29 results on '"Beres, Stephen B."'
Search Results
2. Genetic Basis Underlying the Hyperhemolytic Phenotype of Streptococcus agalactiae Strain CNCTC10/84.
- Author
-
Zhu L, Beres SB, Yerramilli P, Pruitt L, Cantu CC, Olsen RJ, and Musser JM
- Subjects
- Bacterial Proteins genetics, Bacterial Proteins metabolism, Base Sequence, Gene Expression Regulation, Bacterial, Hemolysis, Histidine Kinase genetics, Histidine Kinase metabolism, Humans, Phenotype, Point Mutation, Promoter Regions, Genetic, Streptococcal Infections blood, Streptococcus agalactiae metabolism, Virulence Factors genetics, Virulence Factors metabolism, Streptococcal Infections microbiology, Streptococcus agalactiae genetics
- Abstract
Streptococcus agalactiae (group B streptococcus [GBS]) is a major cause of infections in newborns, pregnant women, and immunocompromised patients. GBS strain CNCTC10/84 is a clinical isolate that has high virulence in animal models of infection and has been used extensively to study GBS pathogenesis. Two unusual features of this strain are hyperhemolytic activity and hypo-CAMP factor activity. These two phenotypes are typical of GBS strains that are functionally deficient in the CovR-CovS two-component regulatory system. A previous whole-genome sequencing study found that strain CNCTC10/84 has intact covR and covS regulatory genes. We investigated CovR-CovS regulation in CNCTC10/84 and discovered that a single-nucleotide insertion in a homopolymeric tract in the covR promoter region underlies the strong hemolytic activity and weak CAMP activity of this strain. Using isogenic mutant strains, we demonstrate that this single-nucleotide insertion confers significantly decreased expression of covR and covS and altered expression of CovR-CovS-regulated genes, including that of genes encoding β-hemolysin and CAMP factor. This single-nucleotide insertion also confers significantly increased GBS survival in human whole blood ex vivo Group B streptococcus (GBS) is the leading cause of neonatal sepsis, pneumonia, and meningitis. GBS strain CNCTC10/84 is a highly virulent blood isolate that has been used extensively to study GBS pathogenesis for over 20 years. Strain CNCTC10/84 has an unusually strong hemolytic activity, but the genetic basis is unknown. In this study, we discovered that a single-nucleotide insertion in an intergenic homopolymeric tract is responsible for the elevated hemolytic activity of CNCTC10/84.IMPORTANCE Group B streptococcus (GBS) is the leading cause of neonatal sepsis, pneumonia, and meningitis. GBS strain CNCTC10/84 is a highly virulent blood isolate that has been used extensively to study GBS pathogenesis for over 20 years. Strain CNCTC10/84 has an unusually strong hemolytic activity, but the genetic basis is unknown. In this study, we discovered that a single-nucleotide insertion in an intergenic homopolymeric tract is responsible for the elevated hemolytic activity of CNCTC10/84., (Copyright © 2020 American Society for Microbiology.)
- Published
- 2020
- Full Text
- View/download PDF
3. Genome-Wide Assessment of Streptococcus agalactiae Genes Required for Survival in Human Whole Blood and Plasma.
- Author
-
Zhu L, Yerramilli P, Pruitt L, Ojeda Saavedra M, Cantu CC, Olsen RJ, Beres SB, Waller AS, and Musser JM
- Subjects
- Bacterial Proteins genetics, Genetic Fitness, Genome, Bacterial genetics, Humans, Microbial Viability genetics, Mutagenesis, Insertional, Mutation, Streptococcus agalactiae growth & development, Streptococcus agalactiae pathogenicity, Virulence genetics, Bacteremia microbiology, Genes, Bacterial, Streptococcal Infections microbiology, Streptococcus agalactiae genetics
- Abstract
Streptococcus agalactiae (group B streptococcus, or GBS) is a common cause of bacteremia and sepsis in newborns, pregnant women, and immunocompromised patients. The molecular mechanisms used by GBS to survive and proliferate in blood are not well understood. Here, using a highly virulent GBS strain and transposon-directed insertion site sequencing (TraDIS), we performed genome-wide screens to discover novel GBS genes required for bacterial survival in human whole blood and plasma. The screen identified 85 and 41 genes that are required for GBS growth in whole blood and plasma, respectively. A common set of 29 genes was required in both whole blood and plasma. Targeted gene deletion confirmed that (i) genes encoding methionine transporter ( metP ) and manganese transporter ( mtsA ) are crucial for GBS survival in whole blood and plasma, (ii) gene W903_1820, encoding a small multidrug export family protein, contributes significantly to GBS survival in whole blood, (iii) the shikimate pathway gene aroA is essential for GBS growth in whole blood and plasma, and (iv) deletion of srr1 , encoding a fibrinogen-binding adhesin, increases GBS survival in whole blood. Our findings provide new insight into the GBS-host interactions in human blood., (Copyright © 2020 American Society for Microbiology.)
- Published
- 2020
- Full Text
- View/download PDF
4. Population Genomic Molecular Epidemiological Study of Macrolide-Resistant Streptococcus pyogenes in Iceland, 1995 to 2016: Identification of a Large Clonal Population with a pbp2x Mutation Conferring Reduced In Vitro β-Lactam Susceptibility.
- Author
-
Southon SB, Beres SB, Kachroo P, Saavedra MO, Erlendsdóttir H, Haraldsson G, Yerramilli P, Pruitt L, Zhu L, Musser JM, and Kristinsson KG
- Subjects
- Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial, Epidemiologic Studies, Genotype, Humans, Iceland epidemiology, Macrolides pharmacology, Metagenomics, Microbial Sensitivity Tests, Mutation, beta-Lactams, Streptococcal Infections epidemiology, Streptococcus pyogenes genetics
- Abstract
Resistance to macrolide antibiotics is a global concern in the treatment of Streptococcus pyogenes (group A Streptococcus [GAS]) infections. In Iceland, since the detection of the first macrolide-resistant isolate in 1998, three epidemic waves of macrolide-resistant GAS infections have occurred, with peaks in 1999, 2004, and 2008. We conducted whole-genome sequencing of all 1,575 available GAS macrolide-resistant clinical isolates of all infection types collected at the national reference laboratory in Reykjavik, Iceland, from 1998 to 2016. Among 1,515 erythromycin-resistant isolates, 90.3% were of only three emm types, emm4 ( n = 713), emm6 ( n = 324), and emm12 ( n = 332), with each being predominant in a distinct epidemic peak. The antibiotic efflux pump genes, mef (A) and msr (D), were present on chimeric mobile genetic elements in 99.3% of the macrolide-resistant isolates of these emm types. Of note, in addition to macrolide resistance, virtually all emm12 isolates had a single amino acid substitution in penicillin-binding protein PBP2X that conferred a 2-fold increased penicillin G and ampicillin MIC among the isolates tested. We conclude that each of the three large epidemic peaks of macrolide-resistant GAS infections occurring in Iceland since 1998 was caused by the emergence and clonal expansion of progenitor strains, with macrolide resistance being conferred predominantly by inducible Mef(A) and Msr(D) drug efflux pumps. The occurrence of emm12 strains with macrolide resistance and decreased beta-lactam susceptibility was unexpected and is of public health concern., (Copyright © 2020 Southon et al.)
- Published
- 2020
- Full Text
- View/download PDF
5. Streptococcus pyogenes genes that promote pharyngitis in primates.
- Author
-
Zhu L, Olsen RJ, Beres SB, Saavedra MO, Kubiak SL, Cantu CC, Jenkins L, Waller AS, Sun Z, Palzkill T, Porter AR, DeLeo FR, and Musser JM
- Subjects
- Animals, Disease Models, Animal, Genome-Wide Association Study, Humans, Macaca fascicularis, Genes, Bacterial, Pharyngitis genetics, Pharyngitis metabolism, Pharyngitis microbiology, Pharyngitis pathology, Streptococcal Infections genetics, Streptococcal Infections metabolism, Streptococcal Infections pathology, Streptococcus pyogenes genetics, Streptococcus pyogenes metabolism, Streptococcus pyogenes pathogenicity, Virulence Factors genetics, Virulence Factors metabolism
- Abstract
Streptococcus pyogenes (group A streptococcus; GAS) causes 600 million cases of pharyngitis annually worldwide. There is no licensed human GAS vaccine despite a century of research. Although the human oropharynx is the primary site of GAS infection, the pathogenic genes and molecular processes used to colonize, cause disease, and persist in the upper respiratory tract are poorly understood. Using dense transposon mutant libraries made with serotype M1 and M28 GAS strains and transposon-directed insertion sequencing, we performed genome-wide screens in the nonhuman primate (NHP) oropharynx. We identified many potentially novel GAS fitness genes, including a common set of 115 genes that contribute to fitness in both genetically distinct GAS strains during experimental NHP pharyngitis. Targeted deletion of 4 identified fitness genes/operons confirmed that our newly identified targets are critical for GAS virulence during experimental pharyngitis. Our screens discovered many surface-exposed or secreted proteins - substrates for vaccine research - that potentially contribute to GAS pharyngitis, including lipoprotein HitA. Pooled human immune globulin reacted with purified HitA, suggesting that humans produce antibodies against this lipoprotein. Our findings provide new information about GAS fitness in the upper respiratory tract that may assist in translational research, including developing novel vaccines.
- Published
- 2020
- Full Text
- View/download PDF
6. Genome-Wide Screens Identify Group A Streptococcus Surface Proteins Promoting Female Genital Tract Colonization and Virulence.
- Author
-
Zhu L, Olsen RJ, Beres SB, Ojeda Saavedra M, Kubiak SL, Cantu CC, Jenkins L, Yerramilli P, Pruitt L, Charbonneau ARL, Waller AS, and Musser JM
- Subjects
- Animals, Bacterial Proteins genetics, Disease Models, Animal, Female, Gene Expression Regulation, Bacterial, Macaca fascicularis, Membrane Proteins genetics, Streptococcal Infections metabolism, Streptococcus pyogenes metabolism, Vaginal Diseases pathology, Virulence, Bacterial Proteins metabolism, Membrane Proteins metabolism, Streptococcal Infections microbiology, Streptococcus pyogenes genetics, Streptococcus pyogenes pathogenicity, Vaginal Diseases microbiology
- Abstract
Group A streptococcus (GAS) is a major pathogen that impacts health and economic affairs worldwide. Although the oropharynx is the primary site of infection, GAS can colonize the female genital tract and cause severe diseases, such as puerperal sepsis, neonatal infections, and necrotizing myometritis. Our understanding of how GAS genes contribute to interaction with the primate female genital tract is limited by the lack of relevant animal models. Using two genome-wide transposon mutagenesis screens, we identified 69 GAS genes required for colonization of the primate vaginal mucosa in vivo and 96 genes required for infection of the uterine wall ex vivo. We discovered a common set of 39 genes important for GAS fitness in both environments. They include genes encoding transporters, surface proteins, transcriptional regulators, and metabolic pathways. Notably, the genes that encode the surface-exclusion protein (SpyAD) and the immunogenic secreted protein 2 (Isp2) were found to be crucial for GAS fitness in the female primate genital tract. Targeted gene deletion confirmed that isogenic mutant strains ΔspyAD and Δisp2 are significantly impaired in ability to colonize the primate genital tract and cause uterine wall pathologic findings. Our studies identified novel GAS genes that contribute to female reproductive tract interaction that warrant translational research investigation., (Copyright © 2020 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
7. Genetic heterogeneity of the Spy1336/R28-Spy1337 virulence axis in Streptococcus pyogenes and effect on gene transcript levels and pathogenesis.
- Author
-
Eraso JM, Kachroo P, Olsen RJ, Beres SB, Zhu L, Badu T, Shannon S, Cantu CC, Saavedra MO, Kubiak SL, Porter AR, DeLeo FR, and Musser JM
- Subjects
- Animals, Disease Models, Animal, Fasciitis, Necrotizing pathology, Gene Expression Regulation, Bacterial, Genetic Heterogeneity, Humans, Mice, Polymorphism, Genetic, Streptococcal Infections pathology, Transcriptome, Virulence Factors genetics, Bacterial Proteins genetics, Fasciitis, Necrotizing microbiology, Streptococcal Infections microbiology, Streptococcus pyogenes genetics, Streptococcus pyogenes isolation & purification, Virulence genetics
- Abstract
Streptococcus pyogenes is a strict human pathogen responsible for more than 700 million infections annually worldwide. Strains of serotype M28 S. pyogenes are typically among the five more abundant types causing invasive infections and pharyngitis in adults and children. Type M28 strains also have an unusual propensity to cause puerperal sepsis and neonatal disease. We recently discovered that a one-nucleotide indel in an intergenic homopolymeric tract located between genes Spy1336/R28 and Spy1337 altered virulence in a mouse model of infection. In the present study, we analyzed size variation in this homopolymeric tract and determined the extent of heterogeneity in the number of tandemly-repeated 79-amino acid domains in the coding region of Spy1336/R28 in large samples of strains recovered from humans with invasive infections. Both repeat sequence elements are highly polymorphic in natural populations of M28 strains. Variation in the homopolymeric tract results in (i) changes in transcript levels of Spy1336/R28 and Spy1337 in vitro, (ii) differences in virulence in a mouse model of necrotizing myositis, and (iii) global transcriptome changes as shown by RNAseq analysis of isogenic mutant strains. Variation in the number of tandem repeats in the coding sequence of Spy1336/R28 is responsible for size variation of R28 protein in natural populations. Isogenic mutant strains in which genes encoding R28 or transcriptional regulator Spy1337 are inactivated are significantly less virulent in a nonhuman primate model of necrotizing myositis. Our findings provide impetus for additional studies addressing the role of R28 and Spy1337 variation in pathogen-host interactions., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2020
- Full Text
- View/download PDF
8. RocA Has Serotype-Specific Gene Regulatory and Pathogenesis Activities in Serotype M28 Group A Streptococcus.
- Author
-
Bernard PE, Kachroo P, Zhu L, Beres SB, Eraso JM, Kajani Z, Long SW, Musser JM, and Olsen RJ
- Subjects
- Animals, Colony-Forming Units Assay, Disease Models, Animal, Gene Deletion, Gene Expression Profiling, Mice, Myositis microbiology, Streptococcal Infections microbiology, Streptococcus pyogenes growth & development, Trans-Activators genetics, Virulence Factors biosynthesis, Virulence Factors genetics, Gene Expression Regulation, Bacterial, Myositis pathology, Streptococcal Infections pathology, Streptococcus pyogenes genetics, Streptococcus pyogenes pathogenicity, Trans-Activators metabolism
- Abstract
Serotype M28 group A streptococcus (GAS) is a common cause of infections such as pharyngitis ("strep throat") and necrotizing fasciitis ("flesh-eating" disease). Relatively little is known about the molecular mechanisms underpinning M28 GAS pathogenesis. Whole-genome sequencing studies of M28 GAS strains recovered from patients with invasive infections found an unexpectedly high number of missense (amino acid-changing) and nonsense (protein-truncating) polymorphisms in rocA ( r egulator o f C ov), leading us to hypothesize that altered RocA activity contributes to M28 GAS molecular pathogenesis. To test this hypothesis, an isogenic rocA deletion mutant strain was created. Transcriptome sequencing (RNA-seq) analysis revealed that RocA inactivation significantly alters the level of transcripts for 427 and 323 genes at mid-exponential and early stationary growth phases, respectively, including genes for 41 transcription regulators and 21 virulence factors. In contrast, RocA transcriptomes from other GAS M protein serotypes are much smaller and include fewer transcription regulators. The rocA mutant strain had significantly increased secreted activity of multiple virulence factors and grew to significantly higher colony counts under acid stress in vitro RocA inactivation also significantly increased GAS virulence in a mouse model of necrotizing myositis. Our results demonstrate that RocA is an important regulator of transcription regulators and virulence factors in M28 GAS and raise the possibility that naturally occurring polymorphisms in rocA in some fashion contribute to human invasive infections caused by M28 GAS strains., (Copyright © 2018 American Society for Microbiology.)
- Published
- 2018
- Full Text
- View/download PDF
9. Genome sequence analysis of emm89 Streptococcus pyogenes strains causing infections in Scotland, 2010-2016.
- Author
-
Beres SB, Olsen RJ, Ojeda Saavedra M, Ure R, Reynolds A, Lindsay DSJ, Smith AJ, and Musser JM
- Subjects
- DNA, Bacterial genetics, Humans, Molecular Epidemiology, Retrospective Studies, Scotland epidemiology, Sequence Analysis, DNA, Streptococcus pyogenes classification, Streptococcus pyogenes isolation & purification, Bacterial Proteins genetics, Genome, Bacterial, Streptococcal Infections epidemiology, Streptococcus pyogenes genetics
- Abstract
Purpose: Strains of type emm89 Streptococcus pyogenes have recently increased in frequency as a cause of human infections in several countries in Europe and North America. This increase has been molecular epidemiologically linked with the emergence of a new genetically distinct clone, designated clade 3. We sought to extend our understanding of this epidemic behavior by the genetic characterization of type emm89 strains responsible in recent years for an increased frequency of infections in Scotland., Methodology: We sequenced the genomes of a retrospective cohort of 122 emm89 strains recovered from patients with invasive and noninvasive infections throughout Scotland during 2010 to 2016., Results: All but one of the 122 emm89 infection isolates are of the recently emerged epidemic clade 3 clonal lineage. The Scotland isolates are closely related to and not genetically distinct from recent emm89 strains from England, they constitute a single genetic population., Conclusions: The clade 3 clone causes virtually all-contemporary emm89 infections in Scotland. These findings add Scotland to a growing list of countries of Europe and North America where, by whole genome sequencing, emm89 clade 3 strains have been demonstrated to be the cause of an ongoing epidemic of invasive infections and to be genetically related due to descent from a recent common progenitor.
- Published
- 2017
- Full Text
- View/download PDF
10. Genomic Characteristics Behind the Spread of Bacteremic Group A Streptococcus Type emm89 in Finland, 2004-2014.
- Author
-
Latronico F, Nasser W, Puhakainen K, Ollgren J, Hyyryläinen HL, Beres SB, Lyytikäinen O, Jalava J, Musser JM, and Vuopio J
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Antigens, Bacterial genetics, Bacteremia mortality, Bacterial Outer Membrane Proteins genetics, Carrier Proteins genetics, Child, Child, Preschool, Cluster Analysis, Female, Finland epidemiology, Genome, Bacterial, Genomics, Humans, Infant, Infant, Newborn, Male, Middle Aged, Molecular Diagnostic Techniques methods, Molecular Epidemiology methods, Phylogeny, Polymerase Chain Reaction methods, Streptococcal Infections mortality, Streptococcus pyogenes isolation & purification, Survival Analysis, Young Adult, Bacteremia epidemiology, Bacteremia microbiology, Genotype, Streptococcal Infections epidemiology, Streptococcal Infections microbiology, Streptococcus pyogenes classification, Streptococcus pyogenes genetics
- Abstract
Background: Many countries worldwide have reported increasing numbers of emm89 group A Streptococcus (GAS) infections during last decade. Pathogen genetic factors linked to this increase need assessment., Methods: We investigated epidemiological characteristics of emm89 GAS bacteremic infections, including 7-day and 30-day case-fatality rates, in Finland during 2004-2014 and linked them to whole-genome sequencing data obtained from corresponding strains. The Fisher exact test and exact logistic regression were used to compare differences between bacteremic infections due to emm89 GAS belonging to different genetic clades and subclades., Results: Out of 1928 cases of GAS bacteremic infection, 278 were caused by emm89 GAS. We identified 2 genetically distinct clades, arbitrarily designated clade 2 and clade 3. Both clades were present during 2004-2008, but clade 3 increased rapidly from 2009 onward. Six subclades (designated subclades A-F) were identified within clade 3, based on phylogenetic core genome analysis. The case-fatality rate differed significantly between subclades (P < .05), with subclade D having the highest 30-day estimated case-fatality rate (19% vs 3%-14%)., Conclusions: A new emm89 clone, clade 3, emerged in 2009 and spread rapidly in Finland. Patients infected with certain subclades of clade 3 were significantly more likely to die. A specific polymerase chain reaction assay was developed to follow the spread of subclade D in 2015., (© The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America.)
- Published
- 2016
- Full Text
- View/download PDF
11. Transcriptome Remodeling Contributes to Epidemic Disease Caused by the Human Pathogen Streptococcus pyogenes.
- Author
-
Beres SB, Kachroo P, Nasser W, Olsen RJ, Zhu L, Flores AR, de la Riva I, Paez-Mayorga J, Jimenez FE, Cantu C, Vuopio J, Jalava J, Kristinsson KG, Gottfredsson M, Corander J, Fittipaldi N, Di Luca MC, Petrelli D, Vitali LA, Raiford A, Jenkins L, and Musser JM
- Subjects
- Evolution, Molecular, Gene Transfer, Horizontal, Genome, Bacterial, Genotype, Humans, Immune Evasion, Polymorphism, Single Nucleotide, Recombination, Genetic, Streptococcus pyogenes immunology, Streptococcus pyogenes pathogenicity, Virulence genetics, Virulence Factors genetics, Bacterial Proteins genetics, Epidemics prevention & control, Host-Pathogen Interactions, Streptococcal Infections epidemiology, Streptococcal Infections microbiology, Streptococcus pyogenes genetics, Transcriptome
- Abstract
Unlabelled: For over a century, a fundamental objective in infection biology research has been to understand the molecular processes contributing to the origin and perpetuation of epidemics. Divergent hypotheses have emerged concerning the extent to which environmental events or pathogen evolution dominates in these processes. Remarkably few studies bear on this important issue. Based on population pathogenomic analysis of 1,200 Streptococcus pyogenes type emm89 infection isolates, we report that a series of horizontal gene transfer events produced a new pathogenic genotype with increased ability to cause infection, leading to an epidemic wave of disease on at least two continents. In the aggregate, these and other genetic changes substantially remodeled the transcriptomes of the evolved progeny, causing extensive differential expression of virulence genes and altered pathogen-host interaction, including enhanced immune evasion. Our findings delineate the precise molecular genetic changes that occurred and enhance our understanding of the evolutionary processes that contribute to the emergence and persistence of epidemically successful pathogen clones. The data have significant implications for understanding bacterial epidemics and for translational research efforts to blunt their detrimental effects., Importance: The confluence of studies of molecular events underlying pathogen strain emergence, evolutionary genetic processes mediating altered virulence, and epidemics is in its infancy. Although understanding these events is necessary to develop new or improved strategies to protect health, surprisingly few studies have addressed this issue, in particular, at the comprehensive population genomic level. Herein we establish that substantial remodeling of the transcriptome of the human-specific pathogen Streptococcus pyogenes by horizontal gene flow and other evolutionary genetic changes is a central factor in precipitating and perpetuating epidemic disease. The data unambiguously show that the key outcome of these molecular events is evolution of a new, more virulent pathogenic genotype. Our findings provide new understanding of epidemic disease., (Copyright © 2016 Beres et al.)
- Published
- 2016
- Full Text
- View/download PDF
12. A molecular trigger for intercontinental epidemics of group A Streptococcus.
- Author
-
Zhu L, Olsen RJ, Nasser W, Beres SB, Vuopio J, Kristinsson KG, Gottfredsson M, Porter AR, DeLeo FR, and Musser JM
- Subjects
- Bacterial Proteins, Fasciitis, Necrotizing epidemiology, Fasciitis, Necrotizing genetics, Humans, Leukocytes microbiology, Pharyngitis epidemiology, Pharyngitis genetics, Streptolysins, NAD+ Nucleosidase genetics, Pandemics, Polymorphism, Genetic, Streptococcal Infections epidemiology, Streptococcal Infections genetics, Streptococcus pyogenes genetics, Streptococcus pyogenes pathogenicity, Virulence Factors genetics
- Abstract
The identification of the molecular events responsible for strain emergence, enhanced virulence, and epidemicity has been a long-pursued goal in infectious diseases research. A recent analysis of 3,615 genomes of serotype M1 group A Streptococcus strains (the so-called "flesh-eating" bacterium) identified a recombination event that coincides with the global M1 pandemic beginning in the early 1980s. Here, we have shown that the allelic variation that results from this recombination event, which replaces the chromosomal region encoding secreted NADase and streptolysin O, is the key driver of increased toxin production and enhanced infection severity of the M1 pandemic strains. Using isoallelic mutant strains, we found that 3 polymorphisms in this toxin gene region increase resistance to killing by human polymorphonuclear leukocytes, increase bacterial proliferation, and increase virulence in animal models of pharyngitis and necrotizing fasciitis. Genome sequencing of an additional 1,125 streptococcal strains and virulence studies revealed that a highly similar recombinational replacement event underlies an ongoing intercontinental epidemic of serotype M89 group A Streptococcus infections. By identifying the molecular changes that enhance upper respiratory tract fitness, increased resistance to innate immunity, and increased tissue destruction, we describe a mechanism that underpins epidemic streptococcal infections, which have affected many millions of people.
- Published
- 2015
- Full Text
- View/download PDF
13. Clinical laboratory response to a mock outbreak of invasive bacterial infections: a preparedness study.
- Author
-
Olsen RJ, Fittipaldi N, Kachroo P, Sanson MA, Long SW, Como-Sabetti KJ, Valson C, Cantu C, Lynfield R, Van Beneden C, Beres SB, and Musser JM
- Subjects
- Animals, Canada, Disease Models, Animal, Gene Expression Profiling, Genome, Bacterial, Health Services Research, High-Throughput Nucleotide Sequencing methods, Humans, Mice, Molecular Diagnostic Techniques methods, Streptococcus pyogenes classification, Streptococcus pyogenes genetics, United States, Civil Defense, Disease Outbreaks, Laboratory Proficiency Testing, Streptococcal Infections diagnosis, Streptococcal Infections epidemiology, Streptococcus pyogenes isolation & purification
- Abstract
Large hospital-based clinical laboratories must be prepared to rapidly investigate potential infectious disease outbreaks. To challenge the ability of our molecular diagnostics laboratory to use whole-genome sequencing in a potential outbreak scenario and identify impediments to these efforts, we studied 84 invasive serotype emm59 group A streptococcus (GAS) strains collected in the United States. We performed a rapid-response exercise to the mock outbreak scenario using whole-genome sequencing, genome-wide transcript analysis, and mouse virulence studies. The protocol changes installed in response to the lessons learned were tested in a second iteration. The initial investigation was completed in 9 days. Whole-genome sequencing showed that the invasive infections were caused by multiple subclones of epidemic emm59 GAS strains likely spread to the United States from Canada. The phylogenetic tree showed a strong temporal-spatial structure with diversity in mobile genetic element content, features that are useful for identifying closely related strains and possible transmission events. The genome data informed the epidemiology, identifying multiple patients who likely acquired the organisms through direct person-to-person transmission. Transcriptome analysis unexpectedly revealed significantly altered expression of genes encoding a two-component regulator and the hyaluronic acid capsule virulence factor. Mouse infection studies confirmed a high-virulence capacity of these emm59 organisms. Whole-genome sequencing, coupled with transcriptome analysis and animal virulence studies, can be rapidly performed in a clinical environment to effectively contribute to patient care decisions and public health maneuvers., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)
- Published
- 2014
- Full Text
- View/download PDF
14. Asymptomatic carriage of group A streptococcus is associated with elimination of capsule production.
- Author
-
Flores AR, Jewell BE, Olsen RJ, Shelburne SA 3rd, Fittipaldi N, Beres SB, and Musser JM
- Subjects
- Animals, Bacterial Capsules genetics, Bacterial Proteins genetics, Bacterial Proteins metabolism, Cell Line, Epithelial Cells metabolism, Epithelial Cells microbiology, Female, Humans, Hyaluronic Acid genetics, Hyaluronic Acid metabolism, Mice, Mutation genetics, Operon genetics, Oropharynx metabolism, Oropharynx microbiology, Streptococcal Infections genetics, Streptococcal Infections microbiology, Streptococcus genetics, Virulence Factors genetics, Virulence Factors metabolism, Bacterial Capsules metabolism, Streptococcal Infections metabolism, Streptococcus metabolism
- Abstract
Humans commonly carry pathogenic bacteria asymptomatically, but despite decades of study, the underlying molecular contributors remain poorly understood. Here, we show that a group A streptococcus carriage strain contains a frameshift mutation in the hasA gene resulting in loss of hyaluronic acid capsule biosynthesis. This mutation was repaired by allelic replacement, resulting in restoration of capsule production in the isogenic derivative strain. The "repaired" isogenic strain was significantly more virulent than the carriage strain in a mouse model of necrotizing fasciitis and had enhanced growth ex vivo in human blood. Importantly, the repaired isogenic strain colonized the mouse oropharynx with significantly greater bacterial burden and had significantly reduced ability to internalize into cultured epithelial cells than the acapsular carriage strain. We conducted full-genome sequencing of 81 strains cultured serially from 19 epidemiologically unrelated human subjects and discovered the common theme that mutations negatively affecting capsule biosynthesis arise in vivo in the has operon. The significantly decreased capsule production is a key factor contributing to the molecular détente between pathogen and host. Our discoveries suggest a general model for bacterial pathogens in which mutations that downregulate or ablate virulence factor production contribute to carriage., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)
- Published
- 2014
- Full Text
- View/download PDF
15. Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences.
- Author
-
Nasser W, Beres SB, Olsen RJ, Dean MA, Rice KA, Long SW, Kristinsson KG, Gottfredsson M, Vuopio J, Raisanen K, Caugant DA, Steinbakk M, Low DE, McGeer A, Darenberg J, Henriques-Normark B, Van Beneden CA, Hoffmann S, and Musser JM
- Subjects
- Animals, Base Sequence, Disease Models, Animal, Fasciitis, Necrotizing epidemiology, Fasciitis, Necrotizing genetics, Fasciitis, Necrotizing microbiology, Finland epidemiology, Genes, Bacterial genetics, Genomics, Humans, INDEL Mutation genetics, Pharyngitis epidemiology, Pharyngitis genetics, Pharyngitis microbiology, Polymorphism, Single Nucleotide genetics, Primates microbiology, Selection, Genetic, Serotyping, Streptococcal Infections microbiology, Streptococcus pyogenes isolation & purification, Time Factors, Virulence genetics, Epidemics, Evolution, Molecular, Genome, Bacterial genetics, Streptococcal Infections epidemiology, Streptococcal Infections genetics, Streptococcus pyogenes genetics, Streptococcus pyogenes pathogenicity
- Abstract
We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD(+)-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide.
- Published
- 2014
- Full Text
- View/download PDF
16. Polymorphisms in regulator of protease B (RopB) alter disease phenotype and strain virulence of serotype M3 group A Streptococcus.
- Author
-
Olsen RJ, Laucirica DR, Watkins ME, Feske ML, Garcia-Bustillos JR, Vu C, Cantu C, Shelburne SA 3rd, Fittipaldi N, Kumaraswami M, Shea PR, Flores AR, Beres SB, Lovgren M, Tyrrell GJ, Efstratiou A, Low DE, Van Beneden CA, and Musser JM
- Subjects
- Animals, Bacterial Proteins metabolism, DNA, Bacterial chemistry, DNA, Bacterial genetics, Disease Models, Animal, Fasciitis, Necrotizing microbiology, Fasciitis, Necrotizing pathology, Humans, Mice, Mutant Proteins genetics, Mutant Proteins metabolism, Pharyngitis pathology, Sequence Analysis, DNA, Streptococcal Infections pathology, Streptococcus pyogenes classification, Virulence, Virulence Factors metabolism, Bacterial Proteins genetics, Pharyngitis microbiology, Polymorphism, Genetic, Streptococcal Infections microbiology, Streptococcus pyogenes genetics, Streptococcus pyogenes isolation & purification, Virulence Factors genetics
- Abstract
Whole-genome sequencing of serotype M3 group A streptococci (GAS) from oropharyngeal and invasive infections in Ontario recently showed that the gene encoding regulator of protease B (RopB) is highly polymorphic in this population. To test the hypothesis that ropB is under diversifying selective pressure among all serotype M3 GAS strains, we sequenced this gene in 1178 strains collected from different infection types, geographic regions, and time periods. The results confirmed our hypothesis and discovered a significant association between mutant ropB alleles, decreased activity of its major regulatory target SpeB, and pharyngitis. Additionally, isoallelic strains with ropB polymorphisms were significantly less virulent in a mouse model of necrotizing fasciitis. These studies provide a model strategy for applying whole-genome sequencing followed by deep single-gene sequencing to generate new insight to the rapid evolution and virulence regulation of human pathogens.
- Published
- 2012
- Full Text
- View/download PDF
17. Genomic analysis of emm59 group A Streptococcus invasive strains, United States.
- Author
-
Fittipaldi N, Olsen RJ, Beres SB, Van Beneden C, and Musser JM
- Subjects
- Antigens, Bacterial genetics, Bacterial Outer Membrane Proteins genetics, Carrier Proteins genetics, INDEL Mutation, Molecular Typing standards, Phylogeny, Polymorphism, Single Nucleotide, Population Surveillance, Reference Standards, Sequence Analysis, DNA, Streptococcus pyogenes classification, Streptococcus pyogenes isolation & purification, United States, Genome, Bacterial, Streptococcal Infections microbiology, Streptococcus pyogenes genetics
- Abstract
Genomic analysis of type emm59 group A Streptococcus invasive strains isolated in the United States discovered higher than anticipated genetic heterogeneity among strains and identified a heretofore unrecognized monoclonal cluster of invasive infections in the San Francisco Bay area. Heightened monitoring for a potential shift in the epidemic behavior of emm59 group A Streptococcus is warranted.
- Published
- 2012
- Full Text
- View/download PDF
18. Full-genome dissection of an epidemic of severe invasive disease caused by a hypervirulent, recently emerged clone of group A Streptococcus.
- Author
-
Fittipaldi N, Beres SB, Olsen RJ, Kapur V, Shea PR, Watkins ME, Cantu CC, Laucirica DR, Jenkins L, Flores AR, Lovgren M, Ardanuy C, Liñares J, Low DE, Tyrrell GJ, and Musser JM
- Subjects
- Animals, Canada epidemiology, DNA, Bacterial genetics, Disease Models, Animal, Epidemics, Fasciitis, Necrotizing microbiology, Fasciitis, Necrotizing pathology, Female, Genome, Bacterial, Humans, Inverted Repeat Sequences genetics, Macaca fascicularis, Male, Mice, Mice, Hairless, Pharyngitis epidemiology, Pharyngitis microbiology, Phylogeny, Saliva microbiology, Sequence Analysis, DNA methods, Skin Diseases, Bacterial microbiology, Skin Diseases, Bacterial pathology, Streptococcal Infections microbiology, Streptococcal Infections transmission, Streptococcus pyogenes classification, Streptococcus pyogenes growth & development, Streptococcus pyogenes pathogenicity, United States epidemiology, Virulence genetics, Streptococcal Infections epidemiology, Streptococcus pyogenes genetics
- Abstract
Group A Streptococcus (GAS) causes an exceptionally broad range of infections in humans, from relatively mild pharyngitis and skin infections to life-threatening necrotizing fasciitis and toxic shock syndrome. An epidemic of severe invasive human infections caused by type emm59 GAS, heretofore an exceedingly rare cause of disease, spread west to east across Canada over a 3-year period (2006 to 2008). By sequencing the genomes of 601 epidemic, historic, and other emm59 organisms, we discovered that a recently emerged, genetically distinct emm59 clone is responsible for the Canadian epidemic. Using near-real-time genome sequencing, we were able to show spread of the Canadian epidemic clone into the United States. The extensive genome data permitted us to identify patterns of geographic dissemination as well as links between emm59 subclonal lineages that cause infections. Mouse and nonhuman primate models of infection demonstrated that the emerged clone is unusually virulent. Transmission of epidemic emm59 strains may have occurred primarily by skin contact, as suggested by an experimental model of skin transmission. In addition, the emm59 strains had a significantly impaired ability to persist in human saliva and to colonize the oropharynx of mice, and seldom caused human pharyngitis. Our study contributes new information to the rapidly emerging field of molecular pathogenomics of bacterial epidemics and illustrates how full-genome data can be used to precisely illuminate the landscape of strain dissemination during a bacterial epidemic., (Copyright © 2012 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
19. Group A Streptococcus emm gene types in pharyngeal isolates, Ontario, Canada, 2002-2010.
- Author
-
Shea PR, Ewbank AL, Gonzalez-Lugo JH, Martagon-Rosado AJ, Martinez-Gutierrez JC, Rehman HA, Serrano-Gonzalez M, Fittipaldi N, Beres SB, Flores AR, Low DE, Willey BM, and Musser JM
- Subjects
- Alleles, Child, Child, Preschool, Genotype, Humans, Infant, Ontario epidemiology, Pharynx microbiology, Phylogeography, Streptococcus pyogenes genetics, Streptococcus pyogenes isolation & purification, Antigens, Bacterial genetics, Bacterial Outer Membrane Proteins genetics, Carrier Proteins genetics, Pharyngitis epidemiology, Pharyngitis microbiology, Streptococcal Infections epidemiology, Streptococcus pyogenes classification
- Abstract
Group A Streptococcus (GAS) is a human-adapted pathogen that causes a variety of diseases, including pharyngitis and invasive infections. GAS strains are categorized by variation in the nucleotide sequence of the gene (emm) that encodes the M protein. To identify the emm types of GAS strains causing pharyngitis in Ontario, Canada, we sequenced the hypervariable region of the emm gene in 4,635 pharyngeal GAS isolates collected during 2002-2010. The most prevalent emm types varied little from year to year. In contrast, fine-scale geographic analysis identified inter-site variability in the most common emm types. Additionally, we observed fluctuations in yearly frequency of emm3 strains from pharyngitis patients that coincided with peaks of emm3 invasive infections. We also discovered a striking increase in frequency of emm89 strains among isolates from patients with pharyngitis and invasive disease. These findings about the epidemiology of GAS are potentially useful for vaccine research.
- Published
- 2011
- Full Text
- View/download PDF
20. Evolution of diversity in epidemics revealed by analysis of the human bacterial pathogen group A Streptococcus.
- Author
-
Carroll RK, Beres SB, Sitkiewicz I, Peterson L, Matsunami RK, Engler DA, Flores AR, Sumby P, and Musser JM
- Subjects
- Biodiversity, Biological Evolution, Gene Expression Regulation, Genome, Bacterial genetics, Humans, Microarray Analysis, Phenotype, Proteomics, Streptococcal Infections microbiology, Streptococcus pyogenes classification, Streptococcus pyogenes metabolism, Streptococcus pyogenes pathogenicity, Virulence Factors genetics, Bacterial Proteins genetics, Exotoxins genetics, Polymorphism, Genetic, Streptococcal Infections epidemiology, Streptococcal Infections genetics, Streptococcus pyogenes genetics
- Abstract
Advancements in high-throughput, high-volume data generating techniques increasingly present us with opportunities to probe new areas of biology. In this work we assessed the extent to which four closely related and genetically representative strains of group A Streptococcus causing epidemic disease have differentiated from one another. Comparative genome sequencing, expression microarray analysis, and proteomic studies were used in parallel to assess strain variation. The extent of phenotypic differentiation was unexpectedly large. We found significant associations between genetic polymorphisms and alterations in gene expression allowing us to estimate the frequency with which specific types of polymorphisms alter gene transcription. We identified polymorphisms in the gene (ropB) encoding the RopB regulator that associate with altered transcription of speB and production of the SpeB protein, a critical secreted protease virulence factor. Although these four epidemic strains are closely related, a key discovery is that accumulation of modest genetic changes has rapidly resulted in significant strain phenotypic differentiation, including the extracellular proteome that contains multiple virulence factors. These data provide enhanced understanding of genetic events resulting in strain variation in bacterial epidemics., (Copyright © 2011 Elsevier B.V. All rights reserved.)
- Published
- 2011
- Full Text
- View/download PDF
21. Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations.
- Author
-
Shea PR, Beres SB, Flores AR, Ewbank AL, Gonzalez-Lugo JH, Martagon-Rosado AJ, Martinez-Gutierrez JC, Rehman HA, Serrano-Gonzalez M, Fittipaldi N, Ayers SD, Webb P, Willey BM, Low DE, and Musser JM
- Subjects
- Animals, Female, Genome-Wide Association Study, Humans, Male, Primates, Evolution, Molecular, Genome, Bacterial physiology, Pharyngitis genetics, Phylogeny, Streptococcal Infections genetics, Streptococcus pyogenes genetics
- Abstract
Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is a human-adapted bacterium that causes a range of infections. Much effort has been expended to dissect the molecular basis of invasive (sterile-site) infections, but little is known about the genomes of strains causing pharyngitis (streptococcal "sore throat"). Additionally, there is essentially nothing known about the genetic relationships between populations of invasive and pharyngitis strains. In particular, it is unclear if invasive strains represent a distinct genetic subpopulation of strains that cause pharyngitis. We compared the genomes of 86 serotype M3 GAS pharyngitis strains with those of 215 invasive M3 strains from the same geographical location. The pharyngitis and invasive groups were highly related to each other and had virtually identical phylogenetic structures, indicating they belong to the same genetic pool. Despite the overall high degree of genetic similarity, we discovered that strains from different host environments (i.e., throat, normally sterile sites) have distinct patterns of diversifying selection at the nucleotide level. In particular, the pattern of polymorphisms in the hyaluronic acid capsule synthesis operon was especially different between the two strain populations. This finding was mirrored by data obtained from full-genome analysis of strains sequentially cultured from nonhuman primates. Our results answer the long-standing question of the genetic relationship between GAS pharyngitis and invasive strains. The data provide previously undescribed information about the evolutionary history of pathogenic microbes that cause disease in different anatomical sites.
- Published
- 2011
- Full Text
- View/download PDF
22. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.
- Author
-
Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC, Low DE, McGeer A, Willey BM, Green K, Tyrrell GJ, Goldman TD, Feldgarden M, Birren BW, Fofanov Y, Boos J, Wheaton WD, Honisch C, and Musser JM
- Subjects
- Biological Evolution, Codon, Terminator, Genotype, Humans, Mass Spectrometry, Oligonucleotide Array Sequence Analysis, Ontario epidemiology, Phenotype, Phylogeny, Polymorphism, Single Nucleotide, Streptococcus pyogenes pathogenicity, Virulence, Disease Outbreaks, Genome, Bacterial, Streptococcal Infections epidemiology, Streptococcus pyogenes isolation & purification
- Abstract
Understanding the fine-structure molecular architecture of bacterial epidemics has been a long-sought goal of infectious disease research. We used short-read-length DNA sequencing coupled with mass spectroscopy analysis of SNPs to study the molecular pathogenomics of three successive epidemics of invasive infections involving 344 serotype M3 group A Streptococcus in Ontario, Canada. Sequencing the genome of 95 strains from the three epidemics, coupled with analysis of 280 biallelic SNPs in all 344 strains, revealed an unexpectedly complex population structure composed of a dynamic mixture of distinct clonally related complexes. We discovered that each epidemic is dominated by micro- and macrobursts of multiple emergent clones, some with distinct strain genotype-patient phenotype relationships. On average, strains were differentiated from one another by only 49 SNPs and 11 insertion-deletion events (indels) in the core genome. Ten percent of SNPs are strain specific; that is, each strain has a unique genome sequence. We identified nonrandom temporal-spatial patterns of strain distribution within and between the epidemic peaks. The extensive full-genome data permitted us to identify genes with significantly increased rates of nonsynonymous (amino acid-altering) nucleotide polymorphisms, thereby providing clues about selective forces operative in the host. Comparative expression microarray analysis revealed that closely related strains differentiated by seemingly modest genetic changes can have significantly divergent transcriptomes. We conclude that enhanced understanding of bacterial epidemics requires a deep-sequencing, geographically centric, comparative pathogenomics strategy.
- Published
- 2010
- Full Text
- View/download PDF
23. Genome sequence of a Lancefield group C Streptococcus zooepidemicus strain causing epidemic nephritis: new information about an old disease.
- Author
-
Beres SB, Sesso R, Pinto SW, Hoe NP, Porcella SF, Deleo FR, and Musser JM
- Subjects
- Bacterial Proteins genetics, Chromosome Mapping, Genes, Essential, Genetic Variation, Humans, Proteome, RNA, Bacterial genetics, Species Specificity, Streptococcal Infections complications, Streptococcus equi classification, Genome, Bacterial, Nephritis etiology, Streptococcal Infections microbiology, Streptococcus equi genetics
- Abstract
Outbreaks of disease attributable to human error or natural causes can provide unique opportunities to gain new information about host-pathogen interactions and new leads for pathogenesis research. Poststreptococcal glomerulonephritis (PSGN), a sequela of infection with pathogenic streptococci, is a common cause of preventable kidney disease worldwide. Although PSGN usually occurs after infection with group A streptococci, organisms of Lancefield group C and G also can be responsible. Despite decades of study, the molecular pathogenesis of PSGN is poorly understood. As a first step toward gaining new information about PSGN pathogenesis, we sequenced the genome of Streptococcus equi subsp. zooepidemicus strain MGCS10565, a group C organism that caused a very large and unusually severe epidemic of nephritis in Brazil. The genome is a circular chromosome of 2,024,171 bp. The genome shares extensive gene content, including many virulence factors, with genetically related group A streptococci, but unexpectedly lacks prophages. The genome contains many apparently foreign genes interspersed around the chromosome, consistent with the presence of a full array of genes required for natural competence. An inordinately large family of genes encodes secreted extracellular collagen-like proteins with multiple integrin-binding motifs. The absence of a gene related to speB rules out the long-held belief that streptococcal pyrogenic exotoxin B or antibodies reacting with it singularly cause PSGN. Many proteins previously implicated in GAS PSGN, such as streptokinase, are either highly divergent in strain MGCS10565 or are not more closely related between these species than to orthologs present in other streptococci that do not commonly cause PSGN. Our analysis provides a comparative genomics framework for renewed appraisal of molecular events underlying APSGN pathogenesis.
- Published
- 2008
- Full Text
- View/download PDF
24. Molecular genetic anatomy of inter- and intraserotype variation in the human bacterial pathogen group A Streptococcus.
- Author
-
Beres SB, Richter EW, Nagiec MJ, Sumby P, Porcella SF, DeLeo FR, and Musser JM
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Gene Expression Profiling, Genes, Bacterial, Genome, Bacterial, Genotype, Humans, Mice, Molecular Biology, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Phenotype, Phylogeny, Sequence Alignment, Serotyping, Streptococcus pyogenes pathogenicity, Genetic Variation, Sequence Analysis, DNA, Streptococcal Infections, Streptococcus pyogenes genetics
- Abstract
In recent years we have studied the relationship between strain genotypes and patient phenotypes in group A Streptococcus (GAS), a model human bacterial pathogen that causes extensive morbidity and mortality worldwide. We have concentrated our efforts on serotype M3 organisms because these strains are common causes of pharyngeal and invasive infections, produce unusually severe invasive infections, and can exhibit epidemic behavior. Our studies have been hindered by the lack of genome-scale phylogenies of multiple GAS strains and whole-genome sequences of multiple serotype M3 strains recovered from individuals with defined clinical phenotypes. To remove some of these impediments, we sequenced to closure the genome of four additional GAS strains and conducted comparative genomic resequencing of 12 contemporary serotype M3 strains representing distinct genotypes and phenotypes. Serotype M3 strains are a single phylogenetic lineage. Strains from asymptomatic throat carriers were significantly less virulent for mice than sterile-site isolates and evolved to a less virulent phenotype by multiple genetic pathways. Strain persistence or extinction between epidemics was strongly associated with presence or absence, respectively, of the prophage encoding streptococcal pyrogenic exotoxin A. A serotype M3 clone significantly underrepresented among necrotizing fasciitis cases has a unique frameshift mutation that truncates MtsR, a transcriptional regulator controlling expression of genes encoding iron-acquisition proteins. Expression microarray analysis of this clone confirmed significant alteration in expression of genes encoding iron metabolism proteins. Our analysis provided unprecedented detail about the molecular anatomy of bacterial strain genotype-patient phenotype relationships.
- Published
- 2006
- Full Text
- View/download PDF
25. Genome sequence of a serotype M28 strain of group a streptococcus: potential new insights into puerperal sepsis and bacterial disease specificity.
- Author
-
Green NM, Zhang S, Porcella SF, Nagiec MJ, Barbian KD, Beres SB, LeFebvre RB, and Musser JM
- Subjects
- Antigens, Bacterial genetics, Bacterial Outer Membrane Proteins genetics, Base Sequence, Blotting, Western, Carrier Proteins genetics, DNA, Bacterial chemistry, DNA, Bacterial genetics, Female, Humans, Phylogeny, Polymerase Chain Reaction, Prophages genetics, Recombinant Proteins, Sepsis microbiology, Sequence Alignment, Streptococcus pyogenes pathogenicity, Virulence Factors, Genome, Bacterial, Puerperal Infection microbiology, Streptococcal Infections microbiology, Streptococcus pyogenes genetics
- Abstract
Puerperal sepsis, a major cause of death of young women in Europe in the 1800s, was due predominantly to the gram-positive pathogen group A Streptococcus. Studies conducted during past decades have shown that serotype M28 strains are the major group A Streptococcus organisms responsible for many of these infections. To begin to increase our understanding of their enrichment in puerperal sepsis, we sequenced the genome of a genetically representative strain. This strain has genes encoding a novel array of prophage virulence factors, cell-surface proteins, and other molecules likely to contribute to host-pathogen interactions. Importantly, genes for 7 inferred extracellular proteins are encoded by a 37.4-kb foreign DNA element that is shared with group B Streptococcus and is present in all serotype M28 strains. Proteins encoded by the 37.4-kb element were expressed extracellularly and in human infections. Acquisition of foreign genes has helped create a disease-specialist clone of this pathogen.
- Published
- 2005
- Full Text
- View/download PDF
26. Genetic diversity among type emm28 group A Streptococcus strains causing invasive infections and pharyngitis.
- Author
-
Green NM, Beres SB, Graviss EA, Allison JE, McGeer AJ, Vuopio-Varkila J, LeFebvre RB, and Musser JM
- Subjects
- Chromosome Mapping, Drug Resistance, Bacterial, Genetic Variation, Humans, Macrolides pharmacology, Prophages genetics, Streptococcus pyogenes pathogenicity, Virulence genetics, Antigens, Bacterial genetics, Bacterial Outer Membrane Proteins genetics, Carrier Proteins genetics, Pharyngitis microbiology, Streptococcal Infections microbiology, Streptococcus pyogenes genetics
- Abstract
Genome sequencing of group A Streptococcus (GAS) has revealed that prophages account for the vast majority of gene content differences between strains. Serotype M28 strains are a leading cause of pharyngitis and invasive infections, but little is known about genetic diversity present in natural populations of these organisms. To study this issue, population-based samples of 568 strains from Ontario, Canada; Finland; and Houston, Texas, were analyzed. Special attention was given to analysis of variation in prophage-encoded virulence gene content by a PCR-based method. Thirty and 29 distinct prophage-encoded virulence gene profiles were identified among pharyngitis and invasive infection isolates. Thirteen profiles, representing the majority of the strains, were shared between these two classes of isolates. Significant differences were observed in the frequency of occurrence of certain prophage toxin gene profiles and infection type. M28 strains are highly diverse in prophage-encoded virulence gene content and integration site, supporting the key concept that prophages are critical contributors to GAS genetic diversity and population biology. Nucleotide sequence variation in the emm gene (encodes M protein) was also examined. Only three allelic variants were identified in the hypervariable portion of the emm28 gene. All but one strain had the same inferred amino acid sequence in the first 100 amino acids of the mature M28 protein. In contrast, size differences in the emm28 gene and inferred protein due to variable numbers of C-terminal repeats were common. The presence of macrolide resistance genes (mefA, ermB, and ermTR) was analyzed by PCR, and less than 2% of the strains were positive.
- Published
- 2005
- Full Text
- View/download PDF
27. Genome-wide molecular dissection of serotype M3 group A Streptococcus strains causing two epidemics of invasive infections.
- Author
-
Beres SB, Sylva GL, Sturdevant DE, Granville CN, Liu M, Ricklefs SM, Whitney AR, Parkins LD, Hoe NP, Adams GJ, Low DE, DeLeo FR, McGeer A, and Musser JM
- Subjects
- Antigens, Bacterial genetics, Antigens, Bacterial physiology, Bacterial Outer Membrane Proteins genetics, Bacterial Outer Membrane Proteins physiology, Bacterial Proteins genetics, Canada epidemiology, Carrier Proteins genetics, Carrier Proteins physiology, Chromosome Aberrations, Genetic Variation, Genomics methods, Genotype, Humans, Polymorphism, Single Nucleotide, Population Surveillance, Sequence Analysis, Streptococcal Infections virology, Streptococcus pyogenes immunology, Streptococcus pyogenes pathogenicity, Virulence genetics, Virulence Factors genetics, Disease Outbreaks, Genome, Bacterial, Streptococcal Infections epidemiology, Streptococcus pyogenes genetics
- Abstract
Molecular factors that contribute to the emergence of new virulent bacterial subclones and epidemics are poorly understood. We hypothesized that analysis of a population-based strain sample of serotype M3 group A Streptococcus (GAS) recovered from patients with invasive infection by using genome-wide investigative methods would provide new insight into this fundamental infectious disease problem. Serotype M3 GAS strains (n = 255) cultured from patients in Ontario, Canada, over 11 years and representing two distinct infection peaks were studied. Genetic diversity was indexed by pulsed-field gel electrophoresis, DNA-DNA microarray, whole-genome PCR scanning, prophage genotyping, targeted gene sequencing, and single-nucleotide polymorphism genotyping. All variation in gene content was attributable to acquisition or loss of prophages, a molecular process that generated unique combinations of proven or putative virulence genes. Distinct serotype M3 genotypes experienced rapid population expansion and caused infections that differed significantly in character and severity. Molecular genetic analysis, combined with immunologic studies, implicated a 4-aa duplication in the extreme N terminus of M protein as a factor contributing to an epidemic wave of serotype M3 invasive infections. This finding has implications for GAS vaccine research. Genome-wide analysis of population-based strain samples cultured from clinically well defined patients is crucial for understanding the molecular events underlying bacterial epidemics.
- Published
- 2004
- Full Text
- View/download PDF
28. Intrahost sequence variation in the streptococcal inhibitor of complement gene in patients with human pharyngitis.
- Author
-
Matsumoto M, Hoe NP, Liu M, Beres SB, Sylva GL, Brandt CM, Haase G, and Musser JM
- Subjects
- Acute Disease, Amino Acid Sequence, Base Sequence, Cloning, Molecular, Collagen genetics, Gene Deletion, Genetic Variation, Humans, Microsatellite Repeats, Molecular Sequence Data, Pharynx microbiology, Streptococcus pyogenes chemistry, Bacterial Proteins genetics, Pharyngitis microbiology, Streptococcal Infections microbiology, Streptococcus pyogenes genetics
- Abstract
Selection of new variants of the streptococcal inhibitor of complement protein has been implicated in the perpetuation of epidemics caused by serotype M1 strains of group A Streptococcus (GAS). The frequency at which new streptococcal inhibitor of complement (Sic) variants arise in an infected individual is not known. To study this issue, the sic gene was sequenced in 100 isolates cultured from throat swabs of each of 20 patients with acute pharyngitis caused by serotype M1 GAS. Five patients were infected with GAS populations expressing 2 Sic variants characterized by deletion of a region of the protein. In contrast, no intrahost variation was detected in the number of a pentanucleotide repeat (CAAAA) that controls production of a bacterial cell-surface collagen-like protein by slipped-strand mispairing. Sic variation occurs at a sufficient frequency in vivo to result in mixed infections on the mucosal surface of human hosts, potentially contributing to pathogen survival.
- Published
- 2003
- Full Text
- View/download PDF
29. Genetic evolution of invasive emm28 Streptococcus pyogenes strains and significant association with puerperal infections in young women in Finland
- Author
-
Gröndahl-Yli-Hannuksela, Kirsi, Beres, Stephen B., Hyyryläinen, H.-L., Kallonen, Teemu, Musser, James M., and Vuopio, Jaana
- Subjects
Adult ,Aged, 80 and over ,Whole-genome sequencing ,Antigens, Bacterial ,Adolescent ,Streptococcus pyogenes ,Group A streptococcus ,Infant, Newborn ,Infant ,Bacteremia ,Middle Aged ,Article ,Young Adult ,Pregnancy ,Child, Preschool ,Streptococcal Infections ,Humans ,Puerperal Infection ,Female ,Puerperal sepsis ,Child ,Bacteraemic ,Finland ,Aged ,Retrospective Studies - Abstract
Objectives Streptococcus pyogenes or group A streptococcus (GAS) is a human specific pathogen that annually infects over 700 million individuals. GAS strains of type emm28 are an abundant cause of invasive infections in Europe and North America. Methods We conducted a population-based study on bacteraemic emm28 GAS cases in Finland, from 1995 to 2015. Whole-genome sequencing (WGS) was used to genetically characterize the bacterial isolates. Bayesian analysis of the population structure was used to define genetic clades. Register-linkage analysis was performed to test for association of emm28 GAS with delivery- or postpartum-related infections. A genome-wide association study was used to search for DNA sequences associated with delivery or puerperal infections. Results Among 3060 bacteraemic cases reported during the study period, 714 were caused by emm28. Women comprised a majority of cases (59 %, 422/714), and were significantly over-represented (84.4 %, 162/192, p < 0.0001) among cases in the childbearing age group (20–40 years). Register-linkage analysis revealed strong association (p < 0.0001) of emm28 bacteraemias with delivery and puerperium. In this register-linkage analysis, 120 women with GAS bacteraemia were identified and linked to delivery, infections during delivery or puerperium time. Among these the proportion of cases caused by emm28 was significantly higher than any other emm type (55.8%, 67/120, p < 0.0001). Among the four genetic subclades identified, SC1B has dominated among the bacteraemic cases since 2000. Altogether 620 of 653 (94.9%) isolates belonged to SC1B. No specific sequence or genetic clade was found nonrandomly associated with delivery or puerperal infections. Conclusions Women of childbearing age were significantly overrepresented among bacteraemic emm28 GAS cases, and in particular were strongly associated with delivery and puerperium cases over the 21 years studied. The molecular mechanisms behind these associations are unclear and warrant further investigation.
- Published
- 2020
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.