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Arbaein T, Little B, Monshi S, Al-Wathinani AM, Zaidan A. The variation in preventable hospitalization in patients with type 2 diabetes in Kentucky before and after the Medicaid expansion. Ann Saudi Med 2024; 44:73-83. [PMID: 38615187 PMCID: PMC11016150 DOI: 10.5144/0256-4947.2024.73] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/23/2023] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND Hospitalizations are more resource intensive and expensive than outpatient care. Therefore, type 2 diabetes-related preventable hospitalization are a major topic of research efficiency in the healthcare system. OBJECTIVES Analyze county level variation in type 2 diabetes-related preventable hospitalization rates in Kentucky before the Medicaid expansion (2010-2013) and after the Medicaid expansion (2014-2017). DESIGN Geographic mapping and cluster analysis. SETTING Data for a state of the United States of America. METHODS We used the KID data to generate geographic mapping for type 2 diabetes-related preventable hospitalizations to visualize rates. We included all Kentucky discharges of age 18 years and older with the ICD9/10 principal diagnosis code for type 2 diabetes. Then, we conducted cluster analysis techniques to compare county-level variation in type 2 diabetes-related preventable hospitalization rates across Kentucky counties pre- and post-Medicaid expansion. MAIN OUTCOME AND MEASURES County type 2 diabetes-related preventable hospitalization pre- and post-Medicaid expansion. RESULTS From 2010-2017, type 2 diabetes-related preventable hospitalization discharge rates reduced significantly in the period of the post-Medicaid expansion (P=.001). The spatial statistics analysis revealed a significant spatial clustering of counties with similar rates of type 2 diabetes-related preventable hospitalization in the south, east, and southeastern Kentucky pre- and post-Medicaid expansion (positive z-score and positive Moran's Index value (P>.05). Also, there was a significant clustering of counties with low type 2 diabetes-related preventable hospitalization rates in the north, west, and central regions of the state pre-Medicaid expansion and post-Medicaid expansion (positive z-score and positive Moran's Index value (P>.05). CONCLUSION Kentucky counties in the southeast have experienced a significant clustering of highly avoidable hospitalization rates during both periods. Focusing on the vulnerable counties and the economic inequality in Kentucky could lead to efforts to lowering future type 2 diabetes-related preventable hospitalization rates. LIMITATIONS We used de-identified data which does not provide insights into the frequency of hospitalizations per patient. An individual patient may be hospitalized several times and counted as several individuals.
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Affiliation(s)
- Turky Arbaein
- From the Department of Health Administration and Hospital, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Bert Little
- From the Department of Health Management and System Sciences, University of Louisville, Kentucky, United States
| | - Sarah Monshi
- From the Department of Health Administration and Hospital, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ahmed M. Al-Wathinani
- From the Department of Emergency Medical Services, Prince Sultan bin Abdulaziz for Emergency Medical Services, King Saud University, Riyadh, Saudi Arabia
| | - Amal Zaidan
- From the College of Public Health and Health Informatics, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Abstract
DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.
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Hammond JA, Gordon EA, Socarras KM, Chang Mell J, Ehrlich GD. Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis. Biochem Soc Trans 2020; 48:2437-2455. [PMID: 33245329 PMCID: PMC7752077 DOI: 10.1042/bst20190713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023]
Abstract
The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host-bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.
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Affiliation(s)
- Jocelyn A. Hammond
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Emma A. Gordon
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Kayla M. Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Joshua Chang Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
- Department of Otolaryngology – Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, U.S.A
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Silva JG, Araujo WJ, Leite EL, Dias LM, Vasconcelos PC, Silva NMV, Oliveira RP, Sena MJ, Oliveira CJB, Mota RA. First report of a livestock-associated methicillin-resistant Staphylococcus aureus ST126 harbouring the mecC variant in Brazil. Transbound Emerg Dis 2020; 68:1019-1025. [PMID: 32762020 DOI: 10.1111/tbed.13771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/28/2020] [Accepted: 07/31/2020] [Indexed: 12/28/2022]
Abstract
Staphylococcus aureus is a versatile and highly adaptable pathogen associated with a wide range of infectious diseases in humans and animals. In the last decades, concern has increased worldwide due to the emergence and spread of methicillin-resistant S. aureus (MRSA) strains shortly after this drug became a therapeutic option. In this study, we report the genomic features of the first mecC-mediated, β-lactam resistant MRSA strain associated with livestock in Brazil and in the American continent. Three clonally related phenotypic MRSA isolates originated from a dairy herd were confirmed by polymerase chain reaction as mecC-harbouring MRSA isolates. Whole-genome sequencing was performed by Illumina Miseq platform. Downstream analyses showed that the strain was identified as the sequence type 126 (ST126) and spa type t605. In silico analysis revealed a mecC homolog gene in the orfX region associated with different penicillin-binding proteins. Moreover, genes encoding for efflux pump systems (arlR, mepR, LmrS, norA and mgrA), and antibiotic inactivation enzymes (blaZ and FosB) were also detected. Virulence analyses revealed that the strain harbours genes encoding for exoenzymes (aur, splA, splB and splE), toxin (hlgA, hlgB, hlgC, lukD and lukE) and enterotoxin (sea). The epidemiologic and genomic information provided by this study will support further epidemiological and evolutionary investigations to understand the origin and dissemination of mecC-MRSA among animals and its impact on public health.
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Affiliation(s)
- José Givanildo Silva
- Laboratório de Doenças Infectocontagiosas dos Animais Domésticos, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Wydemberg José Araujo
- Laboratório de Análise de Produtos de Origem Animal, Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Elma Lima Leite
- Laboratório de Análise de Produtos de Origem Animal, Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Larissa Maranhão Dias
- Laboratório de Análise de Produtos de Origem Animal, Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Priscylla Carvalho Vasconcelos
- Laboratório de Análise de Produtos de Origem Animal, Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Núbia Michelle Vieira Silva
- Laboratório de Análise de Produtos de Origem Animal, Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Raylson Pereira Oliveira
- Laboratório de Doenças Infectocontagiosas dos Animais Domésticos, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Maria José Sena
- Laboratório de Doenças Infectocontagiosas dos Animais Domésticos, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Celso José Bruno Oliveira
- Laboratório de Análise de Produtos de Origem Animal, Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, Brazil
| | - Rinaldo Aparecido Mota
- Laboratório de Doenças Infectocontagiosas dos Animais Domésticos, Universidade Federal Rural de Pernambuco, Recife, Brazil
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5
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Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani. BMC Genomics 2020; 21:449. [PMID: 32600255 PMCID: PMC7325237 DOI: 10.1186/s12864-020-06863-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/22/2020] [Indexed: 11/11/2022] Open
Abstract
Background Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.
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Santos-Cortez RLP, Bhutta MF, Earl JP, Hafrén L, Jennings M, Mell JC, Pichichero ME, Ryan AF, Tateossian H, Ehrlich GD. Panel 3: Genomics, precision medicine and targeted therapies. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109835. [PMID: 32007292 PMCID: PMC7155947 DOI: 10.1016/j.ijporl.2019.109835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media. DATA SOURCES PubMed articles published since the last meeting in June 2015 up to June 2019. REVIEW METHODS A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. CONCLUSION Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media. IMPLICATIONS FOR PRACTICE In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19 Ave., Aurora, CO 80045, USA
| | - Mahmood F. Bhutta
- Department of ENT, Royal Sussex County Hospital, Eastern Road, Brighton BN2 5BE, UK
| | - Joshua P. Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Tukholmankatu 8A, 00290 Helsinki, Finland
| | - Michael Jennings
- Institute for Glycomics, Gold Coast campus, Griffith University, QLD 4222, Australia
| | - Joshua C. Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Michael E. Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, 1425 Portland Ave., Rochester, NY 14621, USA
| | - Allen F. Ryan
- Department of Surgery/Otolaryngology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Hilda Tateossian
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell, Oxford, Didcot OX11 0RD, UK
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
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7
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Tsang RSW, Shuel M, Ahmad T, Hayden K, Knox N, Van Domselaar G, Hoang L, Tyrrell GJ, Minion J, Van Caeseele P, Kus JV, Ulanova M, Lefebvre B, Haldane D, Garceau R, German G, Zahariadis G, Hanley B, Kandola K, Patterson M. Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada. Can J Microbiol 2019; 66:99-110. [PMID: 31661630 DOI: 10.1139/cjm-2019-0406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study examined the phylogenetic structure of serotype a Haemophilus influenzae (Hia) isolates recovered from patients in Canada. Hia isolates from 490 separate patients and an American Type Culture Collection (ATCC) strain were analyzed by multilocus sequence typing (MLST), with 18 different sequence types (STs) identified. Most (85.7%) Hia patient isolates were typed as ST-23 and another 12.7% belonged to 14 different STs with 6, 5, or 4 MLST gene loci related to ST-23 (ST-23 complex). Core genome single-nucleotide variation phylogeny (SNVPhyl) on whole genome sequence (WGS) data of 121 Hia patient isolates representing all identified STs and the ATCC strain revealed 2 phylogenetic populations, with all the ST-23 complex isolates within 1 population. The other phylogenetic population contained only the ATCC strain and 3 patient isolates. Concatenated hitABC sequences retrieved from WGS data and analyzed by MEGA (Molecular Evolutionary Genetic Analysis) alignment confirmed the phylogeny obtained by SNVPhyl. The sodC gene was found only in isolates in the minor phylogenetic population. The 2 phylogenetic populations of the Canadian Hia isolates are similar to the 2 clonal divisions described for serotype b H. influenzae. Combining MLST, core SNVPhyl, and hitABC gene sequence alignment showed that most (99.4%) Canadian Hia patient isolates belonged to 1 major phylogenetic population.
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Affiliation(s)
- Raymond S W Tsang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michelle Shuel
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Tauqeer Ahmad
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kristy Hayden
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Natalie Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Linda Hoang
- BC Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
| | | | - Jessica Minion
- Roy Romanow Provincial Laboratory, Regina, Saskatchewan, Canada
| | | | - Julianne V Kus
- Public Health Ontario, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Marina Ulanova
- Northern Ontario School of Medicine, Thunder Bay, Ontario, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - David Haldane
- Nova Scotia Health Authority, Halifax, Nova Scotia, Canada.,Dalhousie University, Halifax, Nova Scotia, Canada
| | - Richard Garceau
- Communicable Disease Control Unit, Department of Health, Government of New Brunswick, Fredericton, New Brunswick, Canada
| | - Greg German
- Department of Health, Government of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - George Zahariadis
- Provincial Public Health Laboratory, Eastern Health Microbiology Services, St. John's, Newfoundland and Labrador, Canada.,Department of Laboratory Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Brendan Hanley
- Department of Health and Social Services, Government of Yukon, Whitehorse, Yukon, Canada
| | - Kami Kandola
- Department of Health and Social Services, Government of Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Michael Patterson
- Department of Health, Government of Nunavut, Iqaluit, Nunavut, Canada
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Potts CC, Topaz N, Rodriguez-Rivera LD, Hu F, Chang HY, Whaley MJ, Schmink S, Retchless AC, Chen A, Ramos E, Doho GH, Wang X. Genomic characterization of Haemophilus influenzae: a focus on the capsule locus. BMC Genomics 2019; 20:733. [PMID: 31606037 PMCID: PMC6790013 DOI: 10.1186/s12864-019-6145-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/26/2019] [Indexed: 11/19/2022] Open
Abstract
Background Haemophilus influenzae (Hi) can cause invasive diseases such as meningitis, pneumonia, or sepsis. Typeable Hi includes six serotypes (a through f), each expressing a unique capsular polysaccharide. The capsule, encoded by the genes within the capsule locus, is a major virulence factor of typeable Hi. Non-typeable (NTHi) does not express capsule and is associated with invasive and non-invasive diseases. Methods A total of 395 typeable and 293 NTHi isolates were characterized by whole genome sequencing (WGS). Phylogenetic analysis and multilocus sequence typing were used to characterize the overall genetic diversity. Pair-wise comparisons were used to evaluate the capsule loci. A WGS serotyping method was developed to predict the Hi serotype. WGS serotyping results were compared to slide agglutination (SAST) or real-time PCR (rt-PCR) serotyping. Results Isolates of each Hi serotype clustered into one or two subclades, with each subclade being associated with a distinct sequence type (ST). NTHi isolates were genetically diverse, with seven subclades and 125 STs being detected. Regions I and III of the capsule locus were conserved among the six serotypes (≥82% nucleotide identity). In contrast, genes in Region II were less conserved, with only six gene pairs from all serotypes showing ≥56% nucleotide identity. The WGS serotyping method was 99.9% concordant with SAST and 100% concordant with rt-PCR in determining the Hi serotype. Conclusions Genomic analysis revealed a higher degree of genetic diversity among NTHi compared to typeable Hi. The WGS serotyping method accurately predicted the Hi capsule type and can serve as an alternative method for Hi serotyping.
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Affiliation(s)
- Caelin C Potts
- Bacterial Meningitis Laboratory, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-2, Atlanta, GA, 30329, USA
| | | | | | | | | | - Melissa J Whaley
- Bacterial Meningitis Laboratory, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-2, Atlanta, GA, 30329, USA
| | - Susanna Schmink
- Bacterial Meningitis Laboratory, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-2, Atlanta, GA, 30329, USA
| | - Adam C Retchless
- Bacterial Meningitis Laboratory, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-2, Atlanta, GA, 30329, USA
| | - Alexander Chen
- Bacterial Meningitis Laboratory, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-2, Atlanta, GA, 30329, USA
| | | | | | - Xin Wang
- Bacterial Meningitis Laboratory, Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Mailstop H17-2, Atlanta, GA, 30329, USA.
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Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution. Drug Resist Updat 2019; 44:100640. [PMID: 31492517 DOI: 10.1016/j.drup.2019.07.002] [Citation(s) in RCA: 198] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022]
Abstract
Antibiotics are powerful drugs used in the treatment of bacterial infections. The inappropriate use of these medicines has driven the dissemination of antibiotic resistance (AR) in most bacteria. Pseudomonas aeruginosa is an opportunistic pathogen commonly involved in environmental- and difficult-to-treat hospital-acquired infections. This species is frequently resistant to several antibiotics, being in the "critical" category of the WHO's priority pathogens list for research and development of new antibiotics. In addition to a remarkable intrinsic resistance to several antibiotics, P. aeruginosa can acquire resistance through chromosomal mutations and acquisition of AR genes. P. aeruginosa has one of the largest bacterial genomes and possesses a significant assortment of genes acquired by horizontal gene transfer (HGT), which are frequently localized within integrons and mobile genetic elements (MGEs), such as transposons, insertion sequences, genomic islands, phages, plasmids and integrative and conjugative elements (ICEs). This genomic diversity results in a non-clonal population structure, punctuated by specific clones that are associated with significant morbidity and mortality worldwide, the so-called high-risk clones. Acquisition of MGEs produces a fitness cost in the host, that can be eased over time by compensatory mutations during MGE-host coevolution. Even though plasmids and ICEs are important drivers of AR, the underlying evolutionary traits that promote this dissemination are poorly understood. In this review, we provide a comprehensive description of the main strategies involved in AR in P. aeruginosa and the leading drivers of HGT in this species. The most recently developed genomic tools that allowed a better understanding of the features contributing for the success of P. aeruginosa are discussed.
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10
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Botelho J, Grosso F, Peixe L. WITHDRAWN: Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution. Drug Resist Updat 2019. [DOI: 10.1016/j.drup.2019.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Resistance of Synthetic and Biologic Surgical Meshes to Methicillin-Resistant Staphylococcus aureus Biofilm: An In Vitro Investigation. Int J Biomater 2019; 2019:1063643. [PMID: 31001340 PMCID: PMC6436333 DOI: 10.1155/2019/1063643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/16/2019] [Indexed: 11/17/2022] Open
Abstract
Surgical meshes have become the standard procedure for a variety of surgical applications with 20 million meshes being implanted each year. The popularity of mesh usage among surgeons is backed by the multiple studies that support its functionality as a tool for improving surgical outcomes. However, their use has also been associated with infectious surgical complications and many surgeons have turned to biologic meshes. While there have been several studies investigating synthetic meshes, there is limited data comparing synthetic and biologic meshes in vitro in an infection model. This study evaluates the in vitro susceptibility of both synthetic and biologic meshes to single-species methicillin-resistant Staphylococcus aureus (MRSA) biofilms. This research compares biofilm biomass, average thickness, and coverage between the three meshes through florescent in situ hybridization (FISH), confocal scanning microscopy (CSLM), and image analysis. We also report the varying levels of planktonic and attached bacteria through sonication and cfu counts. While the data illustrates increased biofilm formation on biologic mesh in vitro, the study must further be investigated in vivo to confirm the study observations.
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12
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de Carvalho SP, de Almeida JB, de Freitas LM, Guimarães AMS, do Nascimento NC, Dos Santos AP, Campos GB, Messick JB, Timenetsky J, Marques LM. Genomic profile of Brazilian methicillin-resistant Staphylococcus aureus resembles clones dispersed worldwide. J Med Microbiol 2019; 68:693-702. [PMID: 30900970 DOI: 10.1099/jmm.0.000956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Comparative genomic analysis of strains may help us to better understand the wide diversity of their genetic profiles. The aim of this study was to analyse the genomic features of the resistome and virulome of Brazilian first methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to other Brazilian and international MRSA strains. METHODOLOGY The whole genomes of three MRSA strains previously isolated in Vitória da Conquista were sequenced, assembled, annotated and compared with other MRSA genomes. A phylogenetic tree was constructed and the pan-genome and accessory and core genomes were constructed. The resistomes and virulomes of all strains were identified.Results/Key findings. Phylogenetic analysis of all 49 strains indicated different clones showing high similarity. The pan-genome of the analysed strains consisted of 4484 genes, with 31 % comprising the gene portion of the core genome, 47 % comprising the accessory genome and 22 % being singletons. Most strains showed at least one gene related to virulence factors associated with immune system evasion, followed by enterotoxins. The strains showed multiresistance, with the most recurrent genes conferring resistance to beta-lactams, fluoroquinolones, aminoglycosides and macrolides. CONCLUSIONS Our comparative genomic analysis showed that there is no pattern of virulence gene distribution among the clones analysed in the different regions. The Brazilian strains showed similarity with clones from several continents.
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Affiliation(s)
- Suzi P de Carvalho
- Department of Biological Sciences, Santa Cruz State University, Ilhéus-Itabuna Road, km 16 Salobrinho, Ilhéus 45662-900, Bahia State, Brazil
| | - Jéssica B de Almeida
- Department of Biological Sciences, Santa Cruz State University, Ilhéus-Itabuna Road, km 16 Salobrinho, Ilhéus 45662-900, Bahia State, Brazil.,Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil
| | - Leandro M de Freitas
- Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil
| | - Ana Marcia S Guimarães
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, 1374 Professor Lineu Prestes Avenue, Sao Paulo, 05508-900, São Paulo State, Brazil
| | - Naíla C do Nascimento
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA
| | - Andrea P Dos Santos
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA
| | - Guilherme B Campos
- Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil
| | - Joanne B Messick
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA
| | - Jorge Timenetsky
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, 1374 Professor Lineu Prestes Avenue, Sao Paulo, 05508-900, São Paulo State, Brazil
| | - Lucas M Marques
- Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil.,Department of Biological Sciences, Santa Cruz State University, Ilhéus-Itabuna Road, km 16 Salobrinho, Ilhéus 45662-900, Bahia State, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, 1374 Professor Lineu Prestes Avenue, Sao Paulo, 05508-900, São Paulo State, Brazil
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13
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Abstract
The concept of the species ‘pan-genome’, the union of ‘core’ conserved genes and all ‘accessory’ non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining ‘accessory’ gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.
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Affiliation(s)
- Charley G P McCarthy
- 1Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,2Human Health Research Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - David A Fitzpatrick
- 1Genome Evolution Laboratory, Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.,2Human Health Research Institute, Maynooth University, Maynooth, Co. Kildare, Ireland
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14
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Antagonistic Pleiotropy in the Bifunctional Surface Protein FadL (OmpP1) during Adaptation of Haemophilus influenzae to Chronic Lung Infection Associated with Chronic Obstructive Pulmonary Disease. mBio 2018; 9:mBio.01176-18. [PMID: 30254117 PMCID: PMC6156194 DOI: 10.1128/mbio.01176-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Tracking bacterial evolution during chronic infection provides insights into how host selection pressures shape bacterial genomes. The human-restricted opportunistic pathogen nontypeable Haemophilus influenzae (NTHi) infects the lower airways of patients suffering chronic obstructive pulmonary disease (COPD) and contributes to disease progression. To identify bacterial genetic variation associated with bacterial adaptation to the COPD lung, we sequenced the genomes of 92 isolates collected from the sputum of 13 COPD patients over 1 to 9 years. Individuals were colonized by distinct clonal types (CTs) over time, but the same CT was often reisolated at a later time or found in different patients. Although genomes from the same CT were nearly identical, intra-CT variation due to mutation and recombination occurred. Recurrent mutations in several genes were likely involved in COPD lung adaptation. Notably, nearly a third of CTs were polymorphic for null alleles of ompP1 (also called fadL), which encodes a bifunctional membrane protein that both binds the human carcinoembryonic antigen-related cell adhesion molecule 1 (hCEACAM1) receptor and imports long-chain fatty acids (LCFAs). Our computational studies provide plausible three-dimensional models for FadL's interaction with hCEACAM1 and LCFA binding. We show that recurrent fadL mutations are likely a case of antagonistic pleiotropy, since loss of FadL reduces NTHi's ability to infect epithelia but also increases its resistance to bactericidal LCFAs enriched within the COPD lung. Supporting this interpretation, truncated fadL alleles are common in publicly available NTHi genomes isolated from the lower airway tract but rare in others. These results shed light on molecular mechanisms of bacterial pathoadaptation and guide future research toward developing novel COPD therapeutics.IMPORTANCE Nontypeable Haemophilus influenzae is an important pathogen in patients with chronic obstructive pulmonary disease (COPD). To elucidate the bacterial pathways undergoing in vivo evolutionary adaptation, we compared bacterial genomes collected over time from 13 COPD patients and identified recurrent genetic changes arising in independent bacterial lineages colonizing different patients. Besides finding changes in phase-variable genes, we found recurrent loss-of-function mutations in the ompP1 (fadL) gene. We show that loss of OmpP1/FadL function reduces this bacterium's ability to infect cells via the hCEACAM1 epithelial receptor but also increases its resistance to bactericidal fatty acids enriched within the COPD lung, suggesting a case of antagonistic pleiotropy that restricts ΔfadL strains' niche. These results show how H. influenzae adapts to host-generated inflammatory mediators in the COPD airways.
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15
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Zhang X, Liu X, Yang F, Chen L. Pan-Genome Analysis Links the Hereditary Variation of Leptospirillum ferriphilum With Its Evolutionary Adaptation. Front Microbiol 2018; 9:577. [PMID: 29636744 PMCID: PMC5880901 DOI: 10.3389/fmicb.2018.00577] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 01/16/2023] Open
Abstract
Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an 'open' pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Fei Yang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
| | - Lv Chen
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China
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16
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Earl JP, de Vries SPW, Ahmed A, Powell E, Schultz MP, Hermans PWM, Hill DJ, Zhou Z, Constantinidou CI, Hu FZ, Bootsma HJ, Ehrlich GD. Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution. Genome Biol Evol 2016; 8:955-74. [PMID: 26912404 PMCID: PMC4860680 DOI: 10.1093/gbe/evw039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2016] [Indexed: 02/07/2023] Open
Abstract
The bacterial speciesMoraxella catarrhalishas been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages-the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ß-lactamase genes. The four divergent strains aresui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.
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Affiliation(s)
- Joshua P Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Stefan P W de Vries
- Present address: Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Azad Ahmed
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Evan Powell
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Matthew P Schultz
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Peter W M Hermans
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Darryl J Hill
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | - Fen Z Hu
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA
| | - Hester J Bootsma
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA
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17
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Kress-Bennett JM, Hiller NL, Eutsey RA, Powell E, Longwell MJ, Hillman T, Blackwell T, Byers B, Mell JC, Post JC, Hu FZ, Ehrlich GD, Janto BA. Identification and Characterization of msf, a Novel Virulence Factor in Haemophilus influenzae. PLoS One 2016; 11:e0149891. [PMID: 26977929 PMCID: PMC4792463 DOI: 10.1371/journal.pone.0149891] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 02/05/2016] [Indexed: 12/11/2022] Open
Abstract
Haemophilus influenzae is an opportunistic pathogen. The emergence of virulent, non-typeable strains (NTHi) emphasizes the importance of developing new interventional targets. We screened the NTHi supragenome for genes encoding surface-exposed proteins suggestive of immune evasion, identifying a large family containing Sel1-like repeats (SLRs). Clustering identified ten SLR-containing gene subfamilies, each with various numbers of SLRs per gene. Individual strains also had varying numbers of SLR-containing genes from one or more of the subfamilies. Statistical genetic analyses of gene possession among 210 NTHi strains typed as either disease or carriage found a significant association between possession of the SlrVA subfamily (which we have termed, macrophage survival factor, msf) and the disease isolates. The PittII strain contains four chromosomally contiguous msf genes. Deleting all four of these genes (msfA1-4) (KO) resulted in a highly significant decrease in phagocytosis and survival in macrophages; which was fully complemented by a single copy of the msfA1 gene. Using the chinchilla model of otitis media and invasive disease, the KO strain displayed a significant decrease in fitness compared to the WT in co-infections; and in single infections, the KO lost its ability to invade the brain. The singly complemented strain showed only a partial ability to compete with the WT suggesting gene dosage is important in vivo. The transcriptional profiles of the KO and WT in planktonic growth were compared using the NTHi supragenome array, which revealed highly significant changes in the expression of operons involved in virulence and anaerobiosis. These findings demonstrate that the msfA1-4 genes are virulence factors for phagocytosis, persistence, and trafficking to non-mucosal sites.
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Affiliation(s)
- Jennifer M. Kress-Bennett
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - N. Luisa Hiller
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Rory A. Eutsey
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Evan Powell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Mark J. Longwell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Todd Hillman
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Tenisha Blackwell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Barbara Byers
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Joshua C. Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - J. Christopher Post
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Fen Z. Hu
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology, Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin A. Janto
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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18
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Chaves-Moreno D, Wos-Oxley ML, Jáuregui R, Medina E, Oxley APA, Pieper DH. Application of a Novel "Pan-Genome"-Based Strategy for Assigning RNAseq Transcript Reads to Staphylococcus aureus Strains. PLoS One 2015; 10:e0145861. [PMID: 26717500 PMCID: PMC4696825 DOI: 10.1371/journal.pone.0145861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/09/2015] [Indexed: 11/19/2022] Open
Abstract
Understanding the behaviour of opportunistic pathogens such as Staphylococcus aureus in their natural human niche holds great medical interest. With the development of sensitive molecular methods and deep-sequencing technology, it is now possible to robustly assess the global transcriptome of bacterial species in their human habitat. However, as the genomes of the colonizing strains are often not available compiling the pan-genome for the species of interest may provide an effective method to reliably and rapidly compile the transcriptome of a bacterial species. The pan-genome of S. aureus and its associated core and accessory components were compiled based on 25 genomes and comprises a total of 65,557 proteins clustering into 4,198 Orthologous Groups (OGs). The generated gene catalogue was used to assign RNAseq-derived sequence reads to S. aureus in a variety of in vitro and in vivo samples. In all cases, the number of reads that could be assigned to S. aureus was greater using the OG database than using a reference genome. Growth of two S. aureus strains in synthetic nasal medium confirmed that both strains experienced strong iron starvation. Traits such as purine metabolism appeared to be more affected in a typical nasal colonizer than in a strain representative of the S. aureus USA300 lineage. Mapping sequencing reads from a metatranscriptome generated from the human anterior nares allowed the identification of genes highly expressed by S. aureus in vivo. The OG database generated in this study represents a useful tool to obtain a snapshot of the functional attributes of S. aureus under different in vitro and in vivo conditions. The approach proved to be advantageous to assign sequencing reads to bacterial strains when RNAseq data is derived from samples where strain information and/or the corresponding genome/s are unavailable.
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Affiliation(s)
- Diego Chaves-Moreno
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Melissa L. Wos-Oxley
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eva Medina
- Infection and Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andrew P. A. Oxley
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Infection and Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
- * E-mail:
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19
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Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 2015; 7:72-85. [PMID: 26442149 PMCID: PMC4552756 DOI: 10.1016/j.nmni.2015.06.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 01/18/2023] Open
Abstract
The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position. Pangenome is a new way of studying pathogenic bacteria. Pangenome can be used as a taxonomic tool. This review describes pangenome in the world of pathogenic bacteria.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - V Merhej
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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20
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Valot B, Guyeux C, Rolland JY, Mazouzi K, Bertrand X, Hocquet D. What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated. PLoS One 2015; 10:e0126468. [PMID: 25961859 PMCID: PMC4427113 DOI: 10.1371/journal.pone.0126468] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/02/2015] [Indexed: 11/19/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. Its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. The size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. Here, we redefined the size and the content of the core genome of P. aeruginosa from fully re-analyzed genomes of 17 reference strains. After the optimization of gene detection and clustering parameters, the core genome was defined at 5,233 orthologs, which represented ~ 88% of the average genome. Extrapolation indicated that our panel was suitable to estimate the core genome that will remain constant even if new genomes are added. The core genome contained resistance determinants to the major antibiotic families as well as most metabolic, respiratory, and virulence genes. Although some virulence genes were accessory, they often related to conserved biological functions. Long-standing prophage elements were subjected to a genetic drift to eventually display a G+C content as higher as that of the core genome. This contrasts with the low G+C content of highly conserved ribosomal genes. The conservation of metabolic and respiratory genes could guarantee the ability of the species to thrive on a variety of carbon sources for energy in aerobiosis and anaerobiosis. Virtually all the strains, of environmental or clinical origin, have the complete toolkit to become resistant to the major antipseudomonal compounds and possess basic pathogenic mechanisms to infect humans. The knowledge of the genes shared by the majority of the P. aeruginosa isolates is a prerequisite for designing effective therapeutics to combat the wide variety of human infections.
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Affiliation(s)
- Benoît Valot
- UMR CNRS 6249, Chrono-environnement, Université de Franche-Comté, Besançon, France
| | - Christophe Guyeux
- UMR CNRS 6174, Institut FEMTO-ST, Département DISC, Université de Franche-Comté, Belfort, France
| | - Julien Yves Rolland
- UMR CNRS 6623, Laboratoire de Mathématiques de Besançon, Université de Franche-Comté, Besançon, France
| | - Kamel Mazouzi
- Mésocentre de calculs, Université de Franche-Comté, Besançon, France
| | - Xavier Bertrand
- UMR CNRS 6249, Chrono-environnement, Université de Franche-Comté, Besançon, France
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Didier Hocquet
- UMR CNRS 6249, Chrono-environnement, Université de Franche-Comté, Besançon, France
- Laboratoire d’Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France
- * E-mail:
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Kadam A, Janto B, Eutsey R, Earl JP, Powell E, Dahlgren ME, Hu FZ, Ehrlich GD, Hiller NL. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression. ACTA ACUST UNITED AC 2015; 36:9D.4.1-9D.4.20. [PMID: 25641101 DOI: 10.1002/9780471729259.mc09d04s36] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome.
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Affiliation(s)
- Anagha Kadam
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Benjamin Janto
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Rory Eutsey
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Joshua P Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Evan Powell
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Margaret E Dahlgren
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Fen Z Hu
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
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Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol 2014; 23:148-54. [PMID: 25483351 DOI: 10.1016/j.mib.2014.11.016] [Citation(s) in RCA: 298] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pan-genome analyses provide a framework for estimating the genomic diversity of the dataset at hand and predicting the number of additional whole genomes sequences that would be necessary to fully characterize that diversity. We review recent implementations of the pan-genome approach, its impact and limits, and we propose possible extensions, including analyses at the whole genome multiple sequence alignment level.
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Affiliation(s)
- George Vernikos
- Novartis (Hellas) S.A.C.I., 12th Km Athens-Lamia North Road, 14451 Metamorfossi, Athens, Greece
| | - Duccio Medini
- Novartis Vaccines Research, Via Fiorentina 1, 53100 Siena, Italy
| | - David R Riley
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA.
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Qin QL, Xie BB, Yu Y, Shu YL, Rong JC, Zhang YJ, Zhao DL, Chen XL, Zhang XY, Chen B, Zhou BC, Zhang YZ. Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation. Environ Microbiol 2014; 16:1642-53. [PMID: 25009843 DOI: 10.1111/1462-2920.12318] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.
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Lobkovsky AE, Wolf YI, Koonin EV. Estimation of prokaryotic supergenome size and composition from gene frequency distributions. BMC Genomics 2014; 15 Suppl 6:S14. [PMID: 25572821 PMCID: PMC4240607 DOI: 10.1186/1471-2164-15-s6-s14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Because prokaryotic genomes experience a rapid flux of genes, selection may act at a higher level than an individual genome. We explore a quantitative model of the distributed genome whereby groups of genomes evolve by acquiring genes from a fixed reservoir which we denote as supergenome. Previous attempts to understand the nature of the supergenome treated genomes as random, independent collections of genes and assumed that the supergenome consists of a small number of homogeneous sub-reservoirs. Here we explore the consequences of relaxing both assumptions. RESULTS We surveyed several methods for estimating the size and composition of the supergenome. The methods assumed that genomes were either random, independent samples of the supergenome or that they evolved from a common ancestor along a known tree via stochastic sampling from the reservoir. The reservoir was assumed to be either a collection of homogeneous sub-reservoirs or alternatively composed of genes with Gamma distributed gain probabilities. Empirical gene frequencies were used to either compute the likelihood of the data directly or first to reconstruct the history of gene gains and then compute the likelihood of the reconstructed numbers of gains. CONCLUSIONS Supergenome size estimates using the empirical gene frequencies directly are not robust with respect to the choice of the model. By contrast, using the gene frequencies and the phylogenetic tree to reconstruct multiple gene gains produces reliable estimates of the supergenome size and indicates that a homogeneous supergenome is more consistent with the data than a supergenome with Gamma distributed gain probabilities.
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Development and validation of an Haemophilus influenzae supragenome hybridization (SGH) array for transcriptomic analyses. PLoS One 2014; 9:e105493. [PMID: 25290153 PMCID: PMC4188559 DOI: 10.1371/journal.pone.0105493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 07/23/2014] [Indexed: 01/04/2023] Open
Abstract
We previously carried out the design and testing of a custom-built Haemophilus influenzae supragenome hybridization (SGH) array that contains probe sequences to 2,890 gene clusters identified by whole genome sequencing of 24 strains of H. influenzae. The array was originally designed as a tool to interrogate the gene content of large numbers of clinical isolates without the need for sequencing, however, the data obtained is quantitative and is thus suitable for transcriptomic analyses. In the current study RNA was extracted from H. influenzae strain CZ4126/02 (which was not included in the design of the array) converted to cDNA, and labelled and hybridized to the SGH arrays to assess the quality and reproducibility of data obtained from these custom-designed chips to serve as a tool for transcriptomics. Three types of experimental replicates were analyzed with all showing very high degrees of correlation, thus validating both the array and the methods used for RNA profiling. A custom filtering pipeline for two-condition unpaired data using five metrics was developed to minimize variability within replicates and to maximize the identification of the most significant true transcriptional differences between two samples. These methods can be extended to transcriptional analysis of other bacterial species utilizing supragenome-based arrays.
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Defining the estimated core genome of bacterial populations using a Bayesian decision model. PLoS Comput Biol 2014; 10:e1003788. [PMID: 25144616 PMCID: PMC4140633 DOI: 10.1371/journal.pcbi.1003788] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 07/01/2014] [Indexed: 02/03/2023] Open
Abstract
The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance. Whole genome sequencing has revolutionised the study of pathogenic microorganisms. It has also become so affordable that hundreds of samples can reasonably be sequenced in an individual project, creating a wealth of data. Estimating the bacterial core genome – traditionally defined as those genes present in all genomes – is an important initial step in population genomics analyses. We developed a simple statistical model to estimate the number of core genes in a bacterial genome dataset, calculated pairwise evolutionary distances (p-distances) based on differences among nucleotide sequences, and plotted the median p-distance for each core gene relative to its genome location. Low p-distance values indicate highly-conserved genes; high values suggest genes under selection and/or undergoing recombination. The genome diagrams depict areas of interest in genomes that can be explored in further detail. Using our method, we analysed five bacterial species comprising a total of 2096 genomes. This revealed new information related to antibiotic resistance and virulence for two bacterial species and demonstrated that the function of many core genes in bacteria is still unknown. Our model provides a highly-accessible, publicly-available tool to use on the vast quantities of genome sequence data now available.
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Hall BG, Kirkup BC, Riley MC, Barlow M. Clustering acinetobacter strains by optical mapping. Genome Biol Evol 2013; 5:1176-84. [PMID: 23739739 PMCID: PMC3698929 DOI: 10.1093/gbe/evt085] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Optical mapping is a technique that produces an ordered restriction map of a bacterial or eukaryotic chromosome. We have developed a new method, the BOP method, to compare experimental optical maps with in silico optical maps of complete genomes to infer the presence/absence of short DNA sequences (bops) in each genome. The BOP method, as implemented by the Optical Mapping suite of four programs, circumvents the necessity of whole-genome multiple alignments and permits reliable strain typing and clustering on the basis of optical maps. We have applied the Optical Mapping Suite to 125 strains of Acinetobacter sp., including 11 completely sequenced genomes and 114 Acinetobacter complex from three US military hospitals. We found that optical mapping completely resolves all 125 strains. Signal to noise analysis showed that when the 125 strains were considered together almost 1/3 of the experimental fragments were misidentified. We found that the set of 125 genomes could be divided into three clusters, two of which included sequenced genomes. Signal to noise analysis after clustering showed that only 3.5% of the experimental restriction fragments were misidentified. Minimum spanning trees of the two clusters that included sequenced genomes are presented. The programs we have developed provide a more rigorous approach for analyzing optical map data than previously existed.
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Affiliation(s)
- Barry G Hall
- Bellingham Research Institute, Bellingham, Washington, USA
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Whitby PW, VanWagoner TM, Seale TW, Morton DJ, Stull TL. Comparison of transcription of the Haemophilus influenzae iron/heme modulon genes in vitro and in vivo in the chinchilla middle ear. BMC Genomics 2013; 14:925. [PMID: 24373462 PMCID: PMC3879429 DOI: 10.1186/1471-2164-14-925] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 12/17/2013] [Indexed: 08/30/2023] Open
Abstract
Background Haemophilus influenzae is a significant cause of childhood otitis media, and also has an absolute growth requirement for heme. Recent microarray studies using three H. influenzae isolates were used to propose a putative core of genes responsive to iron and heme levels. Included in the core modulon were thirty seven genes that are preferentially expressed under iron/heme limitation, most of which are directly involved with iron and or heme acquisition. In this report, the core iron/heme modulon was further refined following microarray analysis of two additional nontypeable H. influenzae isolates from patients with otitis media. The transcriptional status of the genes comprising the refined iron/heme core modulon was then assessed in vivo, in a chinchilla model of otitis media. These in vivo experiments were performed to address the hypothesis that iron and heme regulated genes are both highly expressed in vivo and important, during clinical infection. Results Microarray analysis of two additional H. influenzae strains resulted in the definition of a core of iron/heme responsive genes. This core consisted of 35 genes maximally expressed under heme restriction and a further 20 genes maximally expressed in heme replete conditions. In vivo studies were performed with two nontypeable H. influenzae strains, 86-028NP and HI1722. The majority of operons identified as members of the core modulon by microarray were also actively upregulated in the chinchilla ear during otitis media. In 86-028NP, 70% of the operons were significantly upregulated while in HI1722 100% of the operons were upregulated in samples recovered from the chinchilla middle ear. Conclusion This study elucidates a conserved core of H. influenzae genes the transcription of which is altered by the availability of iron and heme in the growth environment, and further assesses transcription of these genes in vivo. Elucidation of this modulon allows for identification of genes with unrecognized roles in iron/heme acquisition or homeostasis and/or potential roles in virulence. Defining these core genes is also of potential importance in identifying targets for therapeutic and vaccine designs since products of these genes are likely to be preferentially expressed during growth in iron/heme restricted sites of the human body.
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Affiliation(s)
- Paul W Whitby
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City 73104, OK, USA.
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Eutsey RA, Hiller NL, Earl JP, Janto BA, Dahlgren ME, Ahmed A, Powell E, Schultz MP, Gilsdorf JR, Zhang L, Smith A, Murphy TF, Sethi S, Shen K, Post JC, Hu FZ, Ehrlich GD. Design and validation of a supragenome array for determination of the genomic content of Haemophilus influenzae isolates. BMC Genomics 2013; 14:484. [PMID: 23865594 PMCID: PMC3723446 DOI: 10.1186/1471-2164-14-484] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 07/10/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of the airway; it is also less commonly associated with invasive disease. Clinical isolates of H. influenzae display extensive genomic diversity and plasticity. The development of strategies to successfully prevent, diagnose and treat H. influenzae infections depends on tools to ascertain the gene content of individual isolates. RESULTS We describe and validate a Haemophilus influenzae supragenome hybridization (SGH) array that can be used to characterize the full genic complement of any strain within the species, as well as strains from several highly related species. The array contains 31,307 probes that collectively cover essentially all alleles of the 2890 gene clusters identified from the whole genome sequencing of 24 clinical H. influenzae strains. The finite supragenome model predicts that these data include greater than 85% of all non-rare genes (where rare genes are defined as those present in less than 10% of sequenced strains). The veracity of the array was tested by comparing the whole genome sequences of eight strains with their hybridization data obtained using the supragenome array. The array predictions were correct and reproducible for ~ 98% of the gene content of all of the sequenced strains. This technology was then applied to an investigation of the gene content of 193 geographically and clinically diverse H. influenzae clinical strains. These strains came from multiple locations from five different continents and Papua New Guinea and include isolates from: the middle ears of persons with otitis media and otorrhea; lung aspirates and sputum samples from pneumonia and COPD patients, blood specimens from patients with sepsis; cerebrospinal fluid from patients with meningitis, as well as from pharyngeal specimens from healthy persons. CONCLUSIONS These analyses provided the most comprehensive and detailed genomic/phylogenetic look at this species to date, and identified a subset of highly divergent strains that form a separate lineage within the species. This array provides a cost-effective and high-throughput tool to determine the gene content of any H. influenzae isolate or lineage. Furthermore, the method for probe selection can be applied to any species, given a group of available whole genome sequences.
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Affiliation(s)
- Rory A Eutsey
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - N Luisa Hiller
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joshua P Earl
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Benjamin A Janto
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Margaret E Dahlgren
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Azad Ahmed
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Evan Powell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Matthew P Schultz
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Janet R Gilsdorf
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MC, USA
- Department of Pediatrics and Communicable Diseases, University of Michigan School of Public Health, Ann Arbor, MC, USA
| | - Lixin Zhang
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MC, USA
| | - Arnold Smith
- Center for Childhood Infections, Seattle Children’s Hospital Research Institute, Seattle, WA, USA
| | - Timothy F Murphy
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Sanjay Sethi
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Kai Shen
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - J Christopher Post
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Fen Z Hu
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Garth D Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
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Murphy TF, Chonmaitree T, Barenkamp S, Kyd J, Nokso-Koivisto J, Patel JA, Heikkinen T, Yamanaka N, Ogra P, Swords WE, Sih T, Pettigrew MM. Panel 5: Microbiology and immunology panel. Otolaryngol Head Neck Surg 2013; 148:E64-89. [PMID: 23536533 DOI: 10.1177/0194599812459636] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The objective is to perform a comprehensive review of the literature from January 2007 through June 2011 on the virology, bacteriology, and immunology related to otitis media. DATA SOURCES PubMed database of the National Library of Medicine. REVIEW METHODS Three subpanels with co-chairs comprising experts in the virology, bacteriology, and immunology of otitis media were formed. Each of the panels reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a second draft was created. The entire panel met at the 10th International Symposium on Recent Advances in Otitis Media in June 2011 and discussed the review and refined the content further. A final draft was created, circulated, and approved by the panel. CONCLUSION Excellent progress has been made in the past 4 years in advancing an understanding of the microbiology and immunology of otitis media. Advances include laboratory-based basic studies, cell-based assays, work in animal models, and clinical studies. IMPLICATIONS FOR PRACTICE The advances of the past 4 years formed the basis of a series of short-term and long-term research goals in an effort to guide the field. Accomplishing these goals will provide opportunities for the development of novel interventions, including new ways to better treat and prevent otitis media.
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Affiliation(s)
- Timothy F Murphy
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, USA.
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Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core. PLoS One 2013; 8:e55644. [PMID: 23409014 PMCID: PMC3567147 DOI: 10.1371/journal.pone.0055644] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/28/2012] [Indexed: 01/08/2023] Open
Abstract
The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1Ea and a putative secondary metabolite pathway only present in Rubus-infecting strains.
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Bajaj JS, O’Leary JG, Reddy KR, Wong F, Olson JC, Subramanian RM, Brown G, Noble NA, Thacker LR, Kamath PS. Second infections independently increase mortality in hospitalized patients with cirrhosis: the North American consortium for the study of end-stage liver disease (NACSELD) experience. Hepatology 2012; 56:2328-35. [PMID: 22806618 PMCID: PMC3492528 DOI: 10.1002/hep.25947] [Citation(s) in RCA: 296] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/19/2012] [Indexed: 12/12/2022]
Abstract
UNLABELLED Bacterial infections are an important cause of mortality in cirrhosis, but there is a paucity of multicenter studies. The aim was to define factors predisposing to infection-related mortality in hospitalized patients with cirrhosis. A prospective, cohort study of patients with cirrhosis with infections was performed at eight North American tertiary-care hepatology centers. Data were collected on admission vitals, disease severity (model for endstage liver disease [MELD] and sequential organ failure [SOFA] scores), first infection site, type (community-acquired, healthcare-associated [HCA] or nosocomial), and second infection occurrence during hospitalization. The outcome was mortality within 30 days. A multivariate logistic regression model predicting mortality was created. 207 patients (55 years, 60% men, MELD 20) were included. Most first infections were HCA (71%), then nosocomial (15%) and community-acquired (14%). Urinary tract infections (52%), spontaneous bacterial peritonitis (SBP, 23%) and spontaneous bacteremia (21%) formed the majority of the first infections. Second infections were seen in 50 (24%) patients and were largely preventable: respiratory, including aspiration (28%), urinary, including catheter-related (26%), fungal (14%), and Clostridium difficile (12%) infections. Forty-nine patients (23.6%) who died within 30 days had higher admission MELD (25 versus 18, P < 0.0001), lower serum albumin (2.4 g/dL versus 2.8 g/dL, P = 0.002), and second infections (49% versus 16%, P < 0.0001) but equivalent SOFA scores (9.2 versus 9.9, P = 0.86). The case fatality rate was highest for C. difficile (40%), respiratory (37.5%), and spontaneous bacteremia (37%), and lowest for SBP (17%) and urinary infections (15%). The model for mortality included admission MELD (odds ratio [OR]: 1.12), heart rate (OR: 1.03) albumin (OR: 0.5), and second infection (OR: 4.42) as significant variables. CONCLUSION Potentially preventable second infections are predictors of mortality independent of liver disease severity in this multicenter cirrhosis cohort.
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Affiliation(s)
- Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, VA 23249, USA.
| | | | - K. Rajender Reddy
- Division of Gastroenterology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Florence Wong
- Division of Gastroenterology, University of Toronto, Toronto, Ontario, Canada
| | - Jody C Olson
- Biostatistics, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Ram M Subramanian
- Division of Gastroenterology, Emory University Medical Center, Atlanta, Georgia
| | - Geri Brown
- Division of Gastroenterology, University of Texas Southwestern Medical School and Dallas VA Medical Center, Dallas, Texas
| | - Nicole A Noble
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Leroy R Thacker
- Biostatistics, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
| | - Patrick S Kamath
- Biostatistics, Virginia Commonwealth University and McGuire VA Medical Center, Richmond, Virginia
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Power PM, Bentley SD, Parkhill J, Moxon ER, Hood DW. Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants. BMC Microbiol 2012; 12:273. [PMID: 23176117 PMCID: PMC3539920 DOI: 10.1186/1471-2180-12-273] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 10/17/2012] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Haemophilus influenzae is an important human commensal pathogen associated with significant levels of disease. High-throughput DNA sequencing was used to investigate differences in genome content within this species. RESULTS Genomic DNA sequence was obtained from 85 strains of H. influenzae and from other related species, selected based on geographical site of isolation, disease association and documented genotypic and phenotypic differences. When compared by Mauve alignment these indicated groupings of H. influenzae that were consistent with previously published analyses; capsule expressing strains fell into two distinct groups and those of serotype b (Hib) were found in two closely positioned lineages. For 18 Hib strains representing both lineages we found many discrete regions (up to 40% of the total genome) displaying sequence variation when compared to a common reference strain. Evidence that this naturally occurring pattern of inter-strain variation in H. influenzae can be mediated by transformation was obtained through sequencing DNA obtained from a pool of 200 independent transformants of a recipient (strain Rd) using donor DNA from a heterologous Hib strain (Eagan). CONCLUSION Much of the inter-strain variation in genome sequence in H. influenzae is likely the result of inter-strain exchanges of DNA, most plausibly through transformation.
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Affiliation(s)
- Peter M Power
- University of Oxford Department of Paediatrics, Medical Sciences Division, John Radcliffe Hospital, Headington, Oxford, UK.
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Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, Horvath P, Heidenreich J, Perna NT, Barrangou R, Steele JL. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 2012; 13:533. [PMID: 23035691 PMCID: PMC3496567 DOI: 10.1186/1471-2164-13-533] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022] Open
Abstract
Background The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources. Results Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay. Conclusions Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.
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Affiliation(s)
- Jeff R Broadbent
- Department of Nutrition, Dietetics, and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA.
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Zhang L, Xie J, Patel M, Bakhtyar A, Ehrlich GD, Ahmed A, Earl J, Marrs CF, Clemans D, Murphy TF, Gilsdorf JR. Nontypeable Haemophilus influenzae genetic islands associated with chronic pulmonary infection. PLoS One 2012; 7:e44730. [PMID: 22970300 PMCID: PMC3435294 DOI: 10.1371/journal.pone.0044730] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022] Open
Abstract
Background Haemophilus influenzae (Hi) colonizes the human respiratory tract and is an important pathogen associated with chronic obstructive pulmonary disease (COPD). Bacterial factors that interact with the human host may be important in the pathogenesis of COPD. These factors, however, have not been well defined. The overall goal of this study was to identify bacterial genetic elements with increased prevalence among H. influenzae strains isolated from patients with COPD compared to those isolated from the pharynges of healthy individuals. Methodology/Principal Findings Four nontypeable H. influenzae (NTHi) strains, two isolated from the airways of patients with COPD and two from a healthy individual, were subjected to whole genome sequencing using 454 FLX Titanium technology. COPD strain-specific genetic islands greater than 500 bp in size were identified by in silico subtraction. Open reading frames residing within these islands include known Hi virulence genes such as lic2b, hgbA, iga, hmw1 and hmw2, as well as genes encoding urease and other enzymes involving metabolic pathways. The distributions of seven selected genetic islands were assessed among a panel of 421 NTHi strains of both disease and commensal origins using a Library-on-a-Slide high throughput dot blot DNA hybridization procedure. Four of the seven islands screened, containing genes that encode a methyltransferase, a dehydrogenase, a urease synthesis enzyme, and a set of unknown short ORFs, respectively, were more prevalent in COPD strains than in colonizing strains with prevalence ratios ranging from 1.21 to 2.85 (p≤0.0002). Surprisingly, none of these sequences show increased prevalence among NTHi isolated from the airways of patients with cystic fibrosis. Conclusions/Significance Our data suggest that specific bacterial genes, many involved in metabolic functions, are associated with the ability of NTHi strains to survive in the lower airways of patients with COPD.
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Affiliation(s)
- Lixin Zhang
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, United States of America.
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Stoodley P, Sidhu S, Nistico L, Mather M, Boucek A, Hall-Stoodley L, Kathju S. Kinetics and morphology of polymicrobial biofilm formation on polypropylene mesh. ACTA ACUST UNITED AC 2012; 65:283-90. [DOI: 10.1111/j.1574-695x.2012.00948.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 11/30/2022]
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Collins RE, Higgs PG. Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome. Mol Biol Evol 2012; 29:3413-25. [PMID: 22752048 DOI: 10.1093/molbev/mss163] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
When groups of related bacterial genomes are compared, the number of core genes found in all genomes is usually much less than the mean genome size, whereas the size of the pangenome (the set of genes found on at least one of the genomes) is much larger than the mean size of one genome. We analyze 172 complete genomes of Bacilli and compare the properties of the pangenomes and core genomes of monophyletic subsets taken from this group. We then assess the capabilities of several evolutionary models to predict these properties. The infinitely many genes (IMG) model is based on the assumption that each new gene can arise only once. The predictions of the model depend on the shape of the evolutionary tree that underlies the divergence of the genomes. We calculate results for coalescent trees, star trees, and arbitrary phylogenetic trees of predefined fixed branch length. On a star tree, the pangenome size increases linearly with the number of genomes, as has been suggested in some previous studies, whereas on a coalescent tree, it increases logarithmically. The coalescent tree gives a better fit to the data, for all the examples we consider. In some cases, a fixed phylogenetic tree proved better than the coalescent tree at reproducing structure in the gene frequency spectrum, but little improvement was gained in predictions of the core and pangenome sizes. Most of the data are well explained by a model with three classes of gene: an essential class that is found in all genomes, a slow class whose rate of origination and deletion is slow compared with the time of divergence of the genomes, and a fast class showing rapid origination and deletion. Although the majority of genes originating in a genome are in the fast class, these genes are not retained for long periods, and the majority of genes present in a genome are in the slow or essential classes. In general, we show that the IMG model is useful for comparison with experimental genome data both for species level and widely divergent taxonomic groups. Software implementing the described formulae is provided at http://github.com/rec3141/pangenome.
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Affiliation(s)
- R Eric Collins
- Origins Institute and Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada.
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Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars. J Bacteriol 2012; 194:3922-37. [PMID: 22609915 DOI: 10.1128/jb.00056-12] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.
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