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Abdelhadi AA, Elarabi NI, Ibrahim SM, Abdel-Maksoud MA, Abdelhaleem HAR, Almutairi S, Malik A, Kiani BH, Henawy AR, Halema AA. Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain. Funct Integr Genomics 2024; 24:174. [PMID: 39320439 DOI: 10.1007/s10142-024-01441-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/28/2024] [Accepted: 09/03/2024] [Indexed: 09/26/2024]
Abstract
Many organisms have adapted to survive in environments with high levels of arsenic (As), a naturally occurring metalloid with various oxidation states and a common element in human activities. These organisms employ diverse mechanisms to resist the harmful effects of arsenic compounds. Ten arsenic-resistant bacteria were isolated from contaminated wastewater in this study. The most efficient bacterial isolate able to resist 15,000 ppm Na2HAsO4·7H2O was identified using the 16S rRNA gene and whole genome analysis as Enterobacter cloacae FACU. The arsenic E. cloacae FACU biosorption capability was analyzed. To further unravel the genetic determinants of As stress resistance, the whole genome sequence of E. cloacae FACU was performed. The FACU complete genome sequence consists of one chromosome (5.7 Mb) and two plasmids, pENCL 1 and pENCL 2 (755,058 and 1155666 bp, respectively). 7152 CDSs were identified in the E. cloacae FACU genome. The genome consists of 130 genes for tRNA and 21 for rRNAs. The average G + C content was found to be 54%. Sequencing analysis annotated 58 genes related to resistance to many heavy metals, including 16 genes involved in arsenic efflux transporter and arsenic reduction (five arsRDABC genes) and 42 genes related to lead, zinc, mercury, nickel, silver, copper, cadmium and chromium in FACU. Scanning electron microscopy (SEM) confirmed the difference between the morphological responses of the As-treated FACU compared to the control strain. The study highlights the genes involved in the mechanism of As stress resistance, metabolic pathways, and potential activity of E. cloacae FACU at the genetic level.
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Affiliation(s)
- Abdelhadi A Abdelhadi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Nagwa I Elarabi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Saifeldeen M Ibrahim
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
- Bioinformatics Department, Agricultural Genetic Engineering Research Institute, ARC, Giza, Egypt
| | - Mostafa A Abdel-Maksoud
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Heba A R Abdelhaleem
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th October City, Egypt
| | - Saeedah Almutairi
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Bushra Hafeez Kiani
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachuesetts, 01609, USA
| | - Ahmed R Henawy
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Asmaa A Halema
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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2
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Stemwedel K, Haase N, Christ S, Bogdanova N, Rudorf S. Synonymous rpsH variants: the common denominator in Escherichia coli adapting to ionizing radiation. NAR Genom Bioinform 2024; 6:lqae110. [PMID: 39184377 PMCID: PMC11344242 DOI: 10.1093/nargab/lqae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/18/2024] [Accepted: 08/08/2024] [Indexed: 08/27/2024] Open
Abstract
Ionizing radiation (IR) in high doses is generally lethal to most organisms. Investigating mechanisms of radiation resistance is crucial for gaining insights into the underlying cellular responses and understanding the damaging effects of IR. In this study, we conducted a comprehensive analysis of sequencing data from an evolutionary experiment aimed at understanding the genetic adaptations to ionizing radiation in Escherichia coli. By including previously neglected synonymous mutations, we identified the rpsH c.294T > G variant, which emerged in all 17 examined isolates across four subpopulations. The identified variant is a synonymous mutation affecting the 30S ribosomal protein S8, and consistently exhibited high detection and low allele frequencies in all subpopulations. This variant, along with two additional rpsH variants, potentially influences translational control of the ribosomal spc operon. The early emergence and stability of these variants suggest their role in adapting to environmental stress, possibly contributing to radiation resistance. Our findings shed light on the dynamics of ribosomal variants during the evolutionary process and their potential role in stress adaptation, providing valuable implications for understanding clinical radiation sensitivity and improving radiotherapy.
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Affiliation(s)
- Katharina Stemwedel
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
| | - Nadin Haase
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
| | - Simon Christ
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
| | | | - Sophia Rudorf
- Leibniz University Hannover, Institute of Cell Biology and Biophysics, Hannover, 30167, Germany
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Jiang C, Zhao G, Wang H, Zheng W, Zhang R, Wang L, Zheng Z. Comparative genomics analysis and transposon mutagenesis provides new insights into high menaquinone-7 biosynthetic potential of Bacillus subtilis natto. Gene 2024; 907:148264. [PMID: 38346457 DOI: 10.1016/j.gene.2024.148264] [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: 10/06/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
This research combined Whole-Genome sequencing, intraspecific comparative genomics and transposon mutagenesis to investigate the menaquinone-7 (MK-7) synthesis potential in Bacillus subtilis natto. First, Whole-Genome sequencing showed that Bacillus subtilis natto BN-P15-11-1 contains one single circular chromosome in size of 3,982,436 bp with a GC content of 43.85 %, harboring 4,053 predicted coding genes. Next, the comparative genomics analysis among strain BN-P15-11-1 with model Bacillus subtilis 168 and four typical Bacillus subtilis natto strains proves that the closer evolutionary relationship Bacillus subtilis natto BN-P15-11-1 and Bacillus subtilis 168 both exhibit strong biosynthetic potential. To further dig for MK-7 biosynthesis latent capacity of BN-P15-11-1, we constructed a mutant library using transposons and a high throughput screening method using microplates. We obtained a YqgQ deficient high MK-7 yield strain F4 with a yield 3.02 times that of the parent strain. Experiments also showed that the high yield mutants had defects in different transcription and translation regulatory factor genes, indicating that regulatory factor defects may affect the biosynthesis and accumulation of MK-7 by altering the overall metabolic level. The findings of this study will provide more novel insights on the precise identification and rational utilization of the Bacillus subtilis subspecies for biosynthesis latent capacity.
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Affiliation(s)
- Chunxu Jiang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Genhai Zhao
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Han Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Wenqian Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China; University of Science and Technology of China, Hefei, Anhui, PR China
| | - Rui Zhang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Li Wang
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Zhiming Zheng
- Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
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4
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Senavirathna I, Jayasundara D, Warnasekara J, Matthias MA, Vinetz JM, Agampodi S. Complete genome sequences of twelve strains of Leptospira interrogans isolated from humans in Sri Lanka. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105462. [PMID: 37301334 DOI: 10.1016/j.meegid.2023.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
Leptospirosis, a major zoonotic disease caused by pathogenic Leptospira spp. is recognized globally as an emerging zoonotic disease. Whole-genome sequencing reveals hidden messages about Leptospira's pathogenesis. We used Single Molecule Real-Time (SMRT) sequencing to obtain complete genome sequences of twelve L. interrogans isolates from febrile patients from Sri Lanka for a comparative whole genome sequencing study. The sequence data generated 12 genomes with a coverage greater than X600 with sizes ranging from 4.62 Mb to 5.16 Mb, and a G + C content ranging from 35.00% to 35.42%. The total number of coding sequences predicted by the NCBI (National Center for Biotechnology Information) genome assembly platform ranged from 3845 to 4621 for the twelve strains. Leptospira serogroup with similar-sized LPS biosynthetic loci that belonged to the same clade had a close relationship in the phylogenetic analysis. Nonetheless, variations in the genes encoding sugar biosynthesis were found in the serovar determinant region (rfb locus). Type I and Type III CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems were found in all of the strains. Genome BLAST Distance Phylogeny of these sequences allowed for detailed genomic strain typing. These findings may help us better understand the pathogenesis, develop a tools for early diagnosis, comparative genomic analysis and evolution of Leptospira.
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Affiliation(s)
- Indika Senavirathna
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka; Department of Biochemistry, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka.
| | - Dinesha Jayasundara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka; Department of Microbiology, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka
| | - Janith Warnasekara
- Leptospirosis Research Laboratory, Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka; Department of Community Medicine, Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Sri Lanka
| | - Michael A Matthias
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Joseph M Vinetz
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Suneth Agampodi
- Section of Infectious Disease, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA; International Vaccine Institute, Seoul, Republic of Korea
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Kanteh A, Jallow HS, Manneh J, Sanyang B, Kujabi MA, Ndure SL, Jarju S, Sey AP, Damilare K D, Bah Y, Sambou S, Jarju G, Manjang B, Jagne A, Bittaye SO, Bittaye M, Forrest K, Tiruneh DA, Samateh AL, Jagne S, Hué S, Mohammed N, Amambua-Ngwa A, Kampmann B, D'Alessandro U, de Silva TI, Roca A, Sesay AK. Genomic epidemiology of SARS-CoV-2 infections in The Gambia: an analysis of routinely collected surveillance data between March, 2020, and January, 2022. Lancet Glob Health 2023; 11:e414-e424. [PMID: 36796985 PMCID: PMC9928486 DOI: 10.1016/s2214-109x(22)00553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 11/30/2022] [Accepted: 12/14/2022] [Indexed: 02/16/2023]
Abstract
BACKGROUND COVID-19, caused by SARS-CoV-2, is one of the deadliest pandemics of the past 100 years. Genomic sequencing has an important role in monitoring of the evolution of the virus, including the detection of new viral variants. We aimed to describe the genomic epidemiology of SARS-CoV-2 infections in The Gambia. METHODS Nasopharyngeal or oropharyngeal swabs collected from people with suspected cases of COVID-19 and international travellers were tested for SARS-CoV-2 with standard RT-PCR methods. SARS-CoV-2-positive samples were sequenced according to standard library preparation and sequencing protocols. Bioinformatic analysis was done using ARTIC pipelines and Pangolin was used to assign lineages. To construct phylogenetic trees, sequences were first stratified into different COVID-19 waves (waves 1-4) and aligned. Clustering analysis was done and phylogenetic trees constructed. FINDINGS Between March, 2020, and January, 2022, 11 911 confirmed cases of COVID-19 were recorded in The Gambia, and 1638 SARS-CoV-2 genomes were sequenced. Cases were broadly distributed into four waves, with more cases during the waves that coincided with the rainy season (July-October). Each wave occurred after the introduction of new viral variants or lineages, or both, generally those already established in Europe or in other African countries. Local transmission was higher during the first and third waves (ie, those that corresponded with the rainy season), in which the B.1.416 lineage and delta (AY.34.1) were dominant, respectively. The second wave was driven by the alpha and eta variants and the B.1.1.420 lineage. The fourth wave was driven by the omicron variant and was predominantly associated with the BA.1.1 lineage. INTERPRETATION More cases of SARS-CoV-2 infection were recorded in The Gambia during peaks of the pandemic that coincided with the rainy season, in line with transmission patterns for other respiratory viruses. The introduction of new lineages or variants preceded epidemic waves, highlighting the importance of implementing well structured genomic surveillance at a national level to detect and monitor emerging and circulating variants. FUNDING Medical Research Unit The Gambia at London School of Hygiene & Tropical Medicine, UK Research and Innovation, WHO.
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Affiliation(s)
- Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Haruna S Jallow
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Jarra Manneh
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Bakary Sanyang
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Mariama A Kujabi
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sainabou Laye Ndure
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alhagie Papa Sey
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Dabiri Damilare K
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Yaya Bah
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | | | | | | | | | - Karen Forrest
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | | | | | - Sheriffo Jagne
- National Public Health Reference Laboratory, Ministry of Health, Banjul, The Gambia
| | - Stéphane Hué
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Nuredin Mohammed
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Thushan I de Silva
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Anna Roca
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Abdul Karim Sesay
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia.
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Gunasekara CWR, Rajapaksha LGTG, Wimalasena SHMP. Comparative analysis unravels genetic recombination events of Vibrio parahaemolyticus recA gene. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 107:105396. [PMID: 36549419 DOI: 10.1016/j.meegid.2022.105396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/03/2022] [Accepted: 12/18/2022] [Indexed: 12/23/2022]
Abstract
Vibrio parahaemolyticus is a gram-negative bacterium capable of causing diseases in humans and aquatic animals. The global relationships among V. parahaemolyticus genomes have been studied using multilocus sequence typing (MLST). Recently, the MLST gene recA has shown difficulties in amplification and/or a larger PCR fragment for some V. parahaemolyticus genomes due to genetic recombination. We aimed to investigate these recombination events of recA gene by analyzing 500 publicly available whole genomes from the NCBI database. The genomes with untypable recA genes were separated using BIGSdb and CGEMLST 2.0 servers, followed by annotation with RAST and NCBI pipelines. Moreover, the variable nature of V. parahaemolyticus was investigated by wgMLST analysis. The hypothetical proteins in recombinant regions were analyzed with VCIMPred tool. In the results, 3 genomes were detected with recA gene recombination, in which 2 were associated with phages and 1 to an AHPND causing strain. All 3 recombinant regions had a G + C content of 39%-40% with 15-30 ORFs, including a newly incorporated recA gene. These acquired recA genes were closely related to 3 different genera namely Aliivibrio, Photobacterium, and Vibrio. The wgMLST analysis indicated genetic recombination events occur independently among V. parahaemolyticus on a global scale. The in silico analysis revealed 4 hypothetical proteins associated with virulence factors in recombinant regions. The present study confirms, recombination events of V. parahaemolyticus recA gene, are diverse and may have an impact on the evolutionary process. Moreover, understanding these genetic recombination events of the recA gene is necessary to determine their STs and, therefore assessing epidemiological relationships.
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Affiliation(s)
- C W R Gunasekara
- Division of Fisheries Life Sciences, College of Fisheries Sciences, Pukyong National University, Busan 48513, South Korea.
| | - L G T G Rajapaksha
- Veterinary Medical Center and College of Veterinary Medicine, Jeonbuk National University, 54596 Jeonju, South Korea
| | - S H M P Wimalasena
- Veterinary Medical Center and College of Veterinary Medicine, Jeonbuk National University, 54596 Jeonju, South Korea
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Simple and structured model to build sequencing capacity in west Africa. Lancet Glob Health 2022; 10:e1240-e1241. [PMID: 35961343 PMCID: PMC9363037 DOI: 10.1016/s2214-109x(22)00319-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022]
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RoyChowdhury M, Sternhagen J, Xin Y, Lou B, Li X, Li C. Evolution of pathogenicity in obligate fungal pathogens and allied genera. PeerJ 2022; 10:e13794. [PMID: 36042858 PMCID: PMC9420410 DOI: 10.7717/peerj.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 07/06/2022] [Indexed: 01/17/2023] Open
Abstract
Obligate fungal pathogens (ascomycetes and basidiomycetes) and oomycetes are known to cause diseases in cereal crop plants. They feed on living cells and most of them have learned to bypass the host immune machinery. This paper discusses some of the factors that are associated with pathogenicity drawing examples from ascomycetes, basidiomycetes and oomycetes, with respect to their manifestation in crop plants. The comparisons have revealed a striking similarity in the three groups suggesting convergent pathways that have arisen from three lineages independently leading to an obligate lifestyle. This review has been written with the intent, that new information on adaptation strategies of biotrophs, modifications in pathogenicity strategies and population dynamics will improve current strategies for breeding with stable resistance.
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Affiliation(s)
- Moytri RoyChowdhury
- Infectious Diseases Program, California Department of Public Health, Richmond, California, United States of America
| | - Jake Sternhagen
- Riverside School of Medicine, University of California, Riverside, Riverside, CA, United States of America
| | - Ya Xin
- Hangzhou Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Binghai Lou
- Guangxi Academy of Specialty Crops, Guilin, Guangxi, P.R. China
| | - Xiaobai Li
- Zhejiang Academy of Agricultural Sciences, Hangzhou, P.R. China
| | - Chunnan Li
- Hangzhou Academy of Agricultural Sciences, Hangzhou, P.R. China
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9
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Damage-Induced Mutation Clustering in Gram-Positive Bacteria: Preliminary Data. Symmetry (Basel) 2022. [DOI: 10.3390/sym14071431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The phenomenon of a nonrandom distribution of mutations in a genome has been observed for many years. In fact, recent findings have indicated the presence of mutation clusters in different biological systems, including chemically treated yeast, transgenic mice, and human cancer cells. Until now, an asymmetrical distribution of mutations was only described in a single bacterial species. Here, we used ethyl methanesulfonate mutagenesis and a whole-genome sequencing approach to determine if this phenomenon is universal and not confined to Gram-negative bacteria. The Gram-positive bacterium Bacillus subtilis was selected for ethyl methanesulfonate treatment, followed by the next-generation sequencing of several mutagenized B. subtilis genomes. A nonrandom distribution of mutations was observed. This pilot study with a limited number of sequenced clones may indicate not only the universality of the phenomenon of mutation clusters but also the effectiveness of the use of a whole-genome sequencing approach in studying this phenomenon.
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10
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Foster-Nyarko E, Pallen MJ. The microbial ecology of Escherichia coli in the vertebrate gut. FEMS Microbiol Rev 2022; 46:fuac008. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's 'rock star', driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance-including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
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11
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Genomic evolution and adaptation of arthropod-associated Rickettsia. Sci Rep 2022; 12:3807. [PMID: 35264613 PMCID: PMC8907221 DOI: 10.1038/s41598-022-07725-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
Rickettsia species are endosymbionts hosted by arthropods and are known to cause mild to fatal diseases in humans. Here, we analyse the evolution and diversity of 34 Rickettsia species using a pangenomic meta-analysis (80 genomes/41 plasmids). Phylogenomic trees showed that Rickettsia spp. diverged into two Spotted Fever groups, a Typhus group, a Canadensis group and a Bellii group, and may have inherited their plasmids from an ancestral plasmid that persisted in some strains or may have been lost by others. The results suggested that the ancestors of Rickettsia spp. might have infected Acari and/or Insecta and probably diverged by persisting inside and/or switching hosts. Pangenomic analysis revealed that the Rickettsia genus evolved through a strong interplay between genome degradation/reduction and/or expansion leading to possible distinct adaptive trajectories. The genus mainly shared evolutionary relationships with α-proteobacteria, and also with γ/β/δ-proteobacteria, cytophagia, actinobacteria, cyanobacteria, chlamydiia and viruses, suggesting lateral exchanges of several critical genes. These evolutionary processes have probably been orchestrated by an abundance of mobile genetic elements, especially in the Spotted Fever and Bellii groups. In this study, we provided a global evolutionary genomic view of the intracellular Rickettsia that may help our understanding of their diversity, adaptation and fitness.
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12
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Gunasekara AWACWR, Rajapaksha LGTG, Tung TL. Whole-genome sequence analysis through online web interfaces: a review. Genomics Inform 2022; 20:e3. [PMID: 35399002 PMCID: PMC9002002 DOI: 10.5808/gi.20038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/01/2022] [Indexed: 11/20/2022] Open
Abstract
The recent development of whole-genome sequencing technologies paved the way for understanding the genomes of microorganisms. Every whole-genome sequencing (WGS) project requires a considerable cost and a massive effort to address the questions at hand. The final step of WGS is data analysis. The analysis of whole-genome sequence is dependent on highly sophisticated bioinformatics tools that the research personal have to buy. However, many laboratories and research institutions do not have the bioinformatics capabilities to analyze the genomic data and therefore, are unable to take maximum advantage of whole-genome sequencing. In this aspect, this study provides a guide for research personals on a set of bioinformatics tools available online that can be used to analyze whole-genome sequence data of bacterial genomes. The web interfaces described here have many advantages and, in most cases exempting the need for costly analysis tools and intensive computing resources.
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Affiliation(s)
- A W A C W R Gunasekara
- Veterinary Medical Center and College of Veterinary Medicine, Jeonbuk National University, Jeonju 54596, Korea
| | - L G T G Rajapaksha
- Veterinary Medical Center and College of Veterinary Medicine, Jeonbuk National University, Jeonju 54596, Korea
| | - T L Tung
- Department of Botany, Dagon University, 11422 Yangon, Myanmar
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13
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Rodriguez AM, Urrea DA, Prada CF. Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin. PeerJ 2021; 9:e12272. [PMID: 34900406 PMCID: PMC8628625 DOI: 10.7717/peerj.12272] [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: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 01/18/2023] Open
Abstract
Background Helicobacter pylori is a pathogenic bacteria that colonize the gastrointestinal tract from human stomachs and causes diseases including gastritis, peptic ulcers, gastric lymphoma (MALT), and gastric cancer, with a higher prevalence in developing countries. Its high genetic diversity among strains is caused by a high mutation rate, observing virulence factors (VFs) variations in different geographic lineages. This study aimed to postulate the genetic variability associated with virulence factors present in the Helicobacter pylori strains, to identify the relationship of these genes with their phylogeographic origin. Methods The complete genomes of 135 strains available in NCBI, from different population origins, were analyzed using bioinformatics tools, identifying a high rate; as well as reorganization events in 87 virulence factor genes, divided into seven functional groups, to determine changes in position, number of copies, nucleotide identity and size, contrasting them with their geographical lineage and pathogenic phenotype. Results Bioinformatics analyses show a high rate of gene annotation errors in VF. Analysis of genetic variability of VFs shown that there is not a direct relationship between the reorganization and geographic lineage. However, regarding the pathogenic phenotype demonstrated in the analysis of many copies, size, and similarity when dividing the strains that possess and not the cag pathogenicity island (cagPAI), having a higher risk of developing gastritis and peptic ulcer was evidenced. Our data has shown that the analysis of the overall genetic variability of all VFs present in each strain of H. pylori is key information in understanding its pathogenic behavior.
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Affiliation(s)
- Aura M Rodriguez
- Grupo de Investigación de Biología y Ecología de Artrópodos. Facultad de Ciencias, Universidad del Tolima, Ibague, Tolima, Colombia
| | - Daniel A Urrea
- Laboratorio de Investigaciones en Parasitología Tropical. Facultad de Ciencias, Universidad del Tolima, Ibague, Tolima, Colombia
| | - Carlos F Prada
- Grupo de Investigación de Biología y Ecología de Artrópodos. Facultad de Ciencias, Universidad del Tolima, Ibague, Tolima, Colombia
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Edwards DJ, Duchene S, Pope B, Holt KE. SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. Microb Genom 2021; 7:000694. [PMID: 34874243 PMCID: PMC8767352 DOI: 10.1099/mgen.0.000694] [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] [Indexed: 01/18/2023] Open
Abstract
Homoplasic SNPs are considered important signatures of strong (positive) selective pressure, and hence of adaptive evolution for clinically relevant traits such as antibiotic resistance and virulence. Here we present a new tool, SNPPar, for efficient detection and analysis of homoplasic SNPs from large whole genome sequencing datasets (>1000 isolates and/or >100 000 SNPs). SNPPar takes as input an SNP alignment, tree and annotated reference genome, and uses a combination of simple monophyly tests and ancestral state reconstruction (ASR, via TreeTime) to assign mutation events to branches and identify homoplasies. Mutations are annotated at the level of codon and gene, to facilitate analysis of convergent evolution. Testing on simulated data (120 Mycobacterium tuberculosis alignments representing local and global samples) showed SNPPar can detect homoplasic SNPs with very high specificity (zero false-positives in all tests) and high sensitivity (zero false-negatives in 89 % of tests). SNPPar analysis of three empirically sampled datasets (Elizabethkingia anophelis, Burkholderia dolosa and M. tuberculosis) produced results that were in concordance with previous studies, in terms of both individual homoplasies and evidence of convergence at the codon and gene levels. SNPPar analysis of a simulated alignment of ~64 000 genome-wide SNPs from 2000 M. tuberculosis genomes took ~23 min and ~2.6 GB of RAM to generate complete annotated results on a laptop. This analysis required ASR be conducted for only 1.25 % of SNPs, and the ASR step took ~23 s and 0.4 GB of RAM. SNPPar automates the detection and annotation of homoplasic SNPs efficiently and accurately from large SNP alignments. As demonstrated by the examples included here, this information can be readily used to explore the role of homoplasy in parallel and/or convergent evolution at the level of nucleotide, codon and/or gene.
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Affiliation(s)
- David J. Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Sebastián Duchene
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria, Australia
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, 187 Grattan Street, Carlton, Victoria, Australia,Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, 305 Grattan Street, Melbourne, Victoria, Australia,Department of Medicine, Central Clinical School, Monash University, Clayton, Victoria, Australia,Department of Surgery (Royal Melbourne Hospital), Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Victoria, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK,*Correspondence: Kathryn E. Holt,
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15
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Ciprofloxacin induced antibiotic resistance in Salmonella Typhimurium mutants and genome analysis. Arch Microbiol 2021; 203:6131-6142. [PMID: 34585273 DOI: 10.1007/s00203-021-02577-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/07/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
Abstract
Antibiotic resistance of Salmonella species is well reported. Ciprofloxacin is the frontline antibiotic for salmonellosis. The repeated exposure to ciprofloxacin leads to resistant strains. After 20 cycles of antibiotic exposure, resistant bacterial clones were evaluated. The colony size of the mutants was small and had an extended lag phase compared to parent strain. The whole genome sequencing showed 40,513 mutations across the genome. Small percentage (5.2%) of mutations was non-synonymous. Four-fold more transitions were observed than transversions. Ratio of < 1 transition vs transversion showed a positive selection for antibiotic resistant trait. Mutation distribution across the genome was uniform. The native plasmid was an exception and 2 mutations were observed on 90 kb plasmid. The important genes like dnaE, gyrA, iroC, metH and rpoB involved in antibiotic resistance had point mutations. The genome analysis revealed most of the metabolic pathways were affected.
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16
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Ramli SR, Bunk B, Spröer C, Geffers R, Jarek M, Bhuju S, Goris M, Mustakim S, Pessler F. Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes. Pathogens 2021; 10:1198. [PMID: 34578230 PMCID: PMC8467490 DOI: 10.3390/pathogens10091198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 11/16/2022] Open
Abstract
The ability of Leptospirae to persist in environments and animal hosts but to cause clinically highly variable disease in humans has made leptospirosis the most common zoonotic disease. Considering the paucity of data on variation in complete genomes of human pathogenic Leptospirae, we have used a combination of Single Molecule Real-Time (SMRT) and Illumina sequencing to obtain complete genome sequences of six human clinical L. interrogans isolates from Malaysia. All six contained the larger (4.28-4.56 Mb) and smaller (0.34-0.395 Mb) chromosome typical of human pathogenic Leptospirae and 0-7 plasmids. Only 24% of the plasmid sequences could be matched to databases. We identified a chromosomal core genome of 3318 coding sequences and strain-specific accessory genomes of 49-179 coding sequences. These sequences enabled detailed genomic strain typing (Genome BLAST Distance Phylogeny, DNA-DNA hybridization, and multi locus sequence typing) and phylogenetic classification (whole-genome SNP genotyping). Even though there was some shared synteny and collinearity across the six genomes, there was evidence of major genome rearrangement, likely driven by horizontal gene transfer and homologous recombination. Mobile genetic elements were identified in all strains in highly varying numbers, including in the rfb locus, which defines serogroups and contributes to immune escape and pathogenesis. On the other hand, there was high conservation of virulence-associated genes including those relating to sialic acid, alginate, and lipid A biosynthesis. These findings suggest (i) that the antigenic variation, adaption to various host environments, and broad spectrum of virulence of L. interrogans are in part due to a high degree of genomic plasticity and (ii) that human pathogenic strains maintain a core set of genes required for virulence.
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Affiliation(s)
- Siti Roszilawati Ramli
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
- Department of Biotechnology, Technical University Braunschweig, 38106 Braunschweig, Germany
- Bacteriology Unit, Institute for Medical Research, National Institute of Health, Setia Alam 40170, Malaysia
| | - Boyke Bunk
- Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Cathrin Spröer
- Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), 38124 Braunschweig, Germany; (B.B.); (C.S.)
| | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (R.G.); (M.J.); (S.B.)
| | - Michael Jarek
- Genome Analytics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (R.G.); (M.J.); (S.B.)
| | - Sabin Bhuju
- Genome Analytics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; (R.G.); (M.J.); (S.B.)
| | - Marga Goris
- Leptospirosis Reference Centre, Amsterdam Medical Centre, University of Amsterdam, 1100 DD Amsterdam, The Netherlands;
| | - Sahlawati Mustakim
- Department of Pathology, Hospital Tuanku Ampuan Rahimah, Klang 41672, Malaysia;
| | - Frank Pessler
- Research Group Biomarkers for Infectious Diseases, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany;
- Centre for Individualised Infection Medicine, 30625 Hannover, Germany
- Research Group Biomarkers for Infectious Diseases, TWINCORE Center for Experimental and Clinical Infection Research, 30625 Hannover, Germany
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17
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Moreno E. The one hundred year journey of the genus Brucella (Meyer and Shaw 1920). FEMS Microbiol Rev 2021; 45:5917985. [PMID: 33016322 DOI: 10.1093/femsre/fuaa045] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
The genus Brucella, described by Meyer and Shaw in 1920, comprises bacterial pathogens of veterinary and public health relevance. For 36 years, the genus came to include three species that caused brucellosis in livestock and humans. In the second half of the 20th century, bacteriologists discovered five new species and several 'atypical' strains in domestic animals and wildlife. In 1990, the Brucella species were recognized as part of the Class Alphaproteobacteria, clustering with pathogens and endosymbionts of animals and plants such as Bartonella, Agrobacterium and Ochrobactrum; all bacteria that live in close association with eukaryotic cells. Comparisons with Alphaproteobacteria contributed to identify virulence factors and to establish evolutionary relationships. Brucella members have two circular chromosomes, are devoid of plasmids, and display close genetic relatedness. A proposal, asserting that all brucellae belong to a single species with several subspecies debated for over 70 years, was ultimately rejected in 2006 by the subcommittee of taxonomy, based on scientific, practical, and biosafety considerations. Following this, the nomenclature of having multiples Brucella species prevailed and defined according to their molecular characteristics, host preference, and virulence. The 100-year history of the genus corresponds to the chronicle of scientific efforts and the struggle for understanding brucellosis.
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Affiliation(s)
- Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Campues Benjamín Nuñez, Universidad Nacional, Heredia 40104, Costa Rica
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18
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Page AJ, Mather AE, Le-Viet T, Meader EJ, Alikhan NF, Kay GL, de Oliveira Martins L, Aydin A, Baker DJ, Trotter AJ, Rudder S, Tedim AP, Kolyva A, Stanley R, Yasir M, Diaz M, Potter W, Stuart C, Meadows L, Bell A, Gutierrez AV, Thomson NM, Adriaenssens EM, Swingler T, Gilroy RAJ, Griffith L, Sethi DK, Aggarwal D, Brown CS, Davidson RK, Kingsley RA, Bedford L, Coupland LJ, Charles IG, Elumogo N, Wain J, Prakash R, Webber MA, Smith SJL, Chand M, Dervisevic S, O’Grady J, The COVID-19 Genomics UK (COG-UK) Consortium. Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Microb Genom 2021; 7:000589. [PMID: 34184982 PMCID: PMC8461472 DOI: 10.1099/mgen.0.000589] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/19/2021] [Indexed: 01/28/2023] Open
Abstract
The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organizations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1565 positive samples (172 per 100 000 population) from 1376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6 % of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. In total, 1035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region. Furthermore, 100 genetically distinct UK lineages were detected demonstrating local evolution, at a rate of ~2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.
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Affiliation(s)
- Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Emma J. Meader
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | | | - Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | - Alp Aydin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - David J. Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alexander J. Trotter
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Steven Rudder
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Ana P. Tedim
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
| | - Anastasia Kolyva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Rachael Stanley
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Maria Diaz
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Will Potter
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Claire Stuart
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Lizzie Meadows
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Andrew Bell
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | | | | | - Tracey Swingler
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Luke Griffith
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Dheeraj K. Sethi
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Dinesh Aggarwal
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Colin S. Brown
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
| | - Rose K. Davidson
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Luke Bedford
- Ipswich Hospital, Heath Road, Ipswich, IP4 5PD, UK
| | | | - Ian G. Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Reenesh Prakash
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Meera Chand
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
| | - Samir Dervisevic
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Justin O’Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - The COVID-19 Genomics UK (COG-UK) Consortium
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
- Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Ipswich Hospital, Heath Road, Ipswich, IP4 5PD, UK
- Public Health, County Hall, Martineau Lane, Norwich, NR1 2DH, UK
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Bunte K, Kuhn C, Walther C, Peters U, Aarabi G, Smeets R, Beikler T. Clinical significance of ragA, ragB, and PG0982 genes in Porphyromonas gingivalis isolates from periodontitis patients. Eur J Oral Sci 2021; 129:e12776. [PMID: 33667038 DOI: 10.1111/eos.12776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/24/2021] [Accepted: 01/25/2021] [Indexed: 12/14/2022]
Abstract
Consistent detection of ragA, ragB, and PG0982 in the genome of Porphyromonas gingivalis (P. gingivalis) isolates from periodontitis patients suggests that genotypes containing these genes may influence virulence and P. gingivalis-associated periodontitis progression. This study evaluated the prevalence of these genes in P. gingivalis isolates from periodontitis patients (n = 28) and in isolates from periodontally healthy P. gingivalis carriers (n = 34). The association of these genes with progression of periodontitis, in vitro cell invasiveness, and bacterial survival following periodontal therapy was also assessed. Periodontal charting and microbiological sampling were done at baseline, and at 6, 12, and 24 months following subgingival debridement of the periodontitis patients. Healthy controls were assessed at baseline for comparison. P. gingivalis isolates were analysed by ragA, ragB, and PG0982 specific polymerase chain reaction (PCR) and Sanger sequencing. Primary human gingival fibroblasts were used for invasion experiments. Results showed that 25% of the tested isolates from the periodontitis group had ragB detected, whereas this gene was undetected in isolates from healthy participants. However, none of the selected genes was associated with an increased cell invasiveness in vitro, with bacterial survival, or with significant clinical periodontal parameter changes. Identification of genes that influence P.gingivalis virulence and therapeutic outcome may have a diagnostic or prognostic value.
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Affiliation(s)
- Kübra Bunte
- Department of Periodontics, Preventive and Restorative Dentistry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Carolin Walther
- Department of Prosthetic Dentistry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrike Peters
- Department of Periodontics, Preventive and Restorative Dentistry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ghazal Aarabi
- Department of Prosthetic Dentistry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Smeets
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Division of Regenerative Orofacial Medicine, Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Beikler
- Department of Periodontics, Preventive and Restorative Dentistry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Vashistha H, Kohram M, Salman H. Non-genetic inheritance restraint of cell-to-cell variation. eLife 2021; 10:64779. [PMID: 33523801 PMCID: PMC7932692 DOI: 10.7554/elife.64779] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/28/2021] [Indexed: 12/22/2022] Open
Abstract
Heterogeneity in physical and functional characteristics of cells (e.g. size, cycle time, growth rate, protein concentration) proliferates within an isogenic population due to stochasticity in intracellular biochemical processes and in the distribution of resources during divisions. Conversely, it is limited in part by the inheritance of cellular components between consecutive generations. Here we introduce a new experimental method for measuring proliferation of heterogeneity in bacterial cell characteristics, based on measuring how two sister cells become different from each other over time. Our measurements provide the inheritance dynamics of different cellular properties, and the 'inertia' of cells to maintain these properties along time. We find that inheritance dynamics are property specific and can exhibit long-term memory (∼10 generations) that works to restrain variation among cells. Our results can reveal mechanisms of non-genetic inheritance in bacteria and help understand how cells control their properties and heterogeneity within isogenic cell populations.
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Affiliation(s)
- Harsh Vashistha
- Department of Physics and Astronomy, The Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Maryam Kohram
- Department of Physics and Astronomy, The Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Hanna Salman
- Department of Physics and Astronomy, The Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, United States.,Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
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21
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Al-Mnaser AA, Woodward MJ. Sub-lethal Concentrations of Phytochemicals (Carvacrol and Oregano) Select for Reduced Susceptibility Mutants of Escherichia coli O23:H52. Pol J Microbiol 2020; 69:1-5. [PMID: 32067440 PMCID: PMC7256741 DOI: 10.33073/pjm-2020-003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/05/2019] [Accepted: 12/21/2019] [Indexed: 12/16/2022] Open
Abstract
In vitro studies aimed at studying the mechanism of action of carvacrol and oregano as natural anti-bacterial agents to control multiple antibiotic-resistant avian pathogenic Escherichia coli (APEC) strain O23:H52 isolated from chicken were performed. Derivatives with increased minimum inhibitory concentrations (MIC) to the phytochemicals were selected after growing Escherichia coli (E. coli) strain O23:H52 at sub-lethal concentrations of carvacrol and oregano for a period of 60 days. Whole-genome sequencing (WGS) of two derivatives revealed a missense mutation in cadC and marR: the genes responsible for survival mechanisms and antibiotic resistance by efflux, respectively. In vitro studies aimed at studying the mechanism of action of carvacrol and oregano as natural anti-bacterial agents to control multiple antibiotic-resistant avian pathogenic Escherichia coli (APEC) strain O23:H52 isolated from chicken were performed. Derivatives with increased minimum inhibitory concentrations (MIC) to the phytochemicals were selected after growing Escherichia coli (E. coli) strain O23:H52 at sub-lethal concentrations of carvacrol and oregano for a period of 60 days. Whole-genome sequencing (WGS) of two derivatives revealed a missense mutation in cadC and marR: the genes responsible for survival mechanisms and antibiotic resistance by efflux, respectively.
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22
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Hammond JA, Gordon EA, Socarras KM, Chang Mell J, Ehrlich GD. Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis. Biochem Soc Trans 2020; 48:2437-2455. [PMID: 33245329 PMCID: PMC7752077 DOI: 10.1042/bst20190713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023]
Abstract
The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host-bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.
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Affiliation(s)
- Jocelyn A. Hammond
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Emma A. Gordon
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Kayla M. Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Joshua Chang Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
- Department of Otolaryngology – Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, U.S.A
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Sertbas M, Ulgen KO. Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. Front Cell Dev Biol 2020; 8:566702. [PMID: 33251208 PMCID: PMC7673413 DOI: 10.3389/fcell.2020.566702] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Pathogens give rise to a wide range of diseases threatening global health and hence drawing public health agencies' attention to establish preventative and curative solutions. Genome-scale metabolic modeling is ever increasingly used tool for biomedical applications including the elucidation of antibiotic resistance, virulence, single pathogen mechanisms and pathogen-host interaction systems. With this approach, the sophisticated cellular system of metabolic reactions inside the pathogens as well as between pathogen and host cells are represented in conjunction with their corresponding genes and enzymes. Along with essential metabolic reactions, alternate pathways and fluxes are predicted by performing computational flux analyses for the growth of pathogens in a very short time. The genes or enzymes responsible for the essential metabolic reactions in pathogen growth are regarded as potential drug targets, as a priori guide to researchers in the pharmaceutical field. Pathogens alter the key metabolic processes in infected host, ultimately the objective of these integrative constraint-based context-specific metabolic models is to provide novel insights toward understanding the metabolic basis of the acute and chronic processes of infection, revealing cellular mechanisms of pathogenesis, identifying strain-specific biomarkers and developing new therapeutic approaches including the combination drugs. The reaction rates predicted during different time points of pathogen development enable us to predict active pathways and those that only occur during certain stages of infection, and thus point out the putative drug targets. Among others, fatty acid and lipid syntheses reactions are recent targets of new antimicrobial drugs. Genome-scale metabolic models provide an improved understanding of how intracellular pathogens utilize the existing microenvironment of the host. Here, we reviewed the current knowledge of genome-scale metabolic modeling in pathogen cells as well as pathogen host interaction systems and the promising applications in the extension of curative strategies against pathogens for global preventative healthcare.
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Affiliation(s)
- Mustafa Sertbas
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.,Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Kutlu O Ulgen
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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24
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Sharma V, Mobeen F, Prakash T. In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB). 3 Biotech 2020; 10:376. [PMID: 32802718 PMCID: PMC7406594 DOI: 10.1007/s13205-020-02371-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 07/28/2020] [Indexed: 12/01/2022] Open
Abstract
The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylum Proteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB.
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Affiliation(s)
- Vikas Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, 175005 Himachal Pradesh India
| | - Fauzul Mobeen
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, 175005 Himachal Pradesh India
| | - Tulika Prakash
- School of Basic Sciences, Indian Institute of Technology Mandi, Kamand, Mandi, 175005 Himachal Pradesh India
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25
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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26
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Guimaraes AMS, Zimpel CK. Mycobacterium bovis: From Genotyping to Genome Sequencing. Microorganisms 2020; 8:E667. [PMID: 32375210 PMCID: PMC7285088 DOI: 10.3390/microorganisms8050667] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium bovis is the main pathogen of bovine, zoonotic, and wildlife tuberculosis. Despite the existence of programs for bovine tuberculosis (bTB) control in many regions, the disease remains a challenge for the veterinary and public health sectors, especially in developing countries and in high-income nations with wildlife reservoirs. Current bTB control programs are mostly based on test-and-slaughter, movement restrictions, and post-mortem inspection measures. In certain settings, contact tracing and surveillance has benefited from M. bovis genotyping techniques. More recently, whole-genome sequencing (WGS) has become the preferential technique to inform outbreak response through contact tracing and source identification for many infectious diseases. As the cost per genome decreases, the application of WGS to bTB control programs is inevitable moving forward. However, there are technical challenges in data analyses and interpretation that hinder the implementation of M. bovis WGS as a molecular epidemiology tool. Therefore, the aim of this review is to describe M. bovis genotyping techniques and discuss current standards and challenges of the use of M. bovis WGS for transmission investigation, surveillance, and global lineages distribution. We compiled a series of associated research gaps to be explored with the ultimate goal of implementing M. bovis WGS in a standardized manner in bTB control programs.
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Affiliation(s)
- Ana M. S. Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
| | - Cristina K. Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, University of São Paulo, São Paulo 01246-904, Brazil;
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, São Paulo 01246-904, Brazil
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27
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28
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Reis AC, Kolvenbach BA, Chami M, Gales L, Egas C, Corvini PFX, Nunes OC. Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics 2019; 20:885. [PMID: 31752666 PMCID: PMC6868719 DOI: 10.1186/s12864-019-6206-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/21/2019] [Indexed: 02/01/2023] Open
Abstract
Background Microbial communities recurrently establish metabolic associations resulting in increased fitness and ability to perform complex tasks, such as xenobiotic degradation. In a previous study, we have described a sulfonamide-degrading consortium consisting of a novel low-abundant actinobacterium, named strain GP, and Achromobacter denitrificans PR1. However, we found that strain GP was unable to grow independently and could not be further purified. Results Previous studies suggested that strain GP might represent a new putative species within the Leucobacter genus (16S rRNA gene similarity < 97%). In this study, we found that average nucleotide identity (ANI) with other Leucobacter spp. ranged between 76.8 and 82.1%, further corroborating the affiliation of strain GP to a new provisional species. The average amino acid identity (AAI) and percentage of conserved genes (POCP) values were near the lower edge of the genus delimitation thresholds (65 and 55%, respectively). Phylogenetic analysis of core genes between strain GP and Leucobacter spp. corroborated these findings. Comparative genomic analysis indicates that strain GP may have lost genes related to tetrapyrrole biosynthesis and thiol transporters, both crucial for the correct assembly of cytochromes and aerobic growth. However, supplying exogenous heme and catalase was insufficient to abolish the dependent phenotype. The actinobacterium harbors at least two copies of a novel genetic element containing a sulfonamide monooxygenase (sadA) flanked by a single IS1380 family transposase. Additionally, two homologs of sadB (4-aminophenol monooxygenase) were identified in the metagenome-assembled draft genome of strain GP, but these were not located in the vicinity of sadA nor of mobile or integrative elements. Conclusions Comparative genomics of the genus Leucobacter suggested the absence of some genes encoding for important metabolic traits in strain GP. Nevertheless, although media and culture conditions were tailored to supply its potential metabolic needs, these conditions were insufficient to isolate the PR1-dependent actinobacterium further. This study gives important insights regarding strain GP metabolism; however, gene expression and functional studies are necessary to characterize and further isolate strain GP. Based on our data, we propose to classify strain GP in a provisional new species within the genus Leucobacter, ‘Candidatus Leucobacter sulfamidivorax‘.
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Affiliation(s)
- Ana C Reis
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.,Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Boris A Kolvenbach
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Mohamed Chami
- BioEM lab, C-Cina, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Luís Gales
- Instituto de Investigação e Inovação em Saúde - i3S, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Biologia Molecular e Celular - IBMC, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar - ICBAS, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Faculty of Medicine, Rua Larga, Pólo I, 3004-504, Coimbra, Portugal
| | - Philippe F-X Corvini
- Institute for Ecopreneurship, School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gruendenstrasse 40, 4132, Muttenz, Switzerland
| | - Olga C Nunes
- Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering - LEPABE, Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
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29
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Feng C, Zhang F, Wang B, Zhang L, Dong Y, Shao Y. Genome-wide analysis of fermentation and probiotic trait stability in Lactobacillus plantarum during continuous culture. J Dairy Sci 2019; 103:117-127. [PMID: 31704013 DOI: 10.3168/jds.2019-17049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/11/2019] [Indexed: 01/02/2023]
Abstract
Trait stability of Lactobacillus plantarum was studied following daily subculture over a 90-d period. Acid and bile tolerance, self-aggregation ability, cell hydrophobicity, pathogen inhibition activity, and cholesterol removal ability of cultures subcultured 30 (Lp30), 60 (Lp60), or 90 (Lp90) times were not significantly different from the original strain (Lp0). However, carbohydrate metabolism patterns did change; the Lp0 culture was unable to use d-sorbitol, α-methyl-d-mannose, and d-raffinose, whereas Lp30, Lp60, and Lp90 cultures could. Furthermore, gluconate and gentiobiose were fully used by the Lp0 culture but only poorly used by the Lp30, Lp60, and Lp90 cultures. Milk fermentation test confirmed that L. plantarum was unable to use lactose throughout laboratory evolution. Six non-synonymous mutations in genome of the Lp30, Lp60, and Lp90 cultures were identified by whole-genome sequencing, including mutant gene encoding the phosphoglycerate mutase, which is closely related to the transport and metabolism of carbohydrates. These mutations may play an important role in changes of carbohydrate metabolism patterns observed. Understanding the evolutionary characteristics of L. plantarum will help in development for food industry.
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Affiliation(s)
- Cuijiao Feng
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Fuxin Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China.
| | - Bini Wang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Liyuan Zhang
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yushan Dong
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Yuyu Shao
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China.
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30
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Québatte M, Dehio C. Bartonella gene transfer agent: Evolution, function, and proposed role in host adaptation. Cell Microbiol 2019; 21:e13068. [PMID: 31231937 PMCID: PMC6899734 DOI: 10.1111/cmi.13068] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/09/2019] [Accepted: 06/13/2019] [Indexed: 01/05/2023]
Abstract
The processes underlying host adaptation by bacterial pathogens remain a fundamental question with relevant clinical, ecological, and evolutionary implications. Zoonotic pathogens of the genus Bartonella constitute an exceptional model to study these aspects. Bartonellae have undergone a spectacular diversification into multiple species resulting from adaptive radiation. Specific adaptations of a complex facultative intracellular lifestyle have enabled the colonisation of distinct mammalian reservoir hosts. This remarkable host adaptability has a multifactorial basis and is thought to be driven by horizontal gene transfer (HGT) and recombination among a limited genus‐specific pan genome. Recent functional and evolutionary studies revealed that the conserved Bartonella gene transfer agent (BaGTA) mediates highly efficient HGT and could thus drive this evolution. Here, we review the recent progress made towards understanding BaGTA evolution, function, and its role in the evolution and pathogenesis of Bartonella spp. We notably discuss how BaGTA could have contributed to genome diversification through recombination of beneficial traits that underlie host adaptability. We further address how BaGTA may counter the accumulation of deleterious mutations in clonal populations (Muller's ratchet), which are expected to occur through the recurrent transmission bottlenecks during the complex infection cycle of these pathogens in their mammalian reservoir hosts and arthropod vectors.
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31
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Bos KI, Kühnert D, Herbig A, Esquivel-Gomez LR, Andrades Valtueña A, Barquera R, Giffin K, Kumar Lankapalli A, Nelson EA, Sabin S, Spyrou MA, Krause J. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annu Rev Microbiol 2019; 73:639-666. [PMID: 31283430 DOI: 10.1146/annurev-micro-090817-062436] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.
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Affiliation(s)
- Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Luis Roger Esquivel-Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; .,Faculty of Biological Sciences, Friedrich Schiller University, 07737 Jena, Germany
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Sevillya G, Snir S. Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification. Mol Phylogenet Evol 2019; 136:128-137. [DOI: 10.1016/j.ympev.2019.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 03/07/2019] [Accepted: 03/17/2019] [Indexed: 01/22/2023]
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33
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Zeng Q, Xie J, Li Y, Gao T, Xu C, Wang Q. Comparative genomic and functional analyses of four sequenced Bacillus cereus genomes reveal conservation of genes relevant to plant-growth-promoting traits. Sci Rep 2018; 8:17009. [PMID: 30451927 PMCID: PMC6242881 DOI: 10.1038/s41598-018-35300-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022] Open
Abstract
Some Bacillus strains function as predominant plant-growth-promoting rhizobacteria. Bacillus cereus 905 is a rod-shaped Gram-positive bacterium isolated from wheat rhizosphere and is a rhizobacterium that exhibits significant plant-growth-promoting effects. Species belonging to the genus Bacillus are observed in numerous different habitats. Several papers on B. cereus are related to pathogens that causes food-borne illness and industrial applications. However, genomic analysis of plant-associated B. cereus has yet to be reported. Here, we conducted a genomic analysis comparing strain 905 with three other B. cereus strains and investigate the genomic characteristics and evolution traits of the species in different niches. The genome sizes of four B. cereus strains range from 5.38 M to 6.40 M, and the number of protein-coding genes varies in the four strains. Comparisons of the four B. cereus strains reveal 3,998 core genes. The function of strain-specific genes are related to carbohydrate, amino acid and coenzyme metabolism and transcription. Analysis of single nucleotide polymorphisms (SNPs) indicates local diversification of the four strains. SNPs are unevenly distributed throughout the four genomes, and function interpretation of regions with high SNP density coincides with the function of strain-specific genes. Detailed analysis indicates that certain SNPs contribute to the formation of strain-specific genes. By contrast, genes related to plant-growth-promoting traits are highly conserved. This study shows the genomic differences between four strains from different niches and provides an in-depth understanding of the genome architecture of these species, thus facilitating genetic engineering and agricultural applications in the future.
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Affiliation(s)
- Qingchao Zeng
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Jianbo Xie
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, P. R. China
| | - Yan Li
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Tantan Gao
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Cheng Xu
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China
| | - Qi Wang
- Key Laboratory of Plant Pathology, Ministry of Agriculture, College of Plant Protection, China Agricultural University, Beijing, 100193, P. R. China.
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Gutiérrez R, Markus B, Carstens Marques de Sousa K, Marcos-Hadad E, Mugasimangalam RC, Nachum-Biala Y, Hawlena H, Covo S, Harrus S. Prophage-Driven Genomic Structural Changes Promote Bartonella Vertical Evolution. Genome Biol Evol 2018; 10:3089-3103. [PMID: 30346520 PMCID: PMC6257571 DOI: 10.1093/gbe/evy236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2018] [Indexed: 12/30/2022] Open
Abstract
Bartonella is a genetically diverse group of vector-borne bacteria. Over 40 species have been characterized to date, mainly from mammalian reservoirs and arthropod vectors. Rodent reservoirs harbor one of the largest Bartonella diversity described to date, and novel species and genetic variants are continuously identified from these hosts. Yet, it is still unknown if this significant genetic diversity stems from adaptation to different niches or from intrinsic high mutation rates. Here, we explored the vertical occurrence of spontaneous genomic alterations in 18 lines derived from two rodent-associated Bartonella elizabethae-like strains, evolved in nonselective agar plates under conditions mimicking their vector- and mammalian-associated temperatures, and the transmission cycles between them (i.e., 26 °C, 37 °C, and alterations between the two), using mutation accumulation experiments. After ∼1,000 generations, evolved genomes revealed few point mutations (average of one-point mutation per line), evidencing conserved single-nucleotide mutation rates. Interestingly, three large structural genomic changes (two large deletions and an inversion) were identified over all lines, associated with prophages and surface adhesin genes. Particularly, a prophage, deleted during constant propagation at 37 °C, was associated with an increased autonomous replication at 26 °C (the flea-associated temperature). Complementary molecular analyses of wild strains, isolated from desert rodents and their fleas, further supported the occurrence of structural genomic variations and prophage-associated deletions in nature. Our findings suggest that structural genomic changes represent an effective intrinsic mechanism to generate diversity in slow-growing bacteria and emphasize the role of prophages as promoters of diversity in nature.
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Affiliation(s)
- Ricardo Gutiérrez
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Barak Markus
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | | | - Evgeniya Marcos-Hadad
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Yaarit Nachum-Biala
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Hadas Hawlena
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shimon Harrus
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel
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35
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Ksiezopolska E, Gabaldón T. Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens. Genes (Basel) 2018; 9:genes9090461. [PMID: 30235884 PMCID: PMC6162425 DOI: 10.3390/genes9090461] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023] Open
Abstract
Fungal infections, such as candidiasis caused by Candida, pose a problem of growing medical concern. In developed countries, the incidence of Candida infections is increasing due to the higher survival of susceptible populations, such as immunocompromised patients or the elderly. Existing treatment options are limited to few antifungal drug families with efficacies that vary depending on the infecting species. In this context, the emergence and spread of resistant Candida isolates are being increasingly reported. Understanding how resistance can evolve within naturally susceptible species is key to developing novel, more effective treatment strategies. However, in contrast to the situation of antibiotic resistance in bacteria, few studies have focused on the evolutionary mechanisms leading to drug resistance in fungal species. In this review, we will survey and discuss current knowledge on the genetic bases of resistance to antifungal drugs in Candida opportunistic pathogens. We will do so from an evolutionary genomics perspective, focusing on the possible evolutionary paths that may lead to the emergence and selection of the resistant phenotype. Finally, we will discuss the potential of future studies enabled by current developments in sequencing technologies, in vitro evolution approaches, and the analysis of serial clinical isolates.
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Affiliation(s)
- Ewa Ksiezopolska
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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36
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Ausiannikava D, Mitchell L, Marriott H, Smith V, Hawkins M, Makarova KS, Koonin EV, Nieduszynski CA, Allers T. Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii. Mol Biol Evol 2018; 35:1855-1868. [PMID: 29668953 PMCID: PMC6063281 DOI: 10.1093/molbev/msy075] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: 1) mutational diversification of a multi-copy chromosome; 2) capture of a new chromosome by horizontal transfer; 3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination. The newly generated elements are bona fide chromosomes, because each bears "chromosomal" replication origins, rRNA loci, and essential genes. The new chromosomes were stable during routine growth but additional genetic manipulation, which involves selective bottlenecks, provoked further rearrangements. To the best of our knowledge, rearrangement of a naturally evolved prokaryotic genome to generate two new chromosomes has not been described previously.
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Affiliation(s)
- Darya Ausiannikava
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Laura Mitchell
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Hannah Marriott
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Michelle Hawkins
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
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37
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Dasgupta D, Jasmine J, Mukherji S. Characterization, phylogenetic distribution and evolutionary trajectories of diverse hydrocarbon degrading microorganisms isolated from refinery sludge. 3 Biotech 2018; 8:273. [PMID: 29868311 DOI: 10.1007/s13205-018-1297-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/20/2018] [Indexed: 12/01/2022] Open
Abstract
Phylogenic association between bacteria living under harsh conditions can provide important information on adaptive mechanism, survival strategy and their potential application. Indigenous microorganisms isolated from toxic refinery oily sludge with ability to degrade a diverse range of hydrocarbons were identified and characterized. The strains including Pseudomonas aeruginosa RS1, Microbacterium sp. RS2, Bacillus sp. RS3, Acinetobacter baumannii RS4 and Stenotrophomonas sp. RS5 could utilize n-alkanes, cycloalkanes, polynuclear aromatic hydrocarbons (PAHs) with 2-4 rings and also substituted PAHs as sole substrate. The phylogenetic position of Bacillus sp. RS3 and Pseudomonas sp. RS1 was tested by applying the maximum likelihood (ML) method to the aligned 16S rRNA nucleotide sequences of PAH and aliphatic hydrocarbon degrading strains belonging to the corresponding genus. The base substitution matrix created with each set of organisms capable of degrading aromatic and aliphatic hydrocarbons showed significant transitional event with high values of transition: transversion ratio (R) under all conditions. The guanine-cytosine (GC) content of the hydrocarbon degrading test strains was also found to be highest for the clade which harbored them. The test strains consistently occupied a distinct terminal end within the phylogenetic tree constructed by ML analysis. This study reveals that the refinery sludge imposed environmental stress on the bacterial strains which possibly caused significant genetic alteration and phenotypic adaptation. Due to the divergent evolution of the Pseudomonas and Bacillus strains in the sludge, they appeared distinctly different from other hydrocarbon degrading strains of the same genus.
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Affiliation(s)
- Debdeep Dasgupta
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
- 2Present Address: Amity Institute of Biotechnology, Amity University Mumbai, Bhatan, Post-Somathne, Panvel, Mumbai, Maharashtra 410206 India
| | - Jublee Jasmine
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
| | - Suparna Mukherji
- 1Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076 India
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38
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Kanwar A, Marshall SH, Perez F, Tomas M, Jacobs MR, Hujer AM, Domitrovic TN, Rudin SD, Rojas LJ, Kreiswirth BN, Chen L, Quinones-Mateu M, van Duin D, Bonomo RA. Emergence of Resistance to Colistin During the Treatment of Bloodstream Infection Caused by Klebsiella pneumoniae Carbapenemase-Producing Klebsiella pneumoniae. Open Forum Infect Dis 2018; 5:ofy054. [PMID: 30014001 DOI: 10.1093/ofid/ofy054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/18/2018] [Indexed: 11/14/2022] Open
Abstract
We report the emergence of colistin resistance in Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae after 8 days of colistin-based therapy, resulting in relapse of bloodstream infection and death. Disruption of the mgrB gene by insertion of a mobile genetic element was found to be the mechanism, which was replicated in vitro after exposure to subinhibitory concentrations of colistin and meropenem.
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Affiliation(s)
- Anubhav Kanwar
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio
| | | | - Federico Perez
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Research Service.,Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Myreen Tomas
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Michael R Jacobs
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Andrea M Hujer
- Research Service.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - T Nicholas Domitrovic
- Research Service.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Susan D Rudin
- Research Service.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Laura J Rojas
- Research Service.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Barry N Kreiswirth
- Public Health Research Institute Center New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, New Jersey
| | - Liang Chen
- Public Health Research Institute Center New Jersey Medical School - Rutgers, The State University of New Jersey, Newark, New Jersey
| | - Miguel Quinones-Mateu
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina
| | - Robert A Bonomo
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Research Service.,Geriatric Research Education and Clinical Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio
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39
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Olsen I, Chen T, Tribble GD. Genetic exchange and reassignment in Porphyromonas gingivalis. J Oral Microbiol 2018; 10:1457373. [PMID: 29686783 PMCID: PMC5907639 DOI: 10.1080/20002297.2018.1457373] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/19/2018] [Indexed: 12/30/2022] Open
Abstract
Porphyromonas gingivalis is considered a keystone pathogen in adult periodontitis but has also been associated with systemic diseases. It has a myriad of virulence factors that differ between strains. Genetic exchange and intracellular genome rearrangements may be responsible for the variability in the virulence of P. gingivalis. The present review discusses how the exchange of alleles can convert this bacterium from commensalistic to pathogenic and potentially shapes the host-microbe environment from homeostasis to dysbiosis. It is likely that genotypes of P. gingivalis with increased pathogenic adaptations may spread in the human population with features acquired from a common pool of alleles. The exact molecular mechanisms that trigger this exchange are so far unknown but they may be elicited by environmental pressure.
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Affiliation(s)
- Ingar Olsen
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Tsute Chen
- Department of Microbiology, Forsyth Institute, Cambridge, MA, USA.,Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Gena D Tribble
- Department of Periodontics and Dental Hygiene, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
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40
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Comparative Genomics Shows That Mycobacterium ulcerans Migration and Expansion Preceded the Rise of Buruli Ulcer in Southeastern Australia. Appl Environ Microbiol 2018; 84:AEM.02612-17. [PMID: 29439984 DOI: 10.1128/aem.02612-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/25/2018] [Indexed: 02/07/2023] Open
Abstract
Since 2000, cases of the neglected tropical disease Buruli ulcer, caused by infection with Mycobacterium ulcerans, have increased 100-fold around Melbourne (population 4.4 million), the capital of Victoria, in temperate southeastern Australia. The reasons for this increase are unclear. Here, we used whole-genome sequence comparisons of 178 M. ulcerans isolates obtained primarily from human clinical specimens, spanning 70 years, to model the population dynamics of this pathogen from this region. Using phylogeographic and advanced Bayesian phylogenetic approaches, we found that there has been a migration of the pathogen from the east end of the state, beginning in the 1980s, 300 km west to the major human population center around Melbourne. This move was then followed by a significant increase in M. ulcerans population size. These analyses inform our thinking around Buruli ulcer transmission and control, indicating that M. ulcerans is introduced to a new environment and then expands, rather than it being from the awakening of a quiescent pathogen reservoir.IMPORTANCE Buruli ulcer is a destructive skin and soft tissue infection caused by Mycobacterium ulcerans and is characterized by progressive skin ulceration, which can lead to permanent disfigurement and long-term disability. Despite the majority of disease burden occurring in regions of West and central Africa, Buruli ulcer is also becoming increasingly common in southeastern Australia. Major impediments to controlling disease spread are incomplete understandings of the environmental reservoirs and modes of transmission of M. ulcerans The significance of our research is that we used genomics to assess the population structure of this pathogen at the Australian continental scale. We have then reconstructed a historical bacterial spread and modeled demographic dynamics to reveal bacterial population expansion across southeastern Australia. These findings provide explanations for the observed epidemiological trends with Buruli ulcer and suggest possible management to control disease spread.
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41
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Schürch A, Arredondo-Alonso S, Willems R, Goering R. Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene–based approaches. Clin Microbiol Infect 2018; 24:350-354. [DOI: 10.1016/j.cmi.2017.12.016] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/21/2017] [Accepted: 12/22/2017] [Indexed: 11/30/2022]
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Saha MS, Pal S, Sarkar I, Roy A, Das Mohapatra PK, Sen A. Comparative genomics of Mycobacterium reveals evolutionary trends of M. avium complex. Genomics 2018; 111:426-435. [PMID: 29501678 DOI: 10.1016/j.ygeno.2018.02.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/01/2017] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Abstract
Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done. Further the evolutionary features of M. avium complex also have been revealed. Mycobacterial genes are moderately GC rich showed higher expression level in PPs and significant negative correlation with biosynthetic cost of proteins. Translational selection pressure was observed in mycobacterial genes. MAC showed close relationship with NPs and higher evolutionary rate in MAC revealed their constant evolving nature.
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Affiliation(s)
- Mousumi Sarkar Saha
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | - Shilpee Pal
- Department of Microbiology, Vidyasagar University, Midnapore 721102, India
| | - Indrani Sarkar
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | - Ayan Roy
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India
| | | | - Arnab Sen
- Bioinformatics Facility, Department of Botany, University of North Bengal, Darjeeling 734013, India.
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43
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Guerra PR, Herrero-Fresno A, Pors SE, Ahmed S, Wang D, Thøfner I, Antenucci F, Olsen JE. The membrane transporter PotE is required for virulence in avian pathogenic Escherichia coli (APEC). Vet Microbiol 2018. [PMID: 29519523 DOI: 10.1016/j.vetmic.2018.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Over the last few years, polyamines have been described as key-signal of virulence in pathogenic bacteria. In the current study, we investigated whether the knockout of genes related to polyamine biosynthesis and putrescine transport affected the virulence of an avian pathogenic E. coli (APEC) strain. One-week-old White Leghorn chickens were infected intratracheally with mutants in polyamine biosynthesis (ΔspeB/C and ΔspeD/E) and transport genes (ΔpotE) of a well-characterized APEC strain of ST117 (O83: H4). All polyamine mutants and the wild-type strain were able to infect chicken; however, we observed significantly fewer lesions in the lungs of the chickens infected with the polyamine mutants in comparison with chicken infected with the wild-type. Results derived from histology of infected lungs detected significantly fewer lesions in the lung of birds infected within particular the putrescine transport mutant (ΔpotE). A decrease in colonization levels was observed in the liver and spleen of birds infected with the putrescine biosynthesis mutant ΔspeB/C, and likewise, a decrease of the colonization levels of all organs from birds infected with the ΔpotE was detected. Together, our data demonstrate that the deletion of polyamine genes, and in particular the PotE membrane protein, attenuates the virulence of APEC during infection of chickens.
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Affiliation(s)
- Priscila Regina Guerra
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Susanne Elisabeth Pors
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Shahana Ahmed
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Dan Wang
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ida Thøfner
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - Fabio Antenucci
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Science, University of Copenhagen, Frederiksberg, Denmark.
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Huang K, Wang D, Frederiksen RF, Rensing C, Olsen JE, Fresno AH. Investigation of the Role of Genes Encoding Zinc Exporters zntA, zitB, and fieF during Salmonella Typhimurium Infection. Front Microbiol 2018; 8:2656. [PMID: 29375521 PMCID: PMC5768658 DOI: 10.3389/fmicb.2017.02656] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/20/2017] [Indexed: 02/05/2023] Open
Abstract
The transition metal zinc is involved in crucial biological processes in all living organisms and is essential for survival of Salmonella in the host. However, little is known about the role of genes encoding zinc efflux transporters during Salmonella infection. In this study, we constructed deletion mutants for genes encoding zinc exporters (zntA, zitB, and fieF) in the wild-type (WT) strain Salmonella enterica serovar Typhimurium (S. Typhimurium) 4/74. The mutants 4/74ΔzntA and 4/74ΔzntA/zitB exhibited a dramatic growth delay and abrogated growth ability, respectively, in Luria Bertani medium supplemented with 0.25 mM ZnCl2 or 1.5 mM CuSO4 compared to the WT strain. In order to investigate the role of genes encoding zinc exporters on survival of S. Typhimurium inside cells, amoeba and macrophage infection models were used. No significant differences in uptake or survival were detected for any of the mutants compared to the WT during infection of amoebae. In natural resistance-associated macrophage protein 1 (Nramp1)-negative J774.1 murine macrophages, significantly higher bacterial counts were observed for the mutant strains 4/74ΔzntA and 4/74ΔzntA/zitB compared to the WT at 4 h post-infection although the fold net replication was similar between all the strains. All four tested mutants (4/74ΔzntA, 4/74ΔzitB, 4/74ΔfieF, and 4/74ΔzntA/zitB) showed enhanced intracellular survival capacity within the modified Nramp1-positive murine RAW264.7 macrophages at 20 h post-infection. The fold net replication was also significantly higher for 4/74ΔzntA, 4/74ΔzitB, and 4/74ΔzntA/zitB mutants compared to the WT. Intriguingly, the ability to survive and cause infection was significantly impaired in all the three mutants tested (4/74ΔzntA, 4/74ΔzitB, and 4/74ΔzntA/zitB) in C3H/HeN mice, particularly the double mutant 4/74ΔzntA/zitB was severely attenuated compared to the WT in all the three organs analyzed. These findings suggest that these genes encoding zinc exporters, especially zntA, contribute to the resistance of S. Typhimurium to zinc and copper stresses during infection.
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Affiliation(s)
- Kaisong Huang
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dan Wang
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Rikki F Frederiksen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - John E Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ana H Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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45
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Nesse LL, Simm R. Biofilm: A Hotspot for Emerging Bacterial Genotypes. ADVANCES IN APPLIED MICROBIOLOGY 2018; 103:223-246. [PMID: 29914658 DOI: 10.1016/bs.aambs.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Bacteria have the ability to adapt to changing environments through rapid evolution mediated by modification of existing genetic information, as well as by horizontal gene transfer (HGT). This makes bacteria a highly successful life form when it comes to survival. Unfortunately, this genetic plasticity may result in emergence and dissemination of antimicrobial resistance and virulence genes, and even the creation of multiresistant "superbugs" which may pose serious threats to public health. As bacteria commonly reside in biofilms, there has been an increased interest in studying these phenomena within biofilms in recent years. This review summarizes the present knowledge within this important area of research. Studies on bacterial evolution in biofilms have shown that mature biofilms develop into diverse communities over time. There is growing evidence that the biofilm lifestyle may be more mutagenic than planktonic growth. Furthermore, all three main mechanisms for HGT have been observed in biofilms. This has been shown to occur both within and between bacterial species, and higher transfer rates in biofilms than in planktonic cultures were detected. Of special concern are the observations that mutants with increased antibiotic resistance occur at higher frequency in biofilms than in planktonic cultures even in the absence of antibiotic exposure. Likewise, efficient dissemination of antimicrobial resistance genes, as well as virulence genes, has been observed within the biofilm environment. This new knowledge emphasizes the importance of biofilm awareness and control.
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46
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Kulsum U, Kapil A, Singh H, Kaur P. NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1052:39-49. [DOI: 10.1007/978-981-10-7572-8_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Bragonzi A, Paroni M, Pirone L, Coladarci I, Ascenzioni F, Bevivino A. Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice. Int J Mol Sci 2017; 18:ijms18112417. [PMID: 29135920 PMCID: PMC5713385 DOI: 10.3390/ijms18112417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/08/2017] [Accepted: 11/10/2017] [Indexed: 01/17/2023] Open
Abstract
Burkholderia cenocepacia is an important opportunistic pathogen in cystic fibrosis (CF) patients, and has also been isolated from natural environments. In previous work, we explored the virulence and pathogenic potential of environmental B. cenocepacia strains and demonstrated that they do not differ from clinical strains in some pathogenic traits. Here, we investigated the ability of the environmental B. cenocepacia Mex1 strain, isolated from the maize rhizosphere, to persist and increase its virulence after serial passages in a mouse model of chronic infection. B. cenocepacia Mex1 strain, belonging to the recA lineage IIIA, was embedded in agar beads and challenged into the lung of C57Bl/6 mice. The mice were sacrificed after 28 days from infection and their lungs were tested for bacterial loads. Agar beads containing the pool of B. cenocepacia colonies from the four sequential passages were used to infect the mice. The environmental B. cenocepacia strain showed a low incidence of chronic infection after the first passage; after the second, third and fourth passages in mice, its ability to establish chronic infection increased significantly and progressively up to 100%. Colonial morphology analysis and genetic profiling of the Mex1-derived clones recovered after the fourth passage from infected mice revealed that they were indistinguishable from the challenged strain both at phenotypic and genetic level. By testing the virulence of single clones in the Galleria mellonella infection model, we found that two Mex1-derived clones significantly increased their pathogenicity compared to the parental Mex1 strain and behaved similarly to the clinical and epidemic B. cenocepacia LMG16656T. Our findings suggest that serial passages of the environmental B. cenocepacia Mex1 strain in mice resulted in an increased ability to determine chronic lung infection and the appearance of clonal variants with increased virulence in non-vertebrate hosts.
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Affiliation(s)
- Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
| | - Moira Paroni
- Infections and Cystic Fibrosis Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy.
- Department of Biosciences, University of Milan, 20133 Milan, Italy.
| | - Luisa Pirone
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy.
| | - Ivan Coladarci
- Biology and Biotechnology Department "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Fiorentina Ascenzioni
- Biology and Biotechnology Department "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Annamaria Bevivino
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, 00123 Rome, Italy.
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48
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Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris. mBio 2017; 8:mBio.01780-17. [PMID: 29138306 PMCID: PMC5686539 DOI: 10.1128/mbio.01780-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection.IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.
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Gene Duplication in Pseudomonas aeruginosa Improves Growth on Adenosine. J Bacteriol 2017; 199:JB.00261-17. [PMID: 28808129 DOI: 10.1128/jb.00261-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/05/2017] [Indexed: 11/20/2022] Open
Abstract
The laboratory strain of Pseudomonas aeruginosa, PAO1, activates genes for catabolism of adenosine using quorum sensing (QS). However, this strain is not well-adapted for growth on adenosine, with doubling times greater than 40 h. We previously showed that when PAO1 is grown on adenosine and casein, variants emerge that grow rapidly on adenosine. To understand the mechanism by which this adaptation occurs, we performed whole-genome sequencing of five isolates evolved for rapid growth on adenosine. All five genomes had a gene duplication-amplification (GDA) event covering several genes, including the quorum-regulated nucleoside hydrolase gene, nuh, and PA0148, encoding an adenine deaminase. In addition, two of the growth variants also exhibited a nuh promoter mutation. We recapitulated the rapid growth phenotype with a plasmid containing six genes common to all the GDA events. We also showed that nuh and PA0148, the two genes at either end of the common GDA, were sufficient to confer rapid growth on adenosine. Additionally, we demonstrated that the variant nuh promoter increased basal expression of nuh but maintained its QS regulation. Therefore, GDA in P. aeruginosa confers the ability to grow efficiently on adenosine while maintaining QS regulation of nucleoside catabolism.IMPORTANCEPseudomonas aeruginosa thrives in many habitats and is an opportunistic pathogen of humans. In these diverse environments, P. aeruginosa must adapt to use myriad potential carbon sources. P. aeruginosa PAO1 cannot grow efficiently on nucleosides, including adenosine; however, it can acquire this ability through genetic adaptation. We show that the mechanism of adaptation is by amplification of a specific region of the genome and that the amplification preserves the regulation of the adenosine catabolic pathway by quorum sensing. These results demonstrate an underexplored mechanism of adaptation by P. aeruginosa, with implications for phenotypes such as development of antibiotic resistance.
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Pilla G, McVicker G, Tang CM. Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences. PLoS Genet 2017; 13:e1007014. [PMID: 28945748 PMCID: PMC5629016 DOI: 10.1371/journal.pgen.1007014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/05/2017] [Accepted: 09/08/2017] [Indexed: 11/18/2022] Open
Abstract
Acquisition of a single copy, large virulence plasmid, pINV, led to the emergence of Shigella spp. from Escherichia coli. The plasmid encodes a Type III secretion system (T3SS) on a 30 kb pathogenicity island (PAI), and is maintained in a bacterial population through a series of toxin:antitoxin (TA) systems which mediate post-segregational killing (PSK). The T3SS imposes a significant cost on the bacterium, and strains which have lost the plasmid and/or genes encoding the T3SS grow faster than wild-type strains in the laboratory, and fail to bind the indicator dye Congo Red (CR). Our aim was to define the molecular events in Shigella flexneri that cause loss of Type III secretion (T3S), and to examine whether TA systems exert positional effects on pINV. During growth at 37°C, we found that deletions of regions of the plasmid including the PAI lead to the emergence of CR-negative colonies; deletions occur through intra-molecular recombination events between insertion sequences (ISs) flanking the PAI. Furthermore, by repositioning MvpAT (which belongs to the VapBC family of TA systems) near the PAI, we demonstrate that the location of this TA system alters the rearrangements that lead to loss of T3S, indicating that MvpAT acts both globally (by reducing loss of pINV through PSK) as well as locally (by preventing loss of adjacent sequences). During growth at environmental temperatures, we show for the first time that pINV spontaneously integrates into different sites in the chromosome, and this is mediated by inter-molecular events involving IS1294. Integration leads to reduced PAI gene expression and impaired secretion through the T3SS, while excision of pINV from the chromosome restores T3SS function. Therefore, pINV integration provides a reversible mechanism for Shigella to circumvent the metabolic burden imposed by pINV. Intra- and inter-molecular events between ISs, which are abundant in Shigella spp., mediate plasticity of S. flexneri pINV.
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Affiliation(s)
- Giulia Pilla
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Gareth McVicker
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Christoph M. Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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