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Thirumoorthy TP, Jacob JJ, Velmurugan A, Teekaraman MP, Shah B, Iyer V, Maheshwari G, Trivedi U, Shah A, Patel P, Gaigawale A, M Y, Sathya Narayanan P, Mutreja A, Carey M, John J, Kang G, Veeraraghavan B. Recent emergence of cephalosporin-resistant Salmonella Typhi in India due to the endemic clone acquiring IncFIB(K) plasmid encoding blaCTX-M-15 gene. Microbiol Spectr 2025; 13:e0087524. [PMID: 40208005 PMCID: PMC12054180 DOI: 10.1128/spectrum.00875-24] [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: 04/12/2024] [Accepted: 01/21/2025] [Indexed: 04/11/2025] Open
Abstract
The emergence and spread of Salmonella Typhi (S. Typhi) resistant to third-generation cephalosporins is a serious global health concern. In this study, we genomically characterized 142 cephalosporin-resistant S. Typhi strains isolated from India. Comparative genome analysis revealed the emergence of a new clone of ceftriaxone-resistant S. Typhi harboring three plasmids of the incompatibility groups IncFIB(K), IncX1, and IncFIB(pHCM2). Among these, the IncFIB(K) plasmid confers resistance to third-generation cephalosporins through the blaCTX-M-15 gene, along with other resistance determinants such as aph(3"), aph(6'), sul2, dfrA14, qnrS, and tet(A). Phylogenetic analysis showed that the isolates from Gujarat (n = 140/142) belong to a distinct subclade (genotype 4.3.1.2.2) within genotype 4.3.1.2 (H58 lineage II). Single nucleotide polymorphism-based phylogenetic analysis of the core genes in IncFIB(K) suggested a close relatedness of the plasmid backbone to that of IncFIB(K) from other Enterobacteriales, indicating that H58 lineage II possesses the capability to acquire MDR plasmids from these organisms. This could indicate the potential onset of a new wave of ceftriaxone-resistant S. Typhi in India. The implementation of control measures-such as vaccination and improved water, sanitation, and hygiene systems-is crucial in areas where MDR or extensively drug-resistant S. Typhi strains are prevalent to curb the spread and impact of these resistant strains. IMPORTANCE Typhoid fever remains a global health concern, especially in areas lacking sanitation and clean water. The rise of drug-resistant strains complicates treatment, increasing illness, death, and healthcare expenses. Travel facilitates the spread of these strains worldwide. Multidrug-resistant and extensively drug-resistant (XDR) strains, including those resistant to first-line antibiotics and fluoroquinolones, pose significant challenges. Azithromycin and third-generation cephalosporins are now preferred treatments. Recently, XDR typhoid emerged in Pakistan, resistant even to third-generation cephalosporins. India also faces challenges, with sporadic cases initially declining but now re-emerging. New strains in India show resistance to third-generation cephalosporins due to plasmid acquisition from other bacteria, particularly blaCTX-M-carrying IncFIB(K). Due to the ongoing nature of this outbreak, the data from this study deserve further consideration in order to control its spread in India.
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Affiliation(s)
| | | | | | | | - Bhavini Shah
- Neuberg Supratech Reference Laboratories, Ahmedabad, Gujarat, India
| | - Veena Iyer
- Indian Institute of Public Health, Gandhinagar, Gujarat, India
| | | | - Urmi Trivedi
- Unipath Specialty Laboratory, Akota, Vadodara, Gujarat, India
| | - Anand Shah
- Zydus Hospitals, Ahmedabad, Gujarat, India
| | - Pooja Patel
- Pathocare Pathology Laboratory, Vadodara, Gujarat, India
| | - Anushree Gaigawale
- Suburban Diagnostics India Pvt. Ltd, Andheri (w), Mumbai, Maharashtra, India
| | - Yesudoss M
- Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Megan Carey
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jacob John
- Christian Medical College, Vellore, Tamil Nadu, India
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Piper KR, Souza SSR, Ikhimiukor OO, Workman AA, Martin IW, Andam CP. Lineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli. BMC Genomics 2025; 26:190. [PMID: 39994515 PMCID: PMC11853335 DOI: 10.1186/s12864-025-11367-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Accepted: 02/14/2025] [Indexed: 02/26/2025] Open
Abstract
BACKGROUND The opportunistic bacterium Escherichia coli can invade normally sterile sites in the human body, potentially leading to life-threatening organ dysfunction and even death. However, our understanding of the evolutionary processes that shape its genetic diversity in this sterile environment remains limited. Here, we aim to quantify the frequency and characteristics of homologous recombination in E. coli from bloodstream infections. RESULTS Analysis of 557 short-read genome sequences revealed that the propensity to exchange DNA by homologous recombination varies within a distinct population (bloodstream) at narrow geographic (Dartmouth Hitchcock Medical Center, New Hampshire, USA) and temporal (years 2016 - 2022) scope. We identified the four largest monophyletic sequence clusters in the core genome phylogeny that are represented by prominent sequence types (ST): BAPS1 (mainly ST95), BAPS4 (mainly ST73), BAPS10 (mainly ST131), BAPS14 (mainly ST58). We show that the four dominant clusters vary in different characteristics of recombination: number of single nucleotide polymorphisms due to recombination, number of recombination blocks, cumulative bases in recombination blocks, ratio of probabilities that a given site was altered through recombination and mutation (r/m), and ratio of rates at which recombination and mutation occurred (ρ/θ). Each sequence cluster contains a unique set of antimicrobial resistance (AMR) and virulence genes that have experienced recombination. Common among the four sequence clusters were the recombined virulence genes with functions associated with the Curli secretion channel (csgG) and ferric enterobactin transport (entEF, fepEG). We did not identify any one recombined AMR gene that was present in all four sequence clusters. However, AMR genes mdtABC, baeSR, emrKY and tolC had experienced recombination in sequence clusters BAPS4, BAPS10, and BAPS14. These differences lie in part on the contributions of vertically inherited ancestral recombination and contemporary branch-specific recombination, with some genomes having relatively higher proportions of recombined DNA. CONCLUSIONS Our results highlight the variation in the propensity to exchange DNA via homologous recombination within a distinct population at narrow geographic and temporal ranges. Understanding the sources of the genetic variation in invasive E. coli will help inform the implementation of effective strategies to reduce the burden of disease and AMR.
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Affiliation(s)
- Kathryn R Piper
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Odion O Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Adrienne A Workman
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center and Dartmouth College Geisel School of Medicine, Lebanon, NH, USA.
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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Bouzek H, Srinivasan S, Jones DS, McMahon EF, Strenk SM, Fiedler TL, Fredricks DN, Johnston CD. A Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.19.636902. [PMID: 40027674 PMCID: PMC11870614 DOI: 10.1101/2025.02.19.636902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Bacterial vaginosis (BV) is a prevalent condition associated with an imbalance in the vaginal microbiota, often involving species of Gardnerella . The taxonomic complexity and inconsistent nomenclature of Gardnerella have impeded progress in understanding the role of specific species in health and disease. In this study, we conducted a comprehensive genomic and pangenomic analysis to resolve taxonomic ambiguities and elucidate metabolic and virulence potential across Gardnerella species. We obtained complete, closed genomes for 42 Gardnerella isolates from women with BV and curated publicly available genome sequences (n = 291). Average nucleotide identity (ANI) analysis, digital DNA-DNA hybridization (dDDH), and the cpn60 gene sequences identified nine species and eleven subspecies within Gardnerella , for which we refined species and subspecies boundaries and proposed updated nomenclature. Pangenome analysis revealed species-specific gene clusters linked to metabolic pathways, virulence factors, and niche adaptations, distinguishing species specialized for mucin degradation in the vaginal environment from those potentially adapted to urinary tract colonization. Notably, we identified lineage-specific evolutionary divergence in gene clusters associated with biofilm formation, carbohydrate metabolism, and antimicrobial resistance. We further discovered the first cryptic plasmids naturally present within the Gardnerella genus. Our findings provide a unified framework for Gardnerella taxonomy and nomenclature, and enhance our understanding of species-specific functional capabilities, with implications for Gardnerella research, diagnostics, and targeted therapeutics in BV.
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Williams DJ, Hawkins A, Hernandez RE, Mariano G, Mathers K, Buchanan G, Stonier BJ, Inkster T, Leanord A, Chalmers JD, Thomson NR, Holden MTG, Coulthurst SJ. Competitive behaviors in Serratia marcescens are coordinately regulated by a lifestyle switch frequently inactivated in the clinical environment. Cell Host Microbe 2025; 33:252-266.e5. [PMID: 39884275 DOI: 10.1016/j.chom.2025.01.001] [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: 07/31/2024] [Revised: 12/02/2024] [Accepted: 01/06/2025] [Indexed: 02/01/2025]
Abstract
Opportunistic bacterial pathogens must compete with other bacteria and switch between host- and environment-adapted states. Type VI secretion systems (T6SSs) occur widely in gram-negative bacteria and can efficiently kill neighboring competitors. We determined the distribution of T6SSs across the genus Serratia and observed that a highly conserved antibacterial T6SS is differentially active between closely related clinical isolates of Serratia marcescens. By combining genomic and experimental approaches, we identified a genus-core two-component system, BetR-Reg1-Reg2, that controls T6SS activity and exhibits frequent inactivating mutations, exclusively in S. marcescens isolates of clinical origin. This regulatory system controls a number of lifestyle-related traits at transcriptional and post-translational levels, including T6SS activity, antibiotic production, motility, and adhesion, with loss of BetR increasing virulence in an in vivo infection model. Our data support a model whereby this system represents a conserved, modular switch from sessile to pioneering and aggressive behavior, which is subject to selection pressure in clinical environments.
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Affiliation(s)
- David J Williams
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Ruth E Hernandez
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | | | - Grant Buchanan
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | | | - Teresa Inkster
- Antimicrobial Resistance and Healthcare Associated Infection (ARHAI), Glasgow, Scotland
| | - Alistair Leanord
- School of Infection and Immunity, University of Glasgow, Glasgow G12 8TA, UK; Scottish Microbiology Reference Laboratories, Glasgow G31 2ER, UK
| | | | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
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Sheng H, Zhao L, Suo J, Yang Q, Cao C, Chen J, Cui G, Fan Y, Ma Y, Huo S, Wu X, Yang T, Cui X, Chen S, Cui S, Yang B. Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken. Food Res Int 2024; 197:115299. [PMID: 39577948 DOI: 10.1016/j.foodres.2024.115299] [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: 06/29/2024] [Revised: 10/06/2024] [Accepted: 10/31/2024] [Indexed: 11/24/2024]
Abstract
Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.
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Affiliation(s)
- Huanjing Sheng
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Linna Zhao
- National Institutes for Food and Drug Control, Beijing 100050, China; Beijing AOBOXING Bio-Tech Co., Ltd., Beijing 100050, China
| | - Jia Suo
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Qiuping Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Chenyang Cao
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Jia Chen
- College of Chemical Technology, Shijiazhuang University, Shijiazhuang 050035, China
| | - Guangqing Cui
- Shanxi Inspection and Testing Center, Taiyuan 030001, China
| | - Yiling Fan
- National Medical Products Administration Key Laboratory for Testing Technology of Pharmaceutical Microbiology, Shanghai Institute for Food and Drug Control, Shanghai 201203, China; China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Yi Ma
- Hubei Provincial Institute for Food Supervision and Test, Wuhan 430072, China
| | - Shengnan Huo
- Shandong Institute for Food and Drug Control, Jinan 250101, China
| | - Xin Wu
- Food Inspection and Testing Research Institute of Jiangxi General Institute of Testing and Certification, Nanchang 330052, China
| | - Tao Yang
- Hunan Testing Institute of Product and Commodity, Changsha 410007, China
| | - Xuewen Cui
- Microbiological Inspection Center, Sichuan Institute for Drug Control, Chengdu 611731, China
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom 100872, China.
| | - Shenghui Cui
- National Institutes for Food and Drug Control, Beijing 100050, China.
| | - Baowei Yang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China.
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6
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Foo A, Brettell LE, Nichols HL, 2022 UW-Madison Capstone in Microbiology Students, Medina Muñoz M, Lysne JA, Dhokiya V, Hoque AF, Brackney DE, Caragata EP, Hutchinson ML, Jacobs-Lorena M, Lampe DJ, Martin E, Valiente Moro C, Povelones M, Short SM, Steven B, Xu J, Paustian TD, Rondon MR, Hughes GL, Coon KL, Heinz E. MosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies. PLoS Biol 2024; 22:e3002897. [PMID: 39546548 PMCID: PMC11633956 DOI: 10.1371/journal.pbio.3002897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/11/2024] [Accepted: 10/11/2024] [Indexed: 11/17/2024] Open
Abstract
Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such as Plasmodium spp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterial Mosquito-Associated Isolate Collection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available, both isolates and sequence data, for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of the Enterobacteriaceae comprising 40% of the collection. Phylogenomic analysis of 3 genera, Enterobacter, Serratia, and Elizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species' pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to test for functions connected to mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource for research on bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.
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Affiliation(s)
- Aidan Foo
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Laura E. Brettell
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- School of Science, Engineering and Environment, University of Salford, Manchester, United Kingdom
| | - Holly L. Nichols
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | | | - Miguel Medina Muñoz
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jessica A. Lysne
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Vishaal Dhokiya
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Ananya F. Hoque
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Doug E. Brackney
- Department of Entomology, Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
- Center for Vector Biology and Zoonotic Diseases, Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
| | - Eric P. Caragata
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Vero Beach, Florida, United States of America
| | - Michael L. Hutchinson
- Division of Vector Management, Pennsylvania Department of Environmental Protection, Harrisburg, Pennsylvania, United States of America
- Division of Plant Health, Pennsylvania Department of Agriculture, Harrisburg, Pennsylvania, United States of America
| | - Marcelo Jacobs-Lorena
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - David J. Lampe
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Edwige Martin
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France
| | - Claire Valiente Moro
- Universite Claude Bernard Lyon 1, Laboratoire d'Ecologie Microbienne, UMR CNRS 5557, UMR INRAE 1418, VetAgro Sup, 69622 Villeurbanne, France
| | - Michael Povelones
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sarah M. Short
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
| | - Blaire Steven
- Department of Environmental Science and Forestry, Connecticut Agricultural Experiment Station, New Haven, Connecticut, United States of America
| | - Jiannong Xu
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Timothy D. Paustian
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Michelle R. Rondon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Grant L. Hughes
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Centre for Neglected Tropical Disease, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kerri L. Coon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Eva Heinz
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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7
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Piper KR, Ikhimiukor OO, Souza SSR, Garcia-Aroca T, Andam CP. Evolutionary dynamics of the accessory genomes of Staphylococcus aureus. mSphere 2024; 9:e0075123. [PMID: 38501935 PMCID: PMC11036810 DOI: 10.1128/msphere.00751-23] [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: 12/01/2023] [Accepted: 02/24/2024] [Indexed: 03/20/2024] Open
Abstract
Staphylococcus aureus is a ubiquitous commensal and opportunistic bacterial pathogen that can cause a wide gamut of infections, which are exacerbated by the presence of multidrug-resistant and methicillin-resistant S. aureus. S. aureus is genetically heterogeneous and consists of numerous distinct lineages. Using 558 complete genomes of S. aureus, we aim to determine how the accessory genome content among phylogenetic lineages of S. aureus is structured and has evolved. Bayesian hierarchical clustering identified 10 sequence clusters, of which seven contained major sequence types (ST 1, 5, 8, 30, 59, 239, and 398). The seven sequence clusters differed in their accessory gene content, including genes associated with antimicrobial resistance and virulence. Focusing on the two largest clusters, BAPS8 and BAPS10, and each consisting mostly of ST5 and ST8, respectively, we found that the structure and connected components in the co-occurrence networks of accessory genomes varied between them. These differences are explained, in part, by the variation in the rates at which the two sequence clusters gained and lost accessory genes, with the highest rate of gene accumulation occurring recently in their evolutionary histories. We also identified a divergent group within BAPS10 that has experienced high gene gain and loss early in its history. Together, our results show highly variable and dynamic accessory genomes in S. aureus that are structured by the history of the specific lineages that carry them.IMPORTANCEStaphylococcus aureus is an opportunistic, multi-host pathogen that can cause a variety of benign and life-threatening infections. Our results revealed considerable differences in the structure and evolution of the accessory genomes of major lineages within S. aureus. Such genomic variation within a species can have important implications on disease epidemiology, pathogenesis of infection, and interactions with the vertebrate host. Our findings provide important insights into the underlying genetic basis for the success of S. aureus as a highly adaptable and resistant pathogen, which will inform current efforts to control and treat staphylococcal diseases.
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Affiliation(s)
- Kathryn R. Piper
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Teddy Garcia-Aroca
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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8
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Zepeda-Rivera M, Minot SS, Bouzek H, Wu H, Blanco-Míguez A, Manghi P, Jones DS, LaCourse KD, Wu Y, McMahon EF, Park SN, Lim YK, Kempchinsky AG, Willis AD, Cotton SL, Yost SC, Sicinska E, Kook JK, Dewhirst FE, Segata N, Bullman S, Johnston CD. A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. Nature 2024; 628:424-432. [PMID: 38509359 PMCID: PMC11006615 DOI: 10.1038/s41586-024-07182-w] [Citation(s) in RCA: 121] [Impact Index Per Article: 121.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 02/08/2024] [Indexed: 03/22/2024]
Abstract
Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals1, is enriched in human colorectal cancer (CRC) tumours2-5. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis5-8. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.
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Affiliation(s)
- Martha Zepeda-Rivera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Heather Bouzek
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hanrui Wu
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aitor Blanco-Míguez
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Paolo Manghi
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Ying Wu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elsa F McMahon
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Soon-Nang Park
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun K Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | | | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | | | - Ewa Sicinska
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Floyd E Dewhirst
- Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Nicola Segata
- Department of Computational, Cellular and Integrative Biology, University of Trento, Trento, Italy
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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9
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Dong X, Jia H, Yu Y, Xiang Y, Zhang Y. Genomic revisitation and reclassification of the genus Providencia. mSphere 2024; 9:e0073123. [PMID: 38412041 PMCID: PMC10964429 DOI: 10.1128/msphere.00731-23] [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: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Members of Providencia, although typically opportunistic, can cause severe infections in immunocompromised hosts. Recent advances in genome sequencing provide an opportunity for more precise study of this genus. In this study, we first identified and characterized a novel species named Providencia zhijiangensis sp. nov. It has ≤88.23% average nucleotide identity (ANI) and ≤31.8% in silico DNA-DNA hybridization (dDDH) values with all known Providencia species, which fall significantly below the species-defining thresholds. Interestingly, we found that Providencia stuartii and Providencia thailandensis actually fall under the same species, evidenced by an ANI of 98.59% and a dDDH value of 90.4%. By fusing ANI with phylogeny, we have reclassified 545 genomes within this genus into 20 species, including seven unnamed taxa (provisionally titled Taxon 1-7), which can be further subdivided into 23 lineages. Pangenomic analysis identified 1,550 genus-core genes in Providencia, with coenzymes being the predominant category at 10.56%, suggesting significant intermediate metabolism activity. Resistance analysis revealed that most lineages of the genus (82.61%, 19/23) carry a high number of antibiotic-resistance genes (ARGs) and display diverse resistance profiles. Notably, the majority of ARGs are located on plasmids, underscoring the significant role of plasmids in the resistance evolution within this genus. Three species or lineages (P. stuartii, Taxon 3, and Providencia hangzhouensis L12) that possess the highest number of carbapenem-resistance genes suggest their potential influence on clinical treatment. These findings underscore the need for continued surveillance and study of this genus, particularly due to their role in harboring antibiotic-resistance genes. IMPORTANCE The Providencia genus, known to harbor opportunistic pathogens, has been a subject of interest due to its potential to cause severe infections, particularly in vulnerable individuals. Our research offers groundbreaking insights into this genus, unveiling a novel species, Providencia zhijiangensis sp. nov., and highlighting the need for a re-evaluation of existing classifications. Our comprehensive genomic assessment offers a detailed classification of 545 genomes into distinct species and lineages, revealing the rich biodiversity and intricate species diversity within the genus. The substantial presence of antibiotic-resistance genes in the Providencia genus underscores potential challenges for public health and clinical treatments. Our study highlights the pressing need for increased surveillance and research, enriching our understanding of antibiotic resistance in this realm.
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Affiliation(s)
- Xu Dong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Guangzhou, China
| | - Huiqiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuyun Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanghui Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Guangzhou, China
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10
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Raghuram V, Petit RA, Karol Z, Mehta R, Weissman DB, Read TD. Average Nucleotide Identity based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577756. [PMID: 38352482 PMCID: PMC10862745 DOI: 10.1101/2024.01.29.577756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background ("strain-concentrated") and those highly variable within strains ("strain-diffuse"). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.
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Affiliation(s)
- Vishnu Raghuram
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Robert A Petit
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Zach Karol
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | - Rohan Mehta
- Department of Physics, Emory University, Atlanta, Georgia, USA
| | | | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
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11
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Mehrotra T, Konar D, Pragasam AK, Kumar S, Jana P, Babele P, Paul D, Purohit A, Tanwar S, Bakshi S, Das S, Verma J, Talukdar D, Narendrakumar L, Kothidar A, Karmakar SP, Chaudhuri S, Pal S, Jain K, Srikanth CV, Sankar MJ, Atmakuri K, Agarwal R, Gaind R, Ballal M, Kammili N, Bhadra RK, Ramamurthy T, Nair GB, Das B. Antimicrobial resistance heterogeneity among multidrug-resistant Gram-negative pathogens: Phenotypic, genotypic, and proteomic analysis. Proc Natl Acad Sci U S A 2023; 120:e2305465120. [PMID: 37549252 PMCID: PMC10434301 DOI: 10.1073/pnas.2305465120] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/07/2023] [Indexed: 08/09/2023] Open
Abstract
Microbes evolve rapidly by modifying their genomes through mutations or through the horizontal acquisition of mobile genetic elements (MGEs) linked with fitness traits such as antimicrobial resistance (AMR), virulence, and metabolic functions. We conducted a multicentric study in India and collected different clinical samples for decoding the genome sequences of bacterial pathogens associated with sepsis, urinary tract infections, and respiratory infections to understand the functional potency associated with AMR and its dynamics. Genomic analysis identified several acquired AMR genes (ARGs) that have a pathogen-specific signature. We observed that blaCTX-M-15, blaCMY-42, blaNDM-5, and aadA(2) were prevalent in Escherichia coli, and blaTEM-1B, blaOXA-232, blaNDM-1, rmtB, and rmtC were dominant in Klebsiella pneumoniae. In contrast, Pseudomonas aeruginosa and Acinetobacter baumannii harbored blaVEB, blaVIM-2, aph(3'), strA/B, blaOXA-23, aph(3') variants, and amrA, respectively. Regardless of the type of ARG, the MGEs linked with ARGs were also pathogen-specific. The sequence type of these pathogens was identified as high-risk international clones, with only a few lineages being predominant and region-specific. Whole-cell proteome analysis of extensively drug-resistant K. pneumoniae, A. baumannii, E. coli, and P. aeruginosa strains revealed differential abundances of resistance-associated proteins in the presence and absence of different classes of antibiotics. The pathogen-specific resistance signatures and differential abundance of AMR-associated proteins identified in this study should add value to AMR diagnostics and the choice of appropriate drug combinations for successful antimicrobial therapy.
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Affiliation(s)
- Tanshi Mehrotra
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Dipasri Konar
- Division of Diagnostic Laboratory, Jan Swasthya Sahyog, Ganiyari, Bilaspur495112, India
| | - Agila Kumari Pragasam
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Shakti Kumar
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Pradipta Jana
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Prabhakar Babele
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Deepjyoti Paul
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Ayushi Purohit
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Subhash Tanwar
- Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Susmita Bakshi
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Santanu Das
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Jyoti Verma
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Daizee Talukdar
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Lekshmi Narendrakumar
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Akanksha Kothidar
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Sonali Porey Karmakar
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Susmita Chaudhuri
- Multidisciplinary Clinical and Translational Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Sujoy Pal
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi110029, India
| | - Kajal Jain
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi110029, India
| | - Chittur V. Srikanth
- Laboratory of Gut Infection and Inflammation Biology, Regional Centre for Biotechnology, Faridabad121001, India
| | - M. Jeeva Sankar
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi110029, India
| | - Krishnamohan Atmakuri
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
| | - Ramesh Agarwal
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi110029, India
| | - Rajni Gaind
- Department of Microbiology, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi110029, India
| | - Mamatha Ballal
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal576104, India
| | - Nagamani Kammili
- Department of Microbiology, Pathogen Biology Division, Gandhi Medical College and Hospital, Secunderabad500003, India
| | - Rupak K. Bhadra
- Infectious Diseases and Immunology Division, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700 032, India
| | - Thandavarayan Ramamurthy
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
- Division of Bacteriology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata700010, India
| | - G. Balakrish Nair
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
- Pathogen Biology Division, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram695014, India
| | - Bhabatosh Das
- Infection and Immunology Division, Functional Genomics Laboratory, Centre for Microbial Research, Translational Health Science and Technology Institute, Faridabad121001, India
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12
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Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity. Microbiol Spectr 2022; 10:e0311722. [PMID: 36318042 PMCID: PMC9769869 DOI: 10.1128/spectrum.03117-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The massive quantities of bacterial genomic data being generated have facilitated in-depth analyses of bacteria for pan-genomic studies. However, the pan-genome compositions of one species differed significantly between different studies, so we used Staphylococcus aureus as a model organism to explore the influences driving bacterial pan-genome composition. We selected a series of diverse strains for pan-genomic analysis to explore the pan-genomic composition of S. aureus at the species level and the actual contribution of influencing factors (sequence type [ST], source of isolation, country of isolation, and date of collection) to pan-genome composition. We found that the distribution of core genes in bacterial populations restrained under different conditions differed significantly and showed "local core gene regions" in the same ST. Therefore, we propose that ST may be a key factor driving the dynamic distribution of bacterial genomes and that phylogenetic analyses using whole-genome alignment are no longer appropriate in populations containing multiple ST strains. Pan-genomic analysis showed that some of the housekeeping genes of multilocus sequence typing (MLST) are carried at less than 60% in S. aureus strains. Consequently, we propose a new set of marker genes for the classification of S. aureus, which provides a reference for finding a new set of housekeeping genes to apply to MLST. In this study, we explored the role of driving factors influencing pan-genome composition, providing new insights into the study of bacterial pan-genomes. IMPORTANCE We sought to explore the impact of driving factors influencing pan-genome composition using Staphylococcus aureus as a model organism to provide new insights for the study of bacterial pan-genomes. We believe that the sequence type (ST) of the strains under consideration plays a significant role in the dynamic distribution of bacterial genes. Our findings indicate that there are a certain number of essential genes in Staphylococcus aureus; however, the number of core genes is not as high as previously thought. The new classification method proposed herein suggests that a new set of housekeeping genes more suitable for Staphylococcus aureus must be identified to improve the current classification status of this species.
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13
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Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock. Proc Natl Acad Sci U S A 2022; 119:e2211217119. [PMID: 36469788 PMCID: PMC9897428 DOI: 10.1073/pnas.2211217119] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022] Open
Abstract
Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 y ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialization and industrialization of dairy farming, and older lineages have become globally distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pangenome network analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine-associated genes, consistent with multiple trajectories to host adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic, and gene-level perspective of its remarkable success.
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14
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Cummins EA, Hall RJ, Connor C, McInerney JO, McNally A. Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microb Genom 2022; 8:mgen000903. [PMID: 36748558 PMCID: PMC9836092 DOI: 10.1099/mgen.0.000903] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/02/2022] [Indexed: 11/24/2022] Open
Abstract
The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers.
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Affiliation(s)
- Elizabeth A. Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J. Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chris Connor
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - James O. McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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15
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Ramamurthy T, Pragasam AK, Taylor-Brown A, Will RC, Vasudevan K, Das B, Srivastava SK, Chowdhury G, Mukhopadhyay AK, Dutta S, Veeraraghavan B, Thomson NR, Sharma NC, Nair GB, Takeda Y, Ghosh A, Dougan G, Mutreja A. Vibrio cholerae O139 genomes provide a clue to why it may have failed to usher in the eighth cholera pandemic. Nat Commun 2022; 13:3864. [PMID: 35790755 PMCID: PMC9256687 DOI: 10.1038/s41467-022-31391-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/14/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractCholera is a life-threatening infectious disease that remains an important public health issue in several low and middle-income countries. In 1992, a newly identified O139 Vibrio cholerae temporarily displaced the O1 serogroup. No study has been able to answer why the potential eighth cholera pandemic (8CP) causing V. cholerae O139 emerged so successfully and then died out. We conducted a genomic study, including 330 O139 isolates, covering emergence of the serogroup in 1992 through to 2015. We noted two key genomic evolutionary changes that may have been responsible for the disappearance of genetically distinct but temporally overlapping waves (A-C) of O139. Firstly, as the waves progressed, a switch from a homogenous toxin genotype in wave-A to heterogeneous genotypes. Secondly, a gradual loss of antimicrobial resistance (AMR) with the progression of waves. We hypothesize that these two changes contributed to the eventual epidemiological decline of O139.
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16
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Cummins EA, Hall RJ, McInerney JO, McNally A. Prokaryote pangenomes are dynamic entities. Curr Opin Microbiol 2022; 66:73-78. [PMID: 35104691 DOI: 10.1016/j.mib.2022.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 11/24/2022]
Abstract
Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - James O McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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