Streptococcus suis, and the distribution of ICESsD9-like elements in clinical isolates. J Glob Antimicrob Resist 2016; 7:13-18. [PMID: 27531000 DOI: 10.1016/j.jgar.2016.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 05/07/2016] [Accepted: 05/25/2016] [Indexed: 12/01/2022] Open
Abstract
This study identified a novel integrative and conjugative element (ICESsD9) carrying erm(B) and tet(O) resistance determinants in Streptococcus suis D9 and determined its prevalence in clinical isolates. Comparative genome analysis was performed using Mauve and Artemis Comparison Tool visualisation programs. Inverse PCR was utilised to detect its circular intermediate. The transfer capacity of ICESsD9 was evaluated by mating assays using S. suis A7 and Enterococcus faecalis JH2-2 as recipients. A genome walking approach was employed to analyse the characteristics of integration sites in transconjugants. A total of 118 clinical S. suis isolates were tested by PCR mapping assays to detect ICESsD9-like elements. MLST was performed on isolates containing ICESsD9 variants to determine their clonal relatedness. This 55 683-bp element can actively excise from the chromosome. Additionally, it was capable of transferring both into S. suis and E. faecalis with frequencies of 1.2×10-4 and 5.8×10-6 per donor, respectively. When investigating integration site features, it was found that ICESsD9 can enter S. suis and E. faecalis chromosomes by different sites, generating 15-bp and 3-bp direct repeat sequences, respectively. Twelve isolates mainly belonging to sequence types ST1, ST7 and ST28 were confirmed to harbour ICESsD9-like elements. In conclusion, this study provides the first description of an ICE in S. suis that is capable of transferring both into S. suis and E. faecalis. The presence of different ICESsD9 variants in clinical isolates suggests already wide dissemination of this family element in S. suis in China.
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Affiliation(s)
- Kaisong Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Yajing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Huazhong Agricultural University, Wuhan 430070, China
| | - Meilin Jin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Development of Veterinary Diagnostic Products, Huazhong Agricultural University, Wuhan 430070, China.
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32
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Athey TBT, Teatero S, Lacouture S, Takamatsu D, Gottschalk M, Fittipaldi N. Determining Streptococcus suis serotype from short-read whole-genome sequencing data. BMC Microbiol 2016; 16:162. [PMID: 27449127 PMCID: PMC4957933 DOI: 10.1186/s12866-016-0782-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/15/2016] [Indexed: 11/30/2022] Open
Abstract
Background Streptococcus suis is divided into 29 serotypes based on a serological reaction against the capsular polysaccharide (CPS). Multiplex PCR tests targeting the cps locus are also used to determine S. suis serotypes, but they cannot differentiate between serotypes 1 and 14, and between serotypes 2 and 1/2. Here, we developed a pipeline permitting in silico serotype determination from whole-genome sequencing (WGS) short-read data that can readily identify all 29 S. suis serotypes. Results We sequenced the genomes of 121 strains representing all 29 known S. suis serotypes. We next combined available software into an automated pipeline permitting in silico serotyping of strains by differential alignment of short-read sequencing data to a custom S. suis cps loci database. Strains of serotype pairs 1 and 14, and 2 and 1/2 could be differentiated by a missense mutation in the cpsK gene. We report a 99 % match between coagglutination- and pipeline-determined serotypes for strains in our collection. We used 375 additional S. suis genomes downloaded from the NCBI’s Sequence Read Archive (SRA) to validate the pipeline. Validation with SRA WGS data resulted in a 92 % match. Included pipeline subroutines permitted us to assess strain virulence marker content and obtain multilocus sequence typing directly from WGS data. Conclusions Our pipeline permits rapid and accurate determination of S. suis serotype, and other lineage information, directly from WGS data. By discriminating between serotypes 1 and 14, and between serotypes 2 and 1/2, our approach solves a three-decade longstanding S. suis typing issue. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0782-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Taryn B T Athey
- Public Health Ontario Toronto Laboratory, 661 University Avenue, Toronto, ON, M5G 1M1 Canada
| | - Sarah Teatero
- Public Health Ontario Toronto Laboratory, 661 University Avenue, Toronto, ON, M5G 1M1 Canada
| | - Sonia Lacouture
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC, Canada
| | - Daisuke Takamatsu
- Bacterial and Parasitic Diseases Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan.,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan
| | - Marcelo Gottschalk
- Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, QC, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario Toronto Laboratory, 661 University Avenue, Toronto, ON, M5G 1M1 Canada. .,Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
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33
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Vinogradov E, Goyette-Desjardins G, Okura M, Takamatsu D, Gottschalk M, Segura M. Structure determination of Streptococcus suis serotype 9 capsular polysaccharide and assignment of functions of the cps locus genes involved in its biosynthesis. Carbohydr Res 2016; 433:25-30. [PMID: 27423880 DOI: 10.1016/j.carres.2016.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/24/2016] [Accepted: 07/02/2016] [Indexed: 11/30/2022]
Abstract
Streptococcus suis serotype 9 is the most prevalent S. suis serotype in several European countries. In spite of its pathogenicity for pigs and increasing zoonotic potential, limited information is available on this serotype. Here we determined for the first time the chemical composition and structure of serotype 9 capsular polysaccharide (CPS), a major bacterial virulence factor and the antigen at the origin of S. suis classification into serotypes. Chemical and spectroscopic data gave the repeating unit sequence: [3)Glcol-6-P-3-[D-Gal(α1-2)]D-Gal(β1-3)D-Sug(β1-3)L-Rha(α1-)]n. Compared to previously characterized S. suis CPSs (serotypes 1, 1/2, 2 and 14), serotype 9 CPS does not contain sialic acid but contains a labile 4-keto sugar (2-acetamido-2,6-dideoxy-β-D-xylo-hexopyranos-4-ulose), one particular feature of this serotype. A correlation between S. suis serotype 9 CPS sequence and genes of this serotype cps locus encoding putative glycosyltransferases and polymerase responsible for the biosynthesis of the repeating unit was tentatively established. Knowledge of CPS structure and composition will contribute to better dissect the role of this bacterial component in the pathogenesis of S. suis serotype 9.
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Affiliation(s)
| | | | - Masatoshi Okura
- Bacterial and Parasitic Diseases Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Daisuke Takamatsu
- Bacterial and Parasitic Diseases Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Marcelo Gottschalk
- Laboratory of Research on Streptococcus suis, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, Quebec, Canada
| | - Mariela Segura
- Laboratory of Immunology, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, Quebec, Canada.
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34
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Tian X, Zhang Z, Yang T, Chen M, Li J, Chen F, Yang J, Li W, Zhang B, Zhang Z, Wu J, Zhang C, Long L, Xiao J. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level. Front Microbiol 2016; 7:998. [PMID: 27446038 PMCID: PMC4921485 DOI: 10.3389/fmicb.2016.00998] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 06/13/2016] [Indexed: 11/13/2022] Open
Abstract
Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea's genetic data sources.
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Affiliation(s)
- Xinpeng Tian
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology - Chinese Academy of Sciences Guangzhou, China
| | - Zhewen Zhang
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Tingting Yang
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of SciencesBeijing, China; University of Chinese Academy of SciencesBeijing, China
| | - Meili Chen
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Jie Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology - Chinese Academy of Sciences Guangzhou, China
| | - Fei Chen
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Jin Yang
- Core Genomic Facility, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Wenjie Li
- Core Genomic Facility, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Zhang Zhang
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Jiayan Wu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology - Chinese Academy of Sciences Guangzhou, China
| | - Lijuan Long
- Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology - Chinese Academy of Sciences Guangzhou, China
| | - Jingfa Xiao
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics - Chinese Academy of Sciences Beijing, China
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Gonzalez-Rivera C, Bhatty M, Christie PJ. Mechanism and Function of Type IV Secretion During Infection of the Human Host. Microbiol Spectr 2016; 4:10.1128/microbiolspec.VMBF-0024-2015. [PMID: 27337453 PMCID: PMC4920089 DOI: 10.1128/microbiolspec.vmbf-0024-2015] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Indexed: 02/07/2023] Open
Abstract
Bacterial pathogens employ type IV secretion systems (T4SSs) for various purposes to aid in survival and proliferation in eukaryotic hosts. One large T4SS subfamily, the conjugation systems, confers a selective advantage to the invading pathogen in clinical settings through dissemination of antibiotic resistance genes and virulence traits. Besides their intrinsic importance as principle contributors to the emergence of multiply drug-resistant "superbugs," detailed studies of these highly tractable systems have generated important new insights into the mode of action and architectures of paradigmatic T4SSs as a foundation for future efforts aimed at suppressing T4SS machine function. Over the past decade, extensive work on the second large T4SS subfamily, the effector translocators, has identified a myriad of mechanisms employed by pathogens to subvert, subdue, or bypass cellular processes and signaling pathways of the host cell. An overarching theme in the evolution of many effectors is that of molecular mimicry. These effectors carry domains similar to those of eukaryotic proteins and exert their effects through stealthy interdigitation of cellular pathways, often with the outcome not of inducing irreversible cell damage but rather of reversibly modulating cellular functions. This article summarizes the major developments for the actively studied pathogens with an emphasis on the structural and functional diversity of the T4SSs and the emerging common themes surrounding effector function in the human host.
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Affiliation(s)
- Christian Gonzalez-Rivera
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, Phone: 713-500-5440 (P. J. Christie); 713-500-5441 (C. Gonzalez-Rivera, M. Bhatty)
| | - Minny Bhatty
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, Phone: 713-500-5440 (P. J. Christie); 713-500-5441 (C. Gonzalez-Rivera, M. Bhatty)
| | - Peter J. Christie
- Department of Microbiology and Molecular Genetics, University of Texas Medical School at Houston, 6431 Fannin St, Houston, Texas 77030, Phone: 713-500-5440 (P. J. Christie); 713-500-5441 (C. Gonzalez-Rivera, M. Bhatty)
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Wang Y, Cobb RE, Zhao H. High-Efficiency Genome Editing of Streptomyces Species by an Engineered CRISPR/Cas System. Methods Enzymol 2016; 575:271-84. [PMID: 27417933 DOI: 10.1016/bs.mie.2016.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Next-generation sequencing technologies have rapidly expanded the genomic information of numerous organisms and revealed a rich reservoir of natural product gene clusters from microbial genomes, especially from Streptomyces, the largest genus of known actinobacteria at present. However, genetic engineering of these bacteria is often time consuming and labor intensive, if even possible. In this chapter, we describe the design and construction of pCRISPomyces, an engineered Type II CRISPR/Cas system, for targeted multiplex gene deletions in Streptomyces lividans, Streptomyces albus, and Streptomyces viridochromogenes with editing efficiency ranging from 70% to 100%. We demonstrate pCRISPomyces as a powerful tool for genome editing in Streptomyces.
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Affiliation(s)
- Y Wang
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - R E Cobb
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - H Zhao
- University of Illinois at Urbana-Champaign, Urbana, IL, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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37
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Huang J, Liang Y, Guo D, Shang K, Ge L, Kashif J, Wang L. Comparative Genomic Analysis of the ICESa2603 Family ICEs and Spread of erm(B)- and tet(O)-Carrying Transferable 89K-Subtype ICEs in Swine and Bovine Isolates in China. Front Microbiol 2016; 7:55. [PMID: 26870017 PMCID: PMC4735348 DOI: 10.3389/fmicb.2016.00055] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/13/2016] [Indexed: 11/13/2022] Open
Abstract
Integrative and conjugative elements (ICEs) of the ICESa2603 family have been isolated from several species of Streptococcus spp.; however, the comparative genomic and evolutionary analyses of these particular ICEs are currently only at their initial stages. By investigating 13 ICEs of the ICESa2603 family and two ICESa2603 family-like ICEs derived from diverse hosts and locations, we have determined that ICEs comprised a backbone of 30 identical syntenic core genes and accessory genes that were restricted to the intergenic sites or the 3′-end of the non-conserved domain of core genes to maintain its function. ICESa2603 family integrase IntICESa2603 specifically recognized a 15-bp att sequence (TTATTTAAGAGTAAC) at the 3′-end of rplL, which was highly conserved in genus Streptococcus. Phylogenetic analyses suggest that extensive recombination/insertion and the occurrence of a hybrid/mosaic in the ICESa2603 family were responsible for the significant increase in ICE diversity, thereby broadening its host range. Approximately 42.5 and 38.1% of the tested Streptococcus suis and Streptococcus agalactiae clinical isolates respectively contained ICESa2603 family Type IV secretion system (T4SS) genes, and 80.5 and 62.5% of which also respectively carried intICESa2603, indicating that ICESa2603 family is widely distributed across these bacteria. Sequencing and conjugation transfer of a novel sequence type ST303 clinical S. suis isolate HB1011 demonstrated that the 89K-subtype ICESsuHB1011 retained its transferrable function, thereby conferring tetracycline and macrolide resistance.
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Affiliation(s)
- Jinhu Huang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Yuan Liang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Dawei Guo
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Kexin Shang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Lin Ge
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Jam Kashif
- Department of Veterinary Pharmacology, Sindh Agricultural University Tandojam, Pakistan
| | - Liping Wang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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Jia RZ, Zhang RJ, Wei Q, Chen WF, Cho IK, Chen WX, Li QX. Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry. ACTA ACUST UNITED AC 2015; 8:98-107. [PMID: 26500417 PMCID: PMC4616259 DOI: 10.4172/jpb.1000357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.
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Affiliation(s)
- Rui Zong Jia
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA ; State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; State Key Biotechnology Laboratory for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, Hainan, 571101, China
| | - Rong Juan Zhang
- State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; Dongying Municipal Bureau of Agriculture, Dongying, Shandong, 257091, China
| | - Qing Wei
- State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China ; State Key Biotechnology Laboratory for Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou, Hainan, 571101, China
| | - Wen Feng Chen
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA ; State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Il Kyu Cho
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Wen Xin Chen
- State Key Laboratory of Agro biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qing X Li
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA
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Abstract
Streptococcus suis is a major swine pathogen and an emerging zoonotic agent of human meningitis and streptococcal toxic shock-like syndrome. S. suis is a well-encapsulated pathogen and multiple serotypes have been described based on the capsular polysaccharide antigenic diversity. In addition, high genotypic, phenotypic and geographic variability exits among strains within the same serotype. Besides, S. suis uses an arsenal of virulence factors to evade the host immune system. Together, these characteristics have challenged the development of efficacious vaccines to fight this important pathogen. In this careful and comprehensive review, clinical field information and experimental data have been compiled and compared for the first time to give a precise overview of the current status of vaccine development against S. suis. The candidate antigens and vaccine formulations under research are examined and the feasibility of reaching the goal of a "universal" cross-protective S. suis vaccine discussed.
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Affiliation(s)
- Mariela Segura
- a Laboratory of Immunology, Faculty of Veterinary Medicine , University of Montreal , Saint-Hyacinthe , Quebec , J2S 2M2 Canada
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40
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Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28. PLoS One 2015; 10:e0137760. [PMID: 26375680 PMCID: PMC4574206 DOI: 10.1371/journal.pone.0137760] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 08/21/2015] [Indexed: 11/19/2022] Open
Abstract
Streptococcus suis is a major swine pathogen and a zoonotic agent. Serotype 2 strains are the most frequently associated with disease. However, not all serotype 2 lineages are considered virulent. Indeed, sequence type (ST) 28 serotype 2 S. suis strains have been described as a homogeneous group of low virulence. However, ST28 strains are often isolated from diseased swine in some countries, and at least four human ST28 cases have been reported. Here, we used whole-genome sequencing and animal infection models to test the hypothesis that the ST28 lineage comprises strains of different genetic backgrounds and different virulence. We used 50 S. suis ST28 strains isolated in Canada, the United States and Japan from diseased pigs, and one ST28 strain from a human case isolated in Thailand. We report a complex population structure among the 51 ST28 strains. Diversity resulted from variable gene content, recombination events and numerous genome-wide polymorphisms not attributable to recombination. Phylogenetic analysis using core genome single-nucleotide polymorphisms revealed four discrete clades with strong geographic structure, and a fifth clade formed by US, Thai and Japanese strains. When tested in experimental animal models, strains from this latter clade were significantly more virulent than a Canadian ST28 reference strain, and a closely related Canadian strain. Our results highlight the limitations of MLST for both phylogenetic analysis and virulence prediction and raise concerns about the possible emergence of ST28 strains in human clinical cases.
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41
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Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PLoS One 2015; 10:e0137908. [PMID: 26366735 PMCID: PMC4569324 DOI: 10.1371/journal.pone.0137908] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/22/2015] [Indexed: 01/17/2023] Open
Abstract
Understanding the diversity and robustness of the metabolism of bacteria is fundamental for understanding how bacteria evolve and adapt to different environments. In this study, we characterised 121 Streptococcus strains and studied metabolic diversity from a protein domain perspective. Metabolic pathways were described in terms of the promiscuity of domains participating in metabolic pathways that were inferred to be functional. Promiscuity was defined by adapting existing measures based on domain abundance and versatility. The approach proved to be successful in capturing bacterial metabolic flexibility and species diversity, indicating that it can be described in terms of reuse and sharing functional domains in different proteins involved in metabolic activity. Additionally, we showed striking differences among metabolic organisation of the pathogenic serotype 2 Streptococcus suis and other strains.
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Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 2015; 7:72-85. [PMID: 26442149 PMCID: PMC4552756 DOI: 10.1016/j.nmni.2015.06.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 01/18/2023] Open
Abstract
The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position. Pangenome is a new way of studying pathogenic bacteria. Pangenome can be used as a taxonomic tool. This review describes pangenome in the world of pathogenic bacteria.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - V Merhej
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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Isolation and characterization of a native avirulent strain of Streptococcus suis serotype 2: a perspective for vaccine development. Sci Rep 2015; 5:9835. [PMID: 25891917 PMCID: PMC4402706 DOI: 10.1038/srep09835] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/19/2015] [Indexed: 01/05/2023] Open
Abstract
Streptococcus suis, an emerging infectious pathogen, is the cause of two large-scale outbreaks of human streptococcal toxic shock syndrome in China, and has attracted much attention from the scientific community. The genetic basis of its pathogenesis remains enigmatic, and no effective prevention measures have been established. To better understand the virulence differentiation of S. suis and develop a promising vaccine, we isolated and sequenced a native avirulent S. suis strain (05HAS68). Animal experiments revealed that 05HAS68 is an avirulent strain and could protect piglets from the attack of virulent strains. Comparative genomics analyses demonstrated the genetic basis for the lack of virulence in 05HAS68, which is characterized by the absence of some important virulence-associated factors and the intact 89K pathogenicity island. Lack of virulence was also illustrated by reduced survival of 05HAS68 compared to a virulent strain in pig whole blood. Further investigations revealed a large-scale genomic rearrangement in 05HAS68, which was proposed to be mediated by transposase genes and/or prophages. This genomic rearrangement may have caused the genomic diversity of S. suis, and resulted in biological discrepancies between 05HAS68 and highly virulent S. suis strains.
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A brief review of software tools for pangenomics. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:73-6. [PMID: 25721608 PMCID: PMC4411478 DOI: 10.1016/j.gpb.2015.01.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 01/22/2015] [Accepted: 01/25/2015] [Indexed: 02/06/2023]
Abstract
Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline (PGAP) ranked as the top two most popular packages according to cumulative citations of peer-reviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence.
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45
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GAP-initiated constitutive expression of a novel plectasin-derived peptide MP1106 by Pichia pastoris and its activity against Streptococcus suis. Process Biochem 2015. [DOI: 10.1016/j.procbio.2014.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Quantitative proteomic analysis of sub-MIC erythromycin inhibiting biofilm formation of S. suis in vitro. J Proteomics 2015; 116:1-14. [PMID: 25579403 DOI: 10.1016/j.jprot.2014.12.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/03/2014] [Accepted: 12/21/2014] [Indexed: 01/01/2023]
Abstract
UNLABELLED Streptococcus suis (S. suis) is a swine pathogen and also a zoonotic agent. Biofilms of S. suis may cause persistent infections by the host immune system and antibiotics. Sub-minimal inhibitory concentration (sub-MIC) of erythromycin can inhibit biofilm formation in bacteria. Here, we performed comparative proteomic analyses of cells at two different conditions: sub-MIC erythromycin treated and nontreated cells. Using iTRAQ strategy, we found some novel proteins that involved in biofilm formation. 79 differentially expressed proteins were identified in sub-MIC erythromycin inhibiting planktonic cell when the protein had both a fold-change of more that a ratio >1.2 or <0.8 (p-value <0.05). Several cell surface proteins (such as Primosomal protein N', l-fucose isomerase, and ABC superfamily ATP binding cassette transporter, membrane protein), as well as those involved in Quorum-sensing, were found to be implicated in biofilm formation. Overall, our results indicated that cell surface proteins played an important role in biofilm formation. Quorum-sensing played a crucial role leading to biofilm formation. ABC superfamily ATP binding cassette transporter, membrane protein and comD might act as channels for erythromycin uptake in Quorum-sensing system. Thus, our data analyzed rough regulatory pathways of biofilm formation that might potentially be exploited to deal with biofilm infections of S. suis. This article is part of a Special Issue entitled: Microbial Proteomics. BIOLOGICAL SIGNIFICANCE In this study, we identified many proteins involved in cell transport, biological regulation and signal transduction, stress responses and other metabolic processes that were not previously known to be associated with biofilm formation of S. suis and target spot of erythromycin. Therefore, our manuscript represents the most comprehensive analysis of protein profiles of biofilm formation of S. suis inhibited by sub-MIC erythromycin and provides new proteomic information about biofilm formation.
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47
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Whole-Genome Sequence of Streptococcus suis Serotype 4 Reference Strain 6407. GENOME ANNOUNCEMENTS 2014; 2:2/4/e00770-14. [PMID: 25125641 PMCID: PMC4132617 DOI: 10.1128/genomea.00770-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the second complete genome sequence of Streptococcus suis serotype 4 (strain 6407). The genome is 2,292,360 bp in length, covering 2,239 coding sequences, 58 tRNAs, and 4 rRNA loci.
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48
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Gao XY, Zhi XY, Li HW, Klenk HP, Li WJ. Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups. PLoS One 2014; 9:e101229. [PMID: 24977706 PMCID: PMC4076318 DOI: 10.1371/journal.pone.0101229] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 06/04/2014] [Indexed: 11/18/2022] Open
Abstract
Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.
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Affiliation(s)
- Xiao-Yang Gao
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail: (X-YG); (W-JL)
| | - Xiao-Yang Zhi
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
| | - Hong-Wei Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- The First Hospital of Qujing City, Qujing Affiliated Hospital of Kunming Medical University, Qujing, China
| | - Hans-Peter Klenk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China
- * E-mail: (X-YG); (W-JL)
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Zhang YM, Shao ZQ, Wang J, Wang L, Li X, Wang C, Tang J, Pan X. Prevalent distribution and conservation of Streptococcus suis Lmb protein and its protective capacity against the Chinese highly virulent strain infection. Microbiol Res 2014; 169:395-401. [DOI: 10.1016/j.micres.2013.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 01/04/2023]
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50
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Etzold S, Kober OI, Mackenzie DA, Tailford LE, Gunning AP, Walshaw J, Hemmings AM, Juge N. Structural basis for adaptation of lactobacilli to gastrointestinal mucus. Environ Microbiol 2014; 16:888-903. [PMID: 24373178 DOI: 10.1111/1462-2920.12377] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 12/17/2013] [Accepted: 12/17/2013] [Indexed: 12/01/2022]
Abstract
The mucus layer covering the gastrointestinal (GI) epithelium is critical in selecting and maintaining homeostatic interactions with our gut bacteria. However, the underpinning mechanisms of these interactions are not understood. Here, we provide structural and functional insights into the canonical mucus-binding protein (MUB), a multi-repeat cell-surface adhesin found in Lactobacillus inhabitants of the GI tract. X-ray crystallography together with small-angle X-ray scattering demonstrated a 'beads on a string' arrangement of repeats, generating 174 nm long protein fibrils, as shown by atomic force microscopy. Each repeat consists of tandemly arranged Ig- and mucin-binding protein (MucBP) modules. The binding of full-length MUB was confined to mucus via multiple interactions involving terminal sialylated mucin glycans. While individual MUB domains showed structural similarity to fimbrial proteins from Gram-positive pathogens, the particular organization of MUB provides a structural explanation for the mechanisms in which lactobacilli have adapted to their host niche by maximizing interactions with the mucus receptors, potentiating the retention of bacteria within the mucus layer. Together, this study reveals functional and structural features which may affect tropism of microbes across mucus and along the GI tract, providing unique insights into the mechanisms adopted by commensals and probiotics to adapt to the mucosal environment.
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Affiliation(s)
- Sabrina Etzold
- Institute of Food Research, Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich, NR4 7UA, UK
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