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Song Z, Ge Y, Yu X, Liu R, Liu C, Cheng K, Guo L, Yao S. Development of a single nucleotide polymorphism-based strain-identified method for Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 using pan-genomics analysis. J Dairy Sci 2024; 107:4248-4258. [PMID: 38246550 DOI: 10.3168/jds.2023-23655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
The health benefits conferred by probiotics is specific to individual probiotic strains, highlighting the importance of identifying specific strains for research and production purposes. Streptococcus thermophilus CICC 6038 and Lactobacillus delbrueckii ssp. bulgaricus CICC 6047 are exceedingly valuable for commercial use with an excellent mixed-culture fermentation. To differentiate these 2 strains from other S. thermophilus and L. delbrueckii ssp. bulgaricus, a specific, sensitive, accurate, rapid, convenient, and cost-effective method is required. In this study, we conducted a pan-genome analysis of S. thermophilus and L. delbrueckii ssp. bulgaricus to identify species-specific core genes, along with strain-specific SNPs. These genes were used to develop suitable PCR primers, and the conformity of sequence length and unique SNPs was confirmed by sequencing for qualitative identification at the strain level. The results demonstrated that SNPs analysis of PCR products derived from these primers could distinguish CICC 6038 and CICC 6047 accurately and reproducibly from the other strains of S. thermophilus and L. delbrueckii ssp. bulgaricus, respectively. The strain-specific PCR method based on SNPs herein is universally applicable for probiotics identification. It offers valuable insights into identifying probiotics at the strain level that is fit-for-purpose in quality control and compliance assessment of commercial dairy products.
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Affiliation(s)
- Zhiquan Song
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Yuanyuan Ge
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China; Beijing Forestry University, College of Biological Sciences and Biotechnology, Beijing, 100083, China
| | - Xuejian Yu
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Rui Liu
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Chong Liu
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Kun Cheng
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Lizheng Guo
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China
| | - Su Yao
- China National Research Institute of Food and Fermentation Industries Co. Ltd., China Center of Industrial Culture Collection, Beijing, 100015, China.
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Yu D, Stothard P, Neumann NF. Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments. Sci Rep 2024; 14:13478. [PMID: 38866876 PMCID: PMC11169474 DOI: 10.1038/s41598-024-64241-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
The Escherichia coli species is comprised of several 'ecotypes' inhabiting a wide range of host and natural environmental niches. Recent studies have suggested that novel naturalized ecotypes have emerged across wastewater treatment plants and meat processing facilities. Phylogenetic and multilocus sequence typing analyses clustered naturalized wastewater and meat plant E. coli strains into two main monophyletic clusters corresponding to the ST635 and ST399 sequence types, with several serotypes identified by serotyping, potentially representing distinct lineages that have naturalized across wastewater treatment plants and meat processing facilities. This evidence, taken alongside ecotype prediction analyses that distinguished the naturalized strains from their host-associated counterparts, suggests these strains may collectively represent a novel ecotype that has recently emerged across food- and water-associated engineered environments. Interestingly, pan-genomic analyses revealed that the naturalized strains exhibited an abundance of biofilm formation, defense, and disinfection-related stress resistance genes, but lacked various virulence and colonization genes, indicating that their naturalization has come at the cost of fitness in the original host environment.
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Affiliation(s)
- Daniel Yu
- School of Public Health, University of Alberta, Edmonton, AB, Canada.
- Antimicrobial Resistance-One Health Consortium, Calgary, AB, Canada.
| | - Paul Stothard
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Antimicrobial Resistance-One Health Consortium, Calgary, AB, Canada
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Frantsuzova E, Bogun A, Kopylova O, Vetrova A, Solyanikova I, Streletskii R, Delegan Y. Genomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135. BIOLOGY 2024; 13:339. [PMID: 38785821 PMCID: PMC11117675 DOI: 10.3390/biology13050339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/07/2024] [Accepted: 05/11/2024] [Indexed: 05/25/2024]
Abstract
The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the "panIGRome" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Olga Kopylova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Pushchino Branch of Federal State Budgetary Educational Institution of Higher Education “Russian Biotechnology University (ROSBIOTECH)”, 142290 Pushchino, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
| | - Inna Solyanikova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
- Regional Microbiological Center, Belgorod State University, 308015 Belgorod, Russia
| | - Rostislav Streletskii
- Laboratory of Ecological Soil Science, Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia; (E.F.); (A.B.); (O.K.); (A.V.); (I.S.)
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Garushyants SK, Sane M, Selifanova MV, Agashe D, Bazykin GA, Gelfand MS. Mutational Signatures in Wild Type Escherichia coli Strains Reveal Predominance of DNA Polymerase Errors. Genome Biol Evol 2024; 16:evae035. [PMID: 38401265 PMCID: PMC10995721 DOI: 10.1093/gbe/evae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/26/2024] Open
Abstract
While mutational processes operating in the Escherichia coli genome have been revealed by multiple laboratory experiments, the contribution of these processes to accumulation of bacterial polymorphism and evolution in natural environments is unknown. To address this question, we reconstruct signatures of distinct mutational processes from experimental data on E. coli hypermutators, and ask how these processes contribute to differences between naturally occurring E. coli strains. We show that both mutations accumulated in the course of evolution of wild-type strains in nature and in the lab-grown nonmutator laboratory strains are explained predominantly by the low fidelity of DNA polymerases II and III. By contrast, contributions specific to disruption of DNA repair systems cannot be detected, suggesting that temporary accelerations of mutagenesis associated with such disruptions are unimportant for within-species evolution. These observations demonstrate that accumulation of diversity in bacterial strains in nature is predominantly associated with errors of DNA polymerases.
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Affiliation(s)
- Sofya K Garushyants
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Mrudula Sane
- National Centre for Biological Sciences, Bengaluru, India
| | - Maria V Selifanova
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Deepa Agashe
- National Centre for Biological Sciences, Bengaluru, India
| | - Georgii A Bazykin
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Mikhail S Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
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Mahesh S, Carmelin DS, Muthusamy R. Bacterial Flora and Treatment Strategies in Women With Escherichia coli Urinary Tract Infections. Cureus 2024; 16:e56552. [PMID: 38646229 PMCID: PMC11027953 DOI: 10.7759/cureus.56552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
Introduction This study explores the intricate relationship between bacterial flora and the occurrence of Escherichia coli (E. coli) infections in gynecological patients. It aims to provide insights into the various treatment strategies used to effectively manage bacterial pathogens, especially E. coli infections. By conducting a comprehensive analysis of the bacterial flora in gynecological patients, the study highlights the notable presence of E. coli, prompting further investigation into the factors that contribute to its colonization. The objective of the study is to comprehensively investigate and detect urinary tract infections (UTIs) specifically caused by E. coli among gynecological patients. The study aims to delve into bacterial flora prevalence, antibiotic resistance patterns, and potential virulence factors. Through this analysis, the study intends to identify effective strategies for rapid detection and diagnosis of UTIs caused by E. coli by utilizing advanced microbiological and molecular techniques. Furthermore, the study aims to formulate and propose a strategic treatment approach with a particular emphasis on selecting appropriate antibiotics to reduce the risk of severe infections and associated complications. Materials and methods The methodology employed in this study included the isolation and characterization of bacterial strains from clinical samples obtained from gynecological patients. A total of 52 urine specimens were collected from patients with complaints of infection in the urinary tract and infertility. These samples underwent both preliminary and confirmatory microbiological analysis, such as gram staining, biochemical confirmation test, and antibiotic susceptibility, and further proceeded with the multiplex polymerase chain reaction (PCR) technique. The results of PCR and antibiotic susceptibility revealed the specific gene involvement and resistant characteristics of E. coli. Results The findings revealed a total of 32 specimens positive for E. coli, of which 10 patients had infertility complaints and 22 patients had UTIs. The preliminary test, gram staining, showed the gram-negative bacilli E. coli, and the nutrient agar plate revealed smooth circular translucent colonies; MacConkey agar showed pink-colored lactose-fermented colonies; and the blood and chocolate agar plates showed grayish white moist gamma-hemolytic colonies. The biochemical confirmation of E. coli resulted in positive for indole and methyl red tests and negative for Voges-Proskauer and citrate utilization tests. The multiplex PCR analysis confirmed the E. coli strains with the presence of two target genes, stx2d and stx2e. Conclusion To summarize, this study offers valuable insights into the bacterial flora of gynecological patients impacted by E. coli infections, which provides a foundation for the development of precise and efficient treatment strategies. The results emphasize the importance of personalized treatment approaches that consider both the microbiological characteristics of the infection and the evolving landscape of antibiotic resistance. The implication of this research extends to enhancing clinical outcomes and alleviating the burden of E. coli infections in gynecological settings.
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Affiliation(s)
- Saisri Mahesh
- Center for Global Health Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Durai Singh Carmelin
- Center for Global Health Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
| | - Raman Muthusamy
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Chennai, IND
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Ha EJ, Hong SM, Kim SJ, Ahn SM, Kim HW, Choi KS, Kwon HJ. Tracing the Evolutionary Pathways of Serogroup O78 Avian Pathogenic Escherichia coli. Antibiotics (Basel) 2023; 12:1714. [PMID: 38136748 PMCID: PMC10740950 DOI: 10.3390/antibiotics12121714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/17/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Avian pathogenic E. coli (APEC) causes severe economic losses in the poultry industry, and O78 serogroup APEC strains are prevalent in chickens. In this study, we aimed to understand the evolutionary pathways and relationships between O78 APEC and other E. coli strains. To trace these evolutionary pathways, we classified 3101 E. coli strains into 306 subgenotypes according to the numbers and types of single nucleotide polymorphisms (RST0 to RST63-1) relative to the consensus sequence (RST0) of the RNA polymerase beta subunit gene and performed network analysis. The E. coli strains showed four apparently different evolutionary pathways (I-1, I-2, I-3, and II). The thirty-two Korean O78 APEC strains tested in this study were classified into RST4-4 (45.2%), RST3-1 (32.3%), RST21-1 (12.9%), RST4-5 (3.2%), RST5-1 (3.2%), and RST12-6 (3.2%), and all RSTs except RST21-1 (I-2) may have evolved through the same evolutionary pathway (I-1). A comparative genomic study revealed the highest relatedness between O78 strains of the same RST in terms of genome sequence coverage/identity and the spacer sequences of CRISPRs. The early-appearing RST3-1 and RST4-4 prevalence among O78 APEC strains may reflect the early settlement of O78 E. coli in chickens, after which these bacteria accumulated virulence and antibiotic resistance genes to become APEC strains. The zoonotic risk of the conventional O78 APEC strains is low at present, but the appearance of genetically distinct and multiple virulence gene-bearing RST21-1 O78 APEC strains may alert us to a need to evaluate their virulence in chickens as well as their zoonotic risk.
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Affiliation(s)
- Eun-Jin Ha
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Min Hong
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Seung-Ji Kim
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Sun-Min Ahn
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Ho-Won Kim
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea; (E.-J.H.); (S.-M.H.); (S.-J.K.)
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
| | - Hyuk-Joon Kwon
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul 08826, Republic of Korea; (S.-M.A.); (H.-W.K.)
- Laboratory of Poultry Medicine, Department of Farm Animal Medicine, College of Veterinary Medicine and BK21 PLUS for Veterinary Science, Seoul National University, Seoul 088026, Republic of Korea
- Farm Animal Clinical Training and Research Center (FACTRC), GBST, Seoul National University, Pyeongchang 25354, Republic of Korea
- GeNiner Inc., Seoul 08826, Republic of Korea
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Abstract
Escherichia coli contain a high level of genetic diversity and are generally associated with the guts of warm-blooded animals but have also been isolated from secondary habitats outside hosts. We used E. coli isolates from previous in situ microcosm experiments conducted under actual beach conditions and performed population-level genomic analysis to identify accessory genes associated with survival within the beach sand environment. E. coli strains capable of surviving had been selected for by seeding isolates originating from sand, sewage, and gull waste (n = 528; 176 from each source) into sand, which was sealed in microcosm chambers and buried for 45 days in the backshore beach of Lake Michigan. In the current work, survival-associated genes were identified by comparing the pangenome of viable E. coli populations at the end of the microcosm experiment with the original isolate collection and identifying loci enriched in the out put samples. We found that environmental survival was associated with a wide variety of genetic factors, with the majority corresponding to metabolism enzymes and transport proteins. Of the 414 unique functions identified, most were present across E. coli phylogroups, except B2 which is often associated with human pathogens. Gene modules that were enriched in surviving populations included a betaine biosynthesis pathway, which produces an osmoprotectant, and the GABA (gamma-aminobutyrate) biosynthesis pathway, which aids in pH homeostasis and nutrient use versatility. Overall, these results demonstrate that the genetic flexibility within this species allows for survival in the environment for extended periods. IMPORTANCE Escherichia coli is commonly used as an indicator of recent fecal pollution in recreational water despite its known ability to survive in secondary environments, such as beach sand. These long-term survivors from sand reservoirs can be introduced into the water column through wave action or runoff during precipitation events, thereby impacting the perception of local water quality. Current beach monitoring methods cannot differentiate long-term environmental survivors from E. coli derived from recent fecal input, resulting in inaccurate monitoring results and unnecessary beach closures. This work identified the genetic factors that are associated with long-term survivors, providing insight into the mechanistic basis for E. coli accumulation in beach sand. A greater understanding of the intrinsic ability of E. coli to survive long-term and conditions that promote such survival will provide evidence of the limitations of beach water quality assessments using this indicator.
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Leigh RJ, Corrigan A, Murphy RA, Walsh F. Effect of Mannan-rich fraction supplementation on commercial broiler intestinum tenue and cecum microbiota. Anim Microbiome 2022; 4:66. [PMID: 36536475 PMCID: PMC9762088 DOI: 10.1186/s42523-022-00208-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 10/15/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The broiler gastrointestinal microbiome is a potent flock performance modulator yet may also serve as a reservoir for pathogen entry into the food chain. The goal of this project was to characterise the effect of mannan rich fraction (MRF) supplementation on microbiome diversity and composition of the intestinum tenue and cecum of commercial broilers. This study also aimed to address some of the intrinsic biases that exist in microbiome studies which arise due to the extensive disparity in 16S rRNA gene copy numbers between bacterial species and due to large intersample variation. RESULTS We observed a divergent yet rich microbiome structure between different anatomical sites and observed the explicit effect MRF supplementation had on community structure, diversity, and pathogen modulation. Birds supplemented with MRF displayed significantly higher species richness in the cecum and significantly different bacterial community composition in each gastrointestinal (GI) tract section. Supplemented birds had lower levels of the zoonotic pathogens Escherichia coli and Clostridioides difficile across all three intestinum tenue sites highlighting the potential of MRF supplementation in maintaining food chain integrity. Higher levels of probiotic genera (eg. Lactobacillus and Blautia) were also noted in the MRF supplemented birds. Following MRF supplementation, the cecum displayed higher relative abundances of both short chain fatty acid (SFCA) synthesising bacteria and SCFA concentrations. CONCLUSIONS Mannan rich fraction addition has been observed to reduce the bioburden of pathogens in broilers and to promote greater intestinal tract microbial biodiversity. This study is the first, to our knowledge, to investigate the effect of mannan-rich fraction supplementation on the microbiome associated with different GI tract anatomical geographies. In addition to this novelty, this study also exploited machine learning and biostatistical techniques to correct the intrinsic biases associated with microbiome community studies to enable a more robust understanding of community structure.
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Affiliation(s)
- Robert J. Leigh
- grid.95004.380000 0000 9331 9029Antimicrobial Resistance and Microbiome Research Group, Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Aoife Corrigan
- grid.496915.6Alltech Inc. (Alltech European Bioscience Centre), Summerhill Road, Sarney, Dunboyne, Co. Meath, Ireland
| | - Richard A. Murphy
- grid.496915.6Alltech Inc. (Alltech European Bioscience Centre), Summerhill Road, Sarney, Dunboyne, Co. Meath, Ireland
| | - Fiona Walsh
- grid.95004.380000 0000 9331 9029Antimicrobial Resistance and Microbiome Research Group, Department of Biology, Maynooth University, Co. Kildare, Ireland
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Cummins EA, Hall RJ, Connor C, McInerney JO, McNally A. Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types. Microb Genom 2022; 8:mgen000903. [PMID: 36748558 PMCID: PMC9836092 DOI: 10.1099/mgen.0.000903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/02/2022] [Indexed: 11/24/2022] Open
Abstract
The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers.
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Affiliation(s)
- Elizabeth A. Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J. Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chris Connor
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - James O. McInerney
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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10
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Tantoso E, Eisenhaber B, Kirsch M, Shitov V, Zhao Z, Eisenhaber F. To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. BMC Biol 2022; 20:146. [PMID: 35710371 PMCID: PMC9205054 DOI: 10.1186/s12915-022-01347-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile. RESULTS Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131. CONCLUSIONS This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E. We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.
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Affiliation(s)
- Erwin Tantoso
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Miles Kirsch
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: Northeastern University, Boston, USA
| | - Vladimir Shitov
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Zhiya Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,Present address: The University of Cambridge, Cambridge, UK
| | - Frank Eisenhaber
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, 637551, Singapore, Republic of Singapore.
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11
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Ferrandis-Vila M, Tiwari SK, Mamerow S, Semmler T, Menge C, Berens C. Using unique ORFan genes as strain-specific identifiers for Escherichia coli. BMC Microbiol 2022; 22:135. [PMID: 35585491 PMCID: PMC9118744 DOI: 10.1186/s12866-022-02508-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 03/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial identification at the strain level is a much-needed, but arduous and challenging task. This study aimed to develop a method for identifying and differentiating individual strains among multiple strains of the same bacterial species. The set used for testing the method consisted of 17 Escherichia coli strains picked from a collection of strains isolated in Germany, Spain, the United Kingdom and Vietnam from humans, cattle, swine, wild boars, and chickens. We targeted unique or rare ORFan genes to address the problem of selective and specific strain identification. These ORFan genes, exclusive to each strain, served as templates for developing strain-specific primers. RESULTS Most of the experimental strains (14 out of 17) possessed unique ORFan genes that were used to develop strain-specific primers. The remaining three strains were identified by combining a PCR for a rare gene with a selection step for isolating the experimental strains. Multiplex PCR allowed the successful identification of the strains both in vitro in spiked faecal material in addition to in vivo after experimental infections of pigs and recovery of bacteria from faecal material. In addition, primers for qPCR were also developed and quantitative readout from faecal samples after experimental infection was also possible. CONCLUSIONS The method described in this manuscript using strain-specific unique genes to identify single strains in a mixture of strains proved itself efficient and reliable in detecting and following individual strains both in vitro and in vivo, representing a fast and inexpensive alternative to more costly methods.
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Affiliation(s)
- Marta Ferrandis-Vila
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | | | - Svenja Mamerow
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | | | | | - Christian Menge
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut - Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Naumburger Straße 96a, 07743, Jena, Germany.
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12
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Abstract
The hypervariable residues that compose the major part of proteins’ surfaces are generally considered outside evolutionary control. Yet, these “nonconserved” residues determine the outcome of stochastic encounters in crowded cells. It has recently become apparent that these encounters are not as random as one might imagine, but carefully orchestrated by the intracellular electrostatics to optimize protein diffusion, interactivity, and partner search. The most influential factor here is the protein surface-charge density, which takes different optimal values across organisms with different intracellular conditions. In this study, we examine how far the net-charge density and other physicochemical properties of proteomes will take us in terms of distinguishing organisms in general. The results show that these global proteome properties not only follow the established taxonomical hierarchy, but also provide clues to functional adaptation. In many cases, the proteome–property divergence is even resolved at species level. Accordingly, the variable parts of the genes are not as free to drift as they seem in sequence alignment, but present a complementary tool for functional, taxonomic, and evolutionary assignment.
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13
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An in silico hierarchal approach for drug candidate mining and validation of natural product inhibitors against pyrimidine biosynthesis enzyme in the antibiotic-resistant Shigella flexneri. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 98:105233. [PMID: 35104682 DOI: 10.1016/j.meegid.2022.105233] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 01/20/2022] [Accepted: 01/26/2022] [Indexed: 02/07/2023]
Abstract
Shigella flexneri is the main causative agent of the communicable diarrheal disease, shigellosis. It is estimated that about 80-165 million cases and > 1 million deaths occur every year due to this disease. S. flexneri causes dysentery mostly in young children, elderly and immunocompromised patients, all over the globe. Recently, due to the emergence of S. flexneri antibiotic resistance strains, it is a dire need to predict novel therapeutic drug targets in the bacterium and screen natural products against it, which could eliminate the curse of antibiotic resistance. Therefore, in current study, available antibiotic-resistant genomes (n = 179) of S. flexneri were downloaded from PATRIC database and a pan-genome and resistome analysis was conducted. Around 5059 genes made up the accessory, 2469 genes made up the core, and 1558 genes made up the unique genome fraction, with 44, 34, and 13 antibiotic-resistant genes in each fraction, respectively. Core genome fraction (27% of the pan-genome), which was common to all strains, was used for subtractive genomics and resulted in 384 non-homologous, and 85 druggable targets. Dihydroorotase was chosen for further analysis and docked with natural product libraries (Ayurvedic and Streptomycin compounds), while the control was orotic acid or vitamin B13 (which is a natural binder of this protein). Dynamics simulation of 50 ns was carried out to validate findings for top-scored inhibitors. The current study proposed dihydroorotase as a significant drug target in S. flexneri and 4-tritriacontanone & patupilone compounds as potent drugs against shigellosis. Further experiments are required to ascertain validity of our findings.
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14
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Epi-Gene: An R-Package for Easy Pan-Genome Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5585586. [PMID: 34595238 PMCID: PMC8478537 DOI: 10.1155/2021/5585586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/28/2021] [Indexed: 11/18/2022]
Abstract
The main aim of this study was to develop a set of functions that can analyze the genomic data with less time consumption and memory. Epi-gene is presented as a solution to large sequence file handling and computational time problems. It uses less time and less programming skills in order to work with a large number of genomes. In the current study, some features of the Epi-gene R-package were described and illustrated by using a dataset of the 14 Aeromonas hydrophila genomes. The joining, relabeling, and conversion functions were also included in this package to handle the FASTA formatted sequences. To calculate the subsets of core genes, accessory genes, and unique genes, various Epi-gene functions have been used. Heat maps and phylogenetic genome trees were also constructed. This whole procedure was completed in less than 30 minutes. This package can only work on Windows operating systems. Different functions from other packages such as dplyr and ggtree were also used that were available in R computing environment.
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15
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Horesh G, Taylor-Brown A, McGimpsey S, Lassalle F, Corander J, Heinz E, Thomson NR. Different evolutionary trends form the twilight zone of the bacterial pan-genome. Microb Genom 2021; 7. [PMID: 34559043 PMCID: PMC8715436 DOI: 10.1099/mgen.0.000670] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species’ pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500 Escherichia coli genomes, one of the most-studied bacterial species and used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species’ pan-genome.
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Affiliation(s)
- Gal Horesh
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Alyce Taylor-Brown
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Stephanie McGimpsey
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Florent Lassalle
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Jukka Corander
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.,Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.,Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Eva Heinz
- Departments of Vector Biology and Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.,Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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16
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Colquhoun RM, Hall MB, Lima L, Roberts LW, Malone KM, Hunt M, Letcher B, Hawkey J, George S, Pankhurst L, Iqbal Z. Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs. Genome Biol 2021; 22:267. [PMID: 34521456 PMCID: PMC8442373 DOI: 10.1186/s13059-021-02473-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/19/2021] [Indexed: 12/21/2022] Open
Abstract
We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations. Pandora approximates a sequenced genome as a recombinant of references, detects novel variation and pan-genotypes multiple samples. Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.
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Affiliation(s)
- Rachel M Colquhoun
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Michael B Hall
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Leandro Lima
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Leah W Roberts
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Kerri M Malone
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Martin Hunt
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Brice Letcher
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, 3004, Australia
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Louise Pankhurst
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Zoology, University of Oxford, Mansfield Road, Oxford, UK
| | - Zamin Iqbal
- European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
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17
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Silva de Oliveira M, Thyeska Castro Alves J, Henrique Caracciolo Gomes de Sá P, Veras AADO. PAN2HGENE-tool for comparative analysis and identifying new gene products. PLoS One 2021; 16:e0252414. [PMID: 34048479 PMCID: PMC8162609 DOI: 10.1371/journal.pone.0252414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 05/14/2021] [Indexed: 12/02/2022] Open
Abstract
Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. However, to understand the evolutionary processes of these genes, comparative analysis, which is an important tool for annotation, is required. Using comparative analysis, it is possible to infer the functions of gene contents and identify orthologs and paralogous genes via their homology. Although several comparative analysis tools currently exist, most of them are limited to complete genomes. PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface. The PAN2HGENE have been uploaded to SourceForge and are available via: https://sourceforge.net/projects/pan2hgene-software
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Affiliation(s)
- Mônica Silva de Oliveira
- Postgraduate Program in Applied Computing, Federal University of Pará Campus Tucuruí (CAMTUC-UFPA), Pará, Brazil
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18
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Kakooza S, Muwonge A, Nabatta E, Eneku W, Ndoboli D, Wampande E, Munyiirwa D, Kayaga E, Tumwebaze MA, Afayoa M, Ssajjakambwe P, Tayebwa DS, Tsuchida S, Okubo T, Ushida K, Sakurai K, Mutebi F. A retrospective analysis of antimicrobial resistance in pathogenic Escherichia coli and Salmonella spp. isolates from poultry in Uganda. Int J Vet Sci Med 2021; 9:11-21. [PMID: 34104644 PMCID: PMC8158283 DOI: 10.1080/23144599.2021.1926056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
There are increasing reports of antimicrobial treatment failures for bacterial diseases of poultry in Uganda. The paucity of data on antimicrobial resistance (AMR) of pathogenic bacteria in Uganda is a major setback to AMR control. This study investigated the occurrence of fowl typhoid, colibacillosis, and AMR in associated pathogens from 2012 to 2018. Laboratory records from the Central Diagnostic Laboratory (CDL), a National Veterinary Diagnostic Facility located at Makerere University, were reviewed. Archived isolates of the causative bacteria for the two diseases were also evaluated for AMR. The frequencies of the two disease conditions, their clinical and necropsy presentations and the demographic data of the diagnostic samples were summarized from the records. Archived bacterial isolates were revived before antimicrobial susceptibility testing. This was done on Mueller Hinton agar using the disk diffusion method, against 16 antimicrobials of medical and veterinary importance according to the Clinical Laboratory Standards Institute guidelines. A total of 697 poultry cases were presented for bacteriological investigations in the review period. Colibacillosis and salmonellosis had prevalence rates of 39.7% (277/697) and 16.2% (113/697), respectively. A total of 63 and 92 isolates of Escherichia coli and Salmonella spp., respectively, were archived but 43 (68.3%) E. coli and 47 (51.1%) Salmonella spp. isolates were recovered and evaluated for AMR. Multidrug resistance was more frequent in E. coli (38; 88.4%) than salmonellae (25; 53.2%), (p < 0.001). The high prevalence of colibacillosis, salmonellosis and the AMR of associated pathogens warrants immediate institution of appropriate disease control measures.
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Affiliation(s)
- Steven Kakooza
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Adrian Muwonge
- Department of Genetics and Genomics, the Roslin Institute, University of Edinburgh, Edinburgh, Scotland
| | - Esther Nabatta
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Wilfred Eneku
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dickson Ndoboli
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Eddie Wampande
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Damian Munyiirwa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Edrine Kayaga
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Maria Agnes Tumwebaze
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Mathias Afayoa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Paul Ssajjakambwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Dickson Stuart Tayebwa
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Sayaka Tsuchida
- Chubu University, Academy of Emerging Sciences, Kasugai, Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University Graduate School of Health Sciences, Sapporo, Japan
| | - Kazunari Ushida
- Chubu University, Academy of Emerging Sciences, Kasugai, Japan
| | - Ken'ichi Sakurai
- Faculty of Life and Environmental Sciences, Department of Animal Sciences, Teikyo University of Science, Tokyo, Japan
| | - Francis Mutebi
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda.,College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
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19
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Shaw LP, Chau KK, Kavanagh J, AbuOun M, Stubberfield E, Gweon HS, Barker L, Rodger G, Bowes MJ, Hubbard ATM, Pickford H, Swann J, Gilson D, Smith RP, Hoosdally SJ, Sebra R, Brett H, Peto TEA, Bailey MJ, Crook DW, Read DS, Anjum MF, Walker AS, Stoesser N. Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. SCIENCE ADVANCES 2021; 7:eabe3868. [PMID: 33837077 PMCID: PMC8034854 DOI: 10.1126/sciadv.abe3868] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 02/22/2021] [Indexed: 05/07/2023]
Abstract
Escherichia coli and other Enterobacteriaceae are diverse species with "open" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.
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Affiliation(s)
- Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
| | - Kevin K Chau
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - James Kavanagh
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Emma Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - H Soon Gweon
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK
| | - Leanne Barker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Gillian Rodger
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Mike J Bowes
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Alasdair T M Hubbard
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Hayleah Pickford
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel Gilson
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Richard P Smith
- Department of Epidemiological Sciences, The Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Sarah J Hoosdally
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, 333 Ludlow Street, North Tower, 8th floor, Stamford, CT 06902, USA
| | - Howard Brett
- Thames Water Utilities, Clearwater Court, Vastern Road, Reading RG1 8DB, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Mark J Bailey
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Daniel S Read
- UK Centre for Ecology & Hydrology (UKCEH), Benson Lane, Crowmarsh Gifford, Wallingford OX10 8BB, UK
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford OX4 9DU, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK.
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
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20
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Lee C, Klockgether J, Fischer S, Trcek J, Tümmler B, Römling U. Why? - Successful Pseudomonas aeruginosa clones with a focus on clone C. FEMS Microbiol Rev 2021; 44:740-762. [PMID: 32990729 PMCID: PMC7685784 DOI: 10.1093/femsre/fuaa029] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.
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Affiliation(s)
- Changhan Lee
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Jens Klockgether
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Sebastian Fischer
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Janja Trcek
- Faculty of Natural Sciences and Mathematics, Department of Biology, University of Maribor, Maribor, 2000, Slovenia
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, Clinical Research Group 'Pseudomonas Genomics', Hannover Medical School, D-30625 Hannover, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum C8, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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Sy BM, Tree JJ. Small RNA Regulation of Virulence in Pathogenic Escherichia coli. Front Cell Infect Microbiol 2021; 10:622202. [PMID: 33585289 PMCID: PMC7873438 DOI: 10.3389/fcimb.2020.622202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/10/2020] [Indexed: 11/17/2022] Open
Abstract
Enteric and extraintestinal pathotypes of Escherichia coli utilize a wide range of virulence factors to colonize niches within the human body. During infection, virulence factors such as adhesins, secretions systems, or toxins require precise regulation and coordination to ensure appropriate expression. Additionally, the bacteria navigate rapidly changing environments with fluctuations in pH, temperature, and nutrient levels. Enteric pathogens utilize sophisticated, interleaved systems of transcriptional and post-transcriptional regulation to sense and respond to these changes and modulate virulence gene expression. Regulatory small RNAs and RNA-binding proteins play critical roles in the post-transcriptional regulation of virulence. In this review we discuss how the mosaic genomes of Escherichia coli pathotypes utilize small RNA regulation to adapt to their niche and become successful human pathogens.
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Affiliation(s)
- Brandon M Sy
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jai J Tree
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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22
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Coradini ALV, Hull CB, Ehrenreich IM. Building genomes to understand biology. Nat Commun 2020; 11:6177. [PMID: 33268788 PMCID: PMC7710724 DOI: 10.1038/s41467-020-19753-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic manipulation is one of the central strategies that biologists use to investigate the molecular underpinnings of life and its diversity. Thus, advances in genetic manipulation usually lead to a deeper understanding of biological systems. During the last decade, the construction of chromosomes, known as synthetic genomics, has emerged as a novel approach to genetic manipulation. By facilitating complex modifications to chromosome content and structure, synthetic genomics opens new opportunities for studying biology through genetic manipulation. Here, we discuss different classes of genetic manipulation that are enabled by synthetic genomics, as well as biological problems they each can help solve.
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Affiliation(s)
- Alessandro L V Coradini
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Cara B Hull
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
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23
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Molina F, Simancas A, Tabla R, Gómez A, Roa I, Rebollo JE. Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants. Front Microbiol 2020; 11:564522. [PMID: 33178150 PMCID: PMC7596221 DOI: 10.3389/fmicb.2020.564522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/17/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are highly specific predators that drive bacterial diversity through coevolution while striking tradeoffs among preserving host populations for long-term exploitation and increasing their virulence, structural stability, or host range. Escherichia coli and other coliform bacteria present in the microbiota of milk and during early ripening of raw milk cheeses have been linked to the production of gas, manifested by the appearance of eyes, and the development of off-flavors; thus, they might cause early blowing and cheese spoilage. Here, we report the characterization of coliphages isolated from manure from small ruminant farms and E. coli strains isolated from goat and sheep raw milk cheese. Additionally, the virulence and host range of locally isolated and laboratory collection phages were determined by comparing the susceptibility of E. coli strains from different sources. In agreement with the high genetic diversity found within the species E. coli, clustering analysis of whole-cell protein revealed a total of 13 distinct profiles but none of the raw milk cheese isolates showed inhibition of growth by reference or water-isolated coliphages. Conversely, 10 newly isolated phages had a broad host range (i.e., able to lyse ≥50% of bacterial hosts tested), thus exhibiting utility for biocontrol and only one cheese-isolated E. coli strain was resistant to all the phages. Whereas there was a high positive correlation between bacterial susceptibility range and lysis intensity, the phages virulence decreased as range increased until reaching a plateau. These results suggest local gene-for-gene coevolution between hosts and phages with selective tradeoffs for both resistance and competitive ability of the bacteria and host-range extension and virulence of the phage populations. Hence, different phage cocktail formulations might be required when devising long-term and short-term biocontrol strategies.
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Affiliation(s)
- Felipe Molina
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Alfredo Simancas
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Rafael Tabla
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - Antonia Gómez
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - Isidro Roa
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - José Emilio Rebollo
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
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Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation. BMC Genomics 2020; 21:418. [PMID: 32571204 PMCID: PMC7306931 DOI: 10.1186/s12864-020-06829-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/15/2020] [Indexed: 12/17/2022] Open
Abstract
Background In bacteria, pan-genomes are the result of an evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. Results We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport. Conclusions Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.
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The gut microbes, Enterococcus and Escherichia-Shigella, affect the responses of heart valve replacement patients to the anticoagulant warfarin. Pharmacol Res 2020; 159:104979. [PMID: 32505835 DOI: 10.1016/j.phrs.2020.104979] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
Numerous algorithms based on patient genetic variants have been established with the aim of reducing the risk of GI bleeding and thromboembolism during warfarin administration. However, approximately 35 % of individual warfarin sensitivity still remains unexplained. Few of warfarin algorithms take into account gut microbiota profiles. The identification of certain microbiome will provide new targets and new strategies for reducing the risk of bleeding and thromboembolism during warfarin administration. In this study, we collected plasma and stool samples from 200 inpatients undergoing heart valve replacement (HVR), which were classified as low responder (LR), high responder (HR) and normal responder (NR). Significant differences were observed in the diversity and relative abundance of the gut microbiota among the three groups. The genus Escherichia-Shigella was enriched significantly in the LRs (P = 3.189e-11), while the genus Enterococcus was enriched significantly in the HRs (P = 1.249e-11). The amount of VK2 synthesized by gut microbiota in LR group was much higher than that in HR group (P = 0.005). Whole genome shotgun sequencing indicated that the relative abundance of enzymes and modules associated with VK biosynthesis was significantly higher in LRs than in HRs or NRs. The 12 microbial markers were identified through tenfold cross-validation with a random forest model. The results provided a new microbial diagnostic model that can be used to inform modulation of warfarin dosage on the basis of patient intestinal flora composition.
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Rao RT, Sivakumar N, Jayakumar K. Analyses of Livestock-Associated Staphylococcus aureus Pan-Genomes Suggest Virulence Is Not Primary Interest in Evolution of Its Genome. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 23:224-236. [PMID: 31009331 DOI: 10.1089/omi.2019.0005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Staphylococcus aureus is not only part of normal flora but also an opportunistic pathogen relevant to microbial genomics, public health, and veterinary medicine. In addition to being a well-known human pathogen, S. aureus causes various infections in economically important livestock animals such as cows, sheep, goats, and pigs. There are very few studies that have examined the pan-genome of S. aureus or the host-specific strains' pan-genomes. We report on livestock-associated S. aureus' (LA-SA) pan-genome and suggest that virulence is not the primary interest in evolution of its genome. LA-SA' complete genomes were retrieved from the NCBI and pan-genome was constructed by high-speed Roary pipeline. The pan-genome size was 4637 clusters, whereas 42.46% of the pan-genome was associated with the core genome. We found 1268 genes were associated with the strain-unique genome, and the remaining 1432 cluster with the accessory genome. COG (clusters of orthologous group of proteins) analysis of the core genes revealed 34% of clusters related to metabolism responsible for amino acid and inorganic ion transport (COG categories E and P), followed by carbohydrate metabolism (category G). Virulent gene analysis revealed the core genes responsible for antiphagocytosis and iron uptake. The fluidity of pan-genome was calculated as 0.082 ± 0.025. Importantly, the positive selection analysis suggested a slower rate of evolution among the LA-SA genomes. We call for comparative microbial and pan-genome research between human and LA-SA that can help further understand the evolution of virulence and thus inform future microbial diagnostics and drug discovery.
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Affiliation(s)
- Relangi Tulasi Rao
- 1 Department of Animal Behaviour & Physiology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Natesan Sivakumar
- 2 Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Kannan Jayakumar
- 1 Department of Animal Behaviour & Physiology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu, India
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Sigalova OM, Chaplin AV, Bochkareva OO, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. BMC Genomics 2019; 20:710. [PMID: 31510914 PMCID: PMC6740158 DOI: 10.1186/s12864-019-6059-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/22/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria. RESULTS We report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system. CONCLUSIONS This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.
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Affiliation(s)
- Olga M. Sigalova
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- current address: European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrei V. Chaplin
- Microbiology and Virology Department, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga O. Bochkareva
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- current address: Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Pavel V. Shelyakin
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Vavilov Institute of General Genetics, RAS, Moscow, Russia
| | | | - Evgeny E. Akkuratov
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- current address: Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Valentina Burskaia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail S. Gelfand
- Kharkevich Institute for Information Transmission Problems, RAS, Moscow, Russia
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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Deshpande SV, Reed TM, Sullivan RF, Kerkhof LJ, Beigel KM, Wade MM. Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS). Genes (Basel) 2019; 10:genes10080578. [PMID: 31366182 PMCID: PMC6723491 DOI: 10.3390/genes10080578] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/14/2022] Open
Abstract
Field laboratories interested in using the MinION often need the internet to perform sample analysis. Thus, the lack of internet connectivity in resource-limited or remote locations renders downstream analysis problematic, resulting in a lack of sample identification in the field. Due to this dependency, field samples are generally transported back to the lab for analysis where internet availability for downstream analysis is available. These logistics problems and the time lost in sample characterization and identification, pose a significant problem for field scientists. To address this limitation, we have developed a stand-alone data analysis packet using open source tools developed by the Nanopore community that does not depend on internet availability. Like Oxford Nanopore Technologies’ (ONT) cloud-based What’s In My Pot (WIMP) software, we developed the offline MinION Detection Software (MINDS) based on the Centrifuge classification engine for rapid species identification. Several online bioinformatics applications have been developed surrounding ONT’s framework for analysis of long reads. We have developed and evaluated an offline real time classification application pipeline using open source tools developed by the Nanopore community that does not depend on internet availability. Our application has been tested on ATCC’s 20 strain even mix whole cell (ATCC MSA-2002) sample. Using the Rapid Sequencing Kit (SQK-RAD004), we were able to identify all 20 organisms at species level. The analysis was performed in 15 min using a Dell Precision 7720 laptop. Our offline downstream bioinformatics application provides a cost-effective option as well as quick turn-around time when analyzing samples in the field, thus enabling researchers to fully utilize ONT’s MinION portability, ease-of-use, and identification capability in remote locations.
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Affiliation(s)
- Samir V Deshpande
- Science and Technology Corporation, 111 Bata Blvd, Suite C, Belcamp, MD 21017, USA
| | - Timothy M Reed
- US Army, 20th CBRNE, Aberdeen Proving Ground, MD 21010, USA
| | - Raymond F Sullivan
- US Army, CCDC-Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA
| | - Lee J Kerkhof
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd, New Brunswick, NJ 08901-8521, USA
| | - Keith M Beigel
- US Army, 20th CBRNE, Aberdeen Proving Ground, MD 21010, USA.
| | - Mary M Wade
- US Army, CCDC-Chemical Biological Center, Aberdeen Proving Ground, MD 21010, USA.
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29
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Lima NCB, Tanmoy AM, Westeel E, de Almeida LGP, Rajoharison A, Islam M, Endtz HP, Saha SK, de Vasconcelos ATR, Komurian-Pradel F. Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi. BMC Genomics 2019; 20:530. [PMID: 31253105 PMCID: PMC6599262 DOI: 10.1186/s12864-019-5916-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
Background Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicrobial resistance (AMR) is a serious issue; the list of treatments for typhoid fever is ever-decreasing. In addition to IncHI1-type plasmids, Salmonella genomic island (SGI) 11 has been reported to carry AMR genes. Although reports suggest a recent reduction in multidrug resistance (MDR) in the Indian subcontinent, the corresponding genomic changes in the background are unknown. Results Here, we assembled and annotated complete closed chromosomes and plasmids for 73 S. Typhi isolates using short-length Illumina reads. S. Typhi had an open pan-genome, and the core genome was smaller than previously reported. Considering AMR genes, we identified five variants of SGI11, including the previously reported reference sequence. Five plasmids were identified, including the new plasmids pK91 and pK43; pK43and pHCM2 were not related to AMR. The pHCM1, pPRJEB21992 and pK91 plasmids carried AMR genes and, along with the SGI11 variants, were responsible for resistance phenotypes. pK91 also contained qnr genes, conferred high ciprofloxacin resistance and was related to the H58-sublineage Bdq, which shows the same phenotype. The presence of plasmids (pHCM1 and pK91) and SGI11 were linked to two H58-lineages, Ia and Bd. Loss of plasmids and integration of resistance genes in genomic islands could contribute to the fitness advantage of lineage Ia isolates. Conclusions Such events may explain why lineage Ia is globally widespread, while the Bd lineage is locally restricted. Further studies are required to understand how these S. Typhi AMR elements spread and generate new variants. Preventive measures such as vaccination programs should also be considered in endemic countries; such initiatives could potentially reduce the spread of AMR. Electronic supplementary material The online version of this article (10.1186/s12864-019-5916-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas Costa Barroso Lima
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil.,Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Arif M Tanmoy
- Department of Medical Microbiology & Infectious Diseases, Erasmus MC, Rotterdam, the Netherlands.,Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France.,Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh
| | - Emilie Westeel
- Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France
| | | | - Alain Rajoharison
- Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France
| | - Maksuda Islam
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh
| | - Hubert P Endtz
- Department of Medical Microbiology & Infectious Diseases, Erasmus MC, Rotterdam, the Netherlands.,Fondation Mérieux - Laboratoire des Pathogènes Emergents, Lyon, France
| | - Samir K Saha
- Child Health Research Foundation, Department of Microbiology, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh.,Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, 1207, Bangladesh
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Muthuirulandi Sethuvel DP, Devanga Ragupathi NK, Bakthavatchalam YD, Vijayakumar S, Varghese R, Shankar C, Jacob JJ, Vasudevan K, Elangovan D, Balaji V. Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens. Indian J Med Microbiol 2019; 37:147-162. [PMID: 31745014 DOI: 10.4103/ijmm.ijmm_19_396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.
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Affiliation(s)
| | | | | | - Saranya Vijayakumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Divyaa Elangovan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Veeraraghavan Balaji
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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Araújo CL, Alves J, Nogueira W, Pereira LC, Gomide AC, Ramos R, Azevedo V, Silva A, Folador A. Prediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology. Gene 2019; 702:36-45. [PMID: 30928361 DOI: 10.1016/j.gene.2019.03.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/15/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Corynebacterium pseudotuberculosis is the etiologic agent of veterinary relevance diseases, such as caseous lymphadenitis, affecting different animal species causing damage to the global agribusiness. So far, there are no completely effective treatment methods to overcome the impacts caused by this pathogen. Several genomes of the species are deposited on public databases, allowing the execution of studies related to the pan-genomic approach. In this study, we used an integrated in silico workflow to prospect novel putative targets using the core genome, a set of shared genes among 65 C. pseudotuberculosis strains. Subsequently, through RNA-Seq data of the same abiotic stresses in two strains, we selected only induced genes to compose the reverse vaccinology workflow based in two different strategies. Our results predicted six probable antigens in both analysis, which indicates that they have a strong potential to be used in further studies as vaccine targets against this bacterium.
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Affiliation(s)
- Carlos Leonardo Araújo
- Laboratory of Genomics and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Jorianne Alves
- Laboratory of Genomics and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Wylerson Nogueira
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lino César Pereira
- Laboratory of Genomics and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Anne Cybelle Gomide
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Rommel Ramos
- Laboratory of Genomics and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Vasco Azevedo
- Department of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Laboratory of Genomics and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil
| | - Adriana Folador
- Laboratory of Genomics and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil.
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Shelyakin PV, Bochkareva OO, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow. BMC Evol Biol 2019; 19:83. [PMID: 30917781 PMCID: PMC6437910 DOI: 10.1186/s12862-019-1403-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Background The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae. Results Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions. The total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity. Mapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism. Conclusions Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines. Electronic supplementary material The online version of this article (10.1186/s12862-019-1403-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pavel V Shelyakin
- Vavilov Institute of General Genetics Russian Academy of Sciences, Gubkina str. 3, Moscow, 119991, Russia. .,Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia. .,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
| | - Olga O Bochkareva
- Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Anna A Karan
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail S Gelfand
- Kharkevich Institute for Information Transmission Problems, 19, Bolshoy Karetny per., Moscow, 127051, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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34
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Concepts of the last eukaryotic common ancestor. Nat Ecol Evol 2019; 3:338-344. [DOI: 10.1038/s41559-019-0796-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/03/2019] [Indexed: 12/27/2022]
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Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, Boorgula MP, Chavan S, Vergara C, Ortega VE, Levin AM, Eng C, Yazdanbakhsh M, Wilson JG, Marrugo J, Lange LA, Williams LK, Watson H, Ware LB, Olopade CO, Olopade O, Oliveira RR, Ober C, Nicolae DL, Meyers DA, Mayorga A, Knight-Madden J, Hartert T, Hansel NN, Foreman MG, Ford JG, Faruque MU, Dunston GM, Caraballo L, Burchard EG, Bleecker ER, Araujo MI, Herrera-Paz EF, Campbell M, Foster C, Taub MA, Beaty TH, Ruczinski I, Mathias RA, Barnes KC, Salzberg SL. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nat Genet 2019; 51:30-35. [PMID: 30455414 PMCID: PMC6309586 DOI: 10.1038/s41588-018-0273-y] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 10/08/2018] [Indexed: 12/11/2022]
Abstract
We used a deeply sequenced dataset of 910 individuals, all of African descent, to construct a set of DNA sequences that is present in these individuals but missing from the reference human genome. We aligned 1.19 trillion reads from the 910 individuals to the reference genome (GRCh38), collected all reads that failed to align, and assembled these reads into contiguous sequences (contigs). We then compared all contigs to one another to identify a set of unique sequences representing regions of the African pan-genome missing from the reference genome. Our analysis revealed 296,485,284 bp in 125,715 distinct contigs present in the populations of African descent, demonstrating that the African pan-genome contains ~10% more DNA than the current human reference genome. Although the functional significance of nearly all of this sequence is unknown, 387 of the novel contigs fall within 315 distinct protein-coding genes, and the rest appear to be intergenic.
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Affiliation(s)
- Rachel M Sherman
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Juliet Forman
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Departments of Computer Science, Biology, and Mathematics, Harvey Mudd College, Claremont, CA, USA
| | - Valentin Antonescu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Nicholas Rafaels
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | | | - Sameer Chavan
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | | | - Victor E Ortega
- Department of Internal Medicine, Section on Pulmonary, Critical Care, Allergy and Immunologic Diseases, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Maria Yazdanbakhsh
- Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Javier Marrugo
- Institute for Immunological Research, Universidad de Cartagena, Cartagena, Colombia
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - L Keoki Williams
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Harold Watson
- Faculty of Medical Sciences Cave Hill Campus, The University of the West Indies, Bridgetown, Barbados
| | - Lorraine B Ware
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Christopher O Olopade
- Department of Medicine and Center for Global Health, University of Chicago, Chicago, IL, USA
| | | | - Ricardo R Oliveira
- Laboratório de Patologia Experimental, Centro de Pesquisas Gonçalo Moniz, Salvador, Brazil
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Dan L Nicolae
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Deborah A Meyers
- Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Alvaro Mayorga
- Centro de Neumologia y Alergias, San Pedro Sula, Honduras
| | - Jennifer Knight-Madden
- Caribbean Institute for Health Research, The University of the West Indies, Kingston, Jamaica
| | - Tina Hartert
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Nadia N Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Marilyn G Foreman
- Pulmonary and Critical Care Medicine, Morehouse School of Medicine, Atlanta, GA, USA
| | - Jean G Ford
- Department of Medicine, Einstein Medical Center, Philadelphia, PA, USA
| | - Mezbah U Faruque
- National Human Genome Center, Howard University College of Medicine, Washington, DC, USA
| | - Georgia M Dunston
- Department of Microbiology, Howard University College of Medicine, Washington, DC, USA
| | - Luis Caraballo
- Institute for Immunological Research, Universidad de Cartagena, Cartagena, Colombia
| | - Esteban G Burchard
- Departments of Bioengineering & Therapeutic Sciences and Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Eugene R Bleecker
- Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Maria I Araujo
- Immunology Service, Universidade Federal da Bahia, Salvador, Brazil
| | - Edwin F Herrera-Paz
- Facultad de Ciencias Médicas, Universidad Tecnológica Centroamericana (UNITEC), Tegucigalpa, Honduras
| | - Monica Campbell
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Cassandra Foster
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C Barnes
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
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Bochkareva OO, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics 2018; 19:965. [PMID: 30587126 PMCID: PMC6307245 DOI: 10.1186/s12864-018-5245-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 11/14/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes. RESULTS We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group. CONCLUSIONS This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.
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Affiliation(s)
- Olga O. Bochkareva
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Elena V. Moroz
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
| | - Iakov I. Davydov
- Department of Ecology and Evolution & Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mikhail S. Gelfand
- Kharkevich Institute for Information Transmission Problems, Moscow, Russia
- Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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Argemi X, Matelska D, Ginalski K, Riegel P, Hansmann Y, Bloom J, Pestel-Caron M, Dahyot S, Lebeurre J, Prévost G. Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer. BMC Genomics 2018; 19:621. [PMID: 30126366 PMCID: PMC6102843 DOI: 10.1186/s12864-018-4978-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci. Results We demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system. Conclusion We show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci. Electronic supplementary material The online version of this article (10.1186/s12864-018-4978-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xavier Argemi
- Service des Maladies Infectieuses et Tropicales, Hôpitaux Universitaires, Nouvel Hôpital Civil, 1 Place de l'Hôpital, 67000, Strasbourg, France. .,Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France.
| | - Dorota Matelska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Philippe Riegel
- Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
| | - Yves Hansmann
- Service des Maladies Infectieuses et Tropicales, Hôpitaux Universitaires, Nouvel Hôpital Civil, 1 Place de l'Hôpital, 67000, Strasbourg, France.,Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
| | - Jochen Bloom
- Bioinformatics & Systems Biology, Justus-Liebig-University Gießen, 35392, Gießen, Germany
| | - Martine Pestel-Caron
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Sandrine Dahyot
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Jérémie Lebeurre
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Gilles Prévost
- Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
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38
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Das S, Pettersson BMF, Behra PRK, Mallick A, Cheramie M, Ramesh M, Shirreff L, DuCote T, Dasgupta S, Ennis DG, Kirsebom LA. Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing. Sci Rep 2018; 8:12040. [PMID: 30104693 PMCID: PMC6089878 DOI: 10.1038/s41598-018-30152-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium marinum is the causative agent for the tuberculosis-like disease mycobacteriosis in fish and skin lesions in humans. Ubiquitous in its geographical distribution, M. marinum is known to occupy diverse fish as hosts. However, information about its genomic diversity is limited. Here, we provide the genome sequences for 15 M. marinum strains isolated from infected humans and fish. Comparative genomic analysis of these and four available genomes of the M. marinum strains M, E11, MB2 and Europe reveal high genomic diversity among the strains, leading to the conclusion that M. marinum should be divided into two different clusters, the "M"- and the "Aronson"-type. We suggest that these two clusters should be considered to represent two M. marinum subspecies. Our data also show that the M. marinum pan-genome for both groups is open and expanding and we provide data showing high number of mutational hotspots in M. marinum relative to other mycobacteria such as Mycobacterium tuberculosis. This high genomic diversity might be related to the ability of M. marinum to occupy different ecological niches.
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Affiliation(s)
- Sarbashis Das
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24, Uppsala, Sweden
| | - Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24, Uppsala, Sweden
| | - Amrita Mallick
- Department of Biology, University of Louisiana, Lafayette, Louisiana, USA
| | - Martin Cheramie
- Department of Biology, University of Louisiana, Lafayette, Louisiana, USA
| | - Malavika Ramesh
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24, Uppsala, Sweden
| | - Lisa Shirreff
- Department of Biology, University of Louisiana, Lafayette, Louisiana, USA
| | - Tanner DuCote
- Department of Biology, University of Louisiana, Lafayette, Louisiana, USA
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24, Uppsala, Sweden
| | - Don G Ennis
- Department of Biology, University of Louisiana, Lafayette, Louisiana, USA
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Box 596, Biomedical Centre, SE-751 24, Uppsala, Sweden.
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39
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Mahfouz N, Caucci S, Achatz E, Semmler T, Guenther S, Berendonk TU, Schroeder M. High genomic diversity of multi-drug resistant wastewater Escherichia coli. Sci Rep 2018; 8:8928. [PMID: 29895899 PMCID: PMC5997705 DOI: 10.1038/s41598-018-27292-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
Wastewater treatment plants play an important role in the emergence of antibiotic resistance. They provide a hot spot for exchange of resistance within and between species. Here, we analyse and quantify the genomic diversity of the indicator Escherichia coli in a German wastewater treatment plant and we relate it to isolates’ antibiotic resistance. Our results show a surprisingly large pan-genome, which mirrors how rich an environment a treatment plant is. We link the genomic analysis to a phenotypic resistance screen and pinpoint genomic hot spots, which correlate with a resistance phenotype. Besides well-known resistance genes, this forward genomics approach generates many novel genes, which correlated with resistance and which are partly completely unknown. A surprising overall finding of our analyses is that we do not see any difference in resistance and pan genome size between isolates taken from the inflow of the treatment plant and from the outflow. This means that while treatment plants reduce the amount of bacteria released into the environment, they do not reduce the potential for antibiotic resistance of these bacteria.
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Affiliation(s)
| | - Serena Caucci
- Institute for Hydrobiology, TU Dresden, Dresden, Germany.,United Nations University Institute for Integrated Management of Material Fluxes and of Resources, Dresden, Germany
| | | | - Torsten Semmler
- Institute of Microbiology und Epizootics, FU, Berlin, Germany
| | - Sebastian Guenther
- Institute of Microbiology und Epizootics, FU, Berlin, Germany.,Institut für Pharmazie Pharmazeutische Biologie, Ernst-Moritz-Arndt-Universität Greifswald, Greifswald, Germany
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40
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Bost A, Martinson VG, Franzenburg S, Adair KL, Albasi A, Wells MT, Douglas AE. Functional variation in the gut microbiome of wild
Drosophila
populations. Mol Ecol 2018; 27:2834-2845. [DOI: 10.1111/mec.14728] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/27/2018] [Accepted: 05/14/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Alyssa Bost
- Department of Entomology Cornell University Ithaca New York
| | | | | | - Karen L. Adair
- Department of Entomology Cornell University Ithaca New York
| | - Alice Albasi
- Department of Entomology Cornell University Ithaca New York
| | - Martin T. Wells
- Department of Biological Statistics and Computational Biology Cornell University Ithaca New York
| | - Angela E. Douglas
- Department of Entomology Cornell University Ithaca New York
- Department of Molecular Biology and Genetics Cornell University Ithaca New York
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41
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D'Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat Prod Rep 2018; 35:455-488. [PMID: 29799048 DOI: 10.1039/c8np00009c] [Citation(s) in RCA: 248] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Literature covered: early 2000s to late 2017Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has shown that bacterial genotypes can significantly benefit from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight general principles that underlie the adaptive evolution of interconnected microbial metabolic networks as well as the evolutionary consequences that result for cells living in such communities.
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Affiliation(s)
- Glen D'Souza
- Department of Environmental Systems Sciences, ETH-Zürich, Zürich, Switzerland
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42
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Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol 2018; 45:131-139. [PMID: 29723841 DOI: 10.1016/j.mib.2018.04.004] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 04/15/2018] [Indexed: 11/18/2022]
Abstract
Klebsiella pneumoniae is an opportunistic bacterial pathogen known for its high frequency and diversity of antimicrobial resistance (AMR) genes. In addition to being a significant clinical problem in its own right, K. pneumoniae is the species within which several new AMR genes were first discovered before spreading to other pathogens (e.g. carbapenem-resistance genes KPC, OXA-48 and NDM-1). Whilst K. pneumoniae's contribution to the overall AMR crisis is impossible to quantify, current evidence suggests it has a wider ecological distribution, significantly more varied DNA composition, greater AMR gene diversity and a higher plasmid burden than other Gram negative opportunists. Hence we propose it plays a key role in disseminating AMR genes from environmental microbes to clinically important pathogens.
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Affiliation(s)
- Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia.
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, 30 Flemington Rd, Parkville, Victoria 3010, Australia
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43
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Fitzgerald DM, Smith C, Lapierre P, Wade JT. The evolutionary impact of intragenic FliA promoters in proteobacteria. Mol Microbiol 2018; 108:361-378. [PMID: 29476659 PMCID: PMC5943157 DOI: 10.1111/mmi.13941] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
In Escherichia coli, one sigma factor recognizes the majority of promoters, and six 'alternative' sigma factors recognize specific subsets of promoters. The alternative sigma factor FliA (σ28 ) recognizes promoters upstream of many flagellar genes. We previously showed that most E. coli FliA binding sites are located inside genes. However, it was unclear whether these intragenic binding sites represent active promoters. Here, we construct and assay transcriptional promoter-lacZ fusions for all 52 putative FliA promoters previously identified by ChIP-seq. These experiments, coupled with integrative analysis of published genome-scale transcriptional datasets, strongly suggest that most intragenic FliA binding sites are active promoters that transcribe highly unstable RNAs. Additionally, we show that widespread intragenic FliA-dependent transcription may be a conserved phenomenon, but that specific promoters are not themselves conserved. We conclude that intragenic FliA-dependent promoters and the resulting RNAs are unlikely to have important regulatory functions. Nonetheless, one intragenic FliA promoter is broadly conserved and constrains evolution of the overlapping protein-coding gene. Thus, our data indicate that intragenic regulatory elements can influence bacterial protein evolution and suggest that the impact of intragenic regulatory sequences on genome evolution should be considered more broadly.
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Affiliation(s)
- Devon M. Fitzgerald
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Carol Smith
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Joseph T. Wade
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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Huson DH, Albrecht B, Bağcı C, Bessarab I, Górska A, Jolic D, Williams RBH. MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. Biol Direct 2018; 13:6. [PMID: 29678199 PMCID: PMC5910613 DOI: 10.1186/s13062-018-0208-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/29/2018] [Indexed: 11/15/2022] Open
Abstract
Background There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. There is an increasing interest in using long reads in microbiome sequencing, and there is a need to adapt short read tools to long read datasets. Methods We describe a new LCA-based algorithm for taxonomic binning, and an interval-tree based algorithm for functional binning, that are explicitly designed for long reads and assembled contigs. We provide a new interactive tool for investigating the alignment of long reads against reference sequences. For taxonomic and functional binning, we propose to use LAST to compare long reads against the NCBI-nr protein reference database so as to obtain frame-shift aware alignments, and then to process the results using our new methods. Results All presented methods are implemented in the open source edition of MEGAN, and we refer to this new extension as MEGAN-LR (MEGAN long read). We evaluate the LAST+MEGAN-LR approach in a simulation study, and on a number of mock community datasets consisting of Nanopore reads, PacBio reads and assembled PacBio reads. We also illustrate the practical application on a Nanopore dataset that we sequenced from an anammox bio-rector community. Reviewers This article was reviewed by Nicola Segata together with Moreno Zolfo, Pete James Lockhart and Serghei Mangul. Conclusion This work extends the applicability of the widely-used metagenomic analysis software MEGAN to long reads. Our study suggests that the presented LAST+MEGAN-LR pipeline is sufficiently fast and accurate.
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Affiliation(s)
- Daniel H Huson
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany. .,Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
| | - Benjamin Albrecht
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany
| | - Caner Bağcı
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany.,IMPRS 'From Molecules to Organisms', Tübingen, Germany
| | - Irina Bessarab
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Anna Górska
- Center for Bioinformatics, University of Tübingen, Sand 14, Tübingen, 72076, Germany.,IMPRS 'From Molecules to Organisms', Tübingen, Germany
| | - Dino Jolic
- Max-Planck Institute for Developmental Biology, Tübingen, 72076, Germany.,IMPRS 'From Molecules to Organisms', Tübingen, Germany
| | - Rohan B H Williams
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
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Moldovan MA, Gelfand MS. Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp. Front Microbiol 2018; 9:428. [PMID: 29593678 PMCID: PMC5857598 DOI: 10.3389/fmicb.2018.00428] [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] [Received: 12/10/2017] [Accepted: 02/23/2018] [Indexed: 11/13/2022] Open
Abstract
The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria Prochlorococcus marinus should be divided into two species. As a control we have confirmed the paraphyletic origin of Yersinia pseudotuberculosis (with embedded, monophyletic Y. pestis) and Burkholderia pseudomallei (with B. mallei). We also demonstrate that by our definition and in accordance with recent studies Escherichia coli and Shigella spp. are one species.
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Affiliation(s)
- Mikhail A. Moldovan
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Mikhail S. Gelfand
- A.A.Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences (RAS), Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Faculty of Computer Science, Higher School of Economics, Moscow, Russia
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Costea PI, Coelho LP, Sunagawa S, Munch R, Huerta-Cepas J, Forslund K, Hildebrand F, Kushugulova A, Zeller G, Bork P. Subspecies in the global human gut microbiome. Mol Syst Biol 2017; 13:960. [PMID: 29242367 PMCID: PMC5740502 DOI: 10.15252/msb.20177589] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 11/24/2017] [Accepted: 11/29/2017] [Indexed: 02/06/2023] Open
Abstract
Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.
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Affiliation(s)
- Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Robin Munch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jaime Huerta-Cepas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kristoffer Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Falk Hildebrand
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
- Molecular Medicine Partnership Unit, Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
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Rantsiou K, Kathariou S, Winkler A, Skandamis P, Saint-Cyr MJ, Rouzeau-Szynalski K, Amézquita A. Next generation microbiological risk assessment: opportunities of whole genome sequencing (WGS) for foodborne pathogen surveillance, source tracking and risk assessment. Int J Food Microbiol 2017; 287:3-9. [PMID: 29246458 DOI: 10.1016/j.ijfoodmicro.2017.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/16/2017] [Accepted: 11/12/2017] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) of important foodborne pathogens is a technology under development, but is already employed in routine surveillance by public health agencies and is being increasingly exploited in tracing transmission routes and identifying contamination events (source tracking) that take place in the farm-to-fork continuum. Furthermore, data generated from WGS, complemented by other -omics data, have the potential to be integrated into and strengthen microbiological risk assessment. In this paper, we discuss the contribution of WGS in diverse areas important to food safety and public health. Additionally, an outlook of future WGS applications, which should contribute to our understanding of the ecology and physiology of foodborne microorganisms, is presented.
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Affiliation(s)
- Kalliopi Rantsiou
- Department of Agriculture, Forest and Food Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, Italy.
| | - Sophia Kathariou
- North Carolina State University, Department of Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, USA
| | - Annet Winkler
- Mondelez International, Kraft Foods R&D, Unterbiberger St. 15, D-81737 Munich, Germany
| | - Panos Skandamis
- Laboratory of Food Quality Control & Hygiene, Department of Food Science & Technology, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece
| | | | | | - Alejandro Amézquita
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
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Graves JL, Thomas M, Ewunkem JA. Antimicrobial Nanomaterials: Why Evolution Matters. NANOMATERIALS 2017; 7:nano7100283. [PMID: 28934114 PMCID: PMC5666448 DOI: 10.3390/nano7100283] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 01/25/2023]
Abstract
Due to the widespread occurrence of multidrug resistant microbes there is increasing interest in the use of novel nanostructured materials as antimicrobials. Specifically, metallic nanoparticles such as silver, copper, and gold have been deployed due to the multiple impacts they have on bacterial physiology. From this, many have concluded that such nanomaterials represent steep obstacles against the evolution of resistance. However, we have already shown that this view is fallacious. For this reason, the significance of our initial experiments are beginning to be recognized in the antimicrobial effects of nanomaterials literature. This recognition is not yet fully understood and here we further explain why nanomaterials research requires a more nuanced understanding of core microbial evolution principles.
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Affiliation(s)
- Joseph L Graves
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University and UNC Greensboro, Greensboro, NC 27401, USA.
| | - Misty Thomas
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA.
| | - Jude Akamu Ewunkem
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina A&T State University and UNC Greensboro, Greensboro, NC 27401, USA.
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Vincent AT, Charette SJ. Phylogenetic analysis of the fish pathogen Aeromonas salmonicida underlines the dichotomy between European and Canadian strains for the salmonicida subspecies. JOURNAL OF FISH DISEASES 2017; 40:1241-1247. [PMID: 28105757 DOI: 10.1111/jfd.12595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/06/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Affiliation(s)
- A T Vincent
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC, Canada
| | - S J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Quebec City, QC, Canada
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Quebec City, QC, Canada
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50
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Sloan A, Wang G, Cheng K. Traditional approaches versus mass spectrometry in bacterial identification and typing. Clin Chim Acta 2017; 473:180-185. [PMID: 28866114 DOI: 10.1016/j.cca.2017.08.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 01/09/2023]
Abstract
Biochemical methods such as metabolite testing and serotyping are traditionally used in clinical microbiology laboratories to identify and categorize microorganisms. Due to the large variety of bacteria, identifying representative metabolites is tedious, while raising high-quality antisera or antibodies unique to specific biomarkers used in serotyping is very challenging, sometimes even impossible. Although serotyping is a certified approach for differentiating bacteria such as E. coli and Salmonella at the subspecies level, the method is tedious, laborious, and not practical during an infectious disease outbreak. Mass spectrometry (MS) platforms, especially matrix assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF-MS), have recently become popular in the field of bacterial identification due to their fast speed and low cost. In the past few years, we have used liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based approaches to solve various problems hindering serotyping and have overcome some insufficiencies of the MALDI-TOF-MS platform. The current article aims to review the characteristics, advantages, and disadvantages of MS-based platforms over traditional approaches in bacterial identification and categorization.
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Affiliation(s)
- Angela Sloan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Gehua Wang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Keding Cheng
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Human Anatomy and Cell Sciences, Faculty of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada.
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