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Taitt CR, Leski TA, Compton JR, Chen A, Berk KL, Dorsey RW, Sozhamannan S, Dutt DL, Vora GJ. Impact of template denaturation prior to whole genome amplification on gene detection in high GC-content species, Burkholderia mallei and B. pseudomallei. BMC Res Notes 2024; 17:70. [PMID: 38475810 DOI: 10.1186/s13104-024-06717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
OBJECTIVE In this study, we sought to determine the types and prevalence of antimicrobial resistance determinants (ARDs) in Burkholderia spp. strains using the Antimicrobial Resistance Determinant Microarray (ARDM). RESULTS Whole genome amplicons from 22 B. mallei (BM) and 37 B. pseudomallei (BP) isolates were tested for > 500 ARDs using ARDM v.3.1. ARDM detected the following Burkholderia spp.-derived genes, aac(6), blaBP/MBL-3, blaABPS, penA-BP, and qacE, in both BM and BP while blaBP/MBL-1, macB, blaOXA-42/43 and penA-BC were observed in BP only. The method of denaturing template for whole genome amplification greatly affected the numbers and types of genes detected by the ARDM. BlaTEM was detected in nearly a third of BM and BP amplicons derived from thermally, but not chemically denatured templates. BlaTEM results were confirmed by PCR, with 81% concordance between methods. Sequences from 414-nt PCR amplicons (13 preparations) were 100% identical to the Klebsiella pneumoniae reference gene. Although blaTEM sequences have been observed in B. glumae, B. cepacia, and other undefined Burkholderia strains, this is the first report of such sequences in BM/BP/B. thailandensis (BT) clade. These results highlight the importance of sample preparation in achieving adequate genome coverage in methods requiring untargeted amplification before analysis.
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Affiliation(s)
- Chris R Taitt
- Nova Research Inc., Alexandria, VA, 22308, USA
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Tomasz A Leski
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Jaimee R Compton
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA
| | - Amy Chen
- Karle's Fellow, US Naval Research Laboratory, Washington, DC, USA
| | - Kimberly L Berk
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Robert W Dorsey
- US Army Combat Capabilities Development Command-Chemical Biological Center, Aberdeen Proving Ground, MD, USA
| | - Shanmuga Sozhamannan
- Defense Biological Product Assurance Office, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Frederick, MD, USA
- Joint Research and Development, Inc., Stafford, VA, USA
| | - Dianne L Dutt
- Defense Threat Reduction Agency, Joint Science and Technology Office, Ft. Belvoir, VA, USA
| | - Gary J Vora
- Center for Biomolecular Science & Engineering, US Naval Research Laboratory, Washington, DC, USA.
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Pan-genome analysis of the Burkholderia gladioli PV. Cocovenenans reveal the extent of variation in the toxigenic gene cluster. Food Microbiol 2023; 113:104249. [PMID: 37098416 DOI: 10.1016/j.fm.2023.104249] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/04/2022] [Accepted: 02/26/2023] [Indexed: 03/06/2023]
Abstract
Burkholderia gladioli has been reported as the pathogen responsible for cases of foodborne illness in many countries. The poisonous bongkrekic acid (BA) produced by B. gladioli was linked to a gene cluster absent in non-pathogenic strains. The whole genome sequence of eight bacteria strains, which were screened from the collected 175 raw food and environmental samples, were assembled and analyzed to detect a significant association of 19 protein-coding genes with the pathogenic status. Except for the common BA synthesis-related gene, several other genes, including the toxin-antitoxin genes, were also absent in the non-pathogenic strains. The bacteria strains with the BA gene cluster were found to form a single cluster in the analysis of all B. gladioli genome assemblies for the variants in the gene cluster. Divergence of this cluster was detected in the analysis for both the flanking sequences and those of the whole genome level, which indicates its complex origin. Genome recombination was found to cause a precise sequence deletion in the gene cluster region, which was found to be predominant in the non-pathogenic strains indicating the possible effect of horizontal gene transfer. Our study provided new information and resources for understanding the evolution and divergence of the B. gladioli species.
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Saroha T, Patil PP, Rana R, Kumar R, Kumar S, Singhal L, Gautam V, Patil PB. Genomic features, antimicrobial susceptibility, and epidemiological insights into Burkholderia cenocepacia clonal complex 31 isolates from bloodstream infections in India. Front Cell Infect Microbiol 2023; 13:1151594. [PMID: 37153161 PMCID: PMC10155701 DOI: 10.3389/fcimb.2023.1151594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Introduction Burkholderia cepacia complex (Bcc) clonal complex (CC) 31, the predominant lineage causing devastating outbreaks globally, has been a growing concern of infections in non-cystic fibrosis (NCF) patients in India. B. cenocepacia is very challenging to treat owing to its virulence determinants and antibiotic resistance. Improving the management of these infections requires a better knowledge of their resistance patterns and mechanisms. Methods Whole-genome sequences of 35 CC31 isolates obtained from patient samples, were analyzed against available 210 CC31 genomes in the NCBI database to glean details of resistance, virulence, mobile elements, and phylogenetic markers to study genomic diversity and evolution of CC31 lineage in India. Results Genomic analysis revealed that 35 isolates belonging to CC31 were categorized into 11 sequence types (ST), of which five STs were reported exclusively from India. Phylogenetic analysis classified 245 CC31 isolates into eight distinct clades (I-VIII) and unveiled that NCF isolates are evolving independently from the global cystic fibrosis (CF) isolates forming a distinct clade. The detection rate of seven classes of antibiotic-related genes in 35 isolates was 35 (100%) for tetracyclines, aminoglycosides, and fluoroquinolones; 26 (74.2%) for sulphonamides and phenicols; 7 (20%) for beta-lactamases; and 1 (2.8%) for trimethoprim resistance genes. Additionally, 3 (8.5%) NCF isolates were resistant to disinfecting agents and antiseptics. Antimicrobial susceptibility testing revealed that majority of NCF isolates were resistant to chloramphenicol (77%) and levofloxacin (34%). NCF isolates have a comparable number of virulence genes to CF isolates. A well-studied pathogenicity island of B. cenocepacia, GI11 is present in ST628 and ST709 isolates from the Indian Bcc population. In contrast, genomic island GI15 (highly similar to the island found in B. pseudomallei strain EY1) is exclusively reported in ST839 and ST824 isolates from two different locations in India. Horizontal acquisition of lytic phage ST79 of pathogenic B. pseudomallei is demonstrated in ST628 isolates Bcc1463, Bcc29163, and BccR4654 amongst CC31 lineage. Discussion The study reveals a high diversity of CC31 lineages among B. cenocepacia isolates from India. The extensive information from this study will facilitate the development of rapid diagnostic and novel therapeutic approaches to manage B. cenocepacia infections.
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Affiliation(s)
- Tanu Saroha
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prashant P. Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
| | - Rekha Rana
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Kumar
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
| | - Lipika Singhal
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Vikas Gautam
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
- *Correspondence: Prabhu B. Patil, ; Vikas Gautam,
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, Council of Scientific and Industrial Research (CSIR)-Institute of Microbial Technology, Chandigarh, India
- *Correspondence: Prabhu B. Patil, ; Vikas Gautam,
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Rios-Miguel AB, Smith GJ, Cremers G, van Alen T, Jetten MS, Op den Camp HJ, Welte CU. Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates. WATER RESEARCH X 2022; 16:100152. [PMID: 36042984 PMCID: PMC9420511 DOI: 10.1016/j.wroa.2022.100152] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/13/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.
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Key Words
- 4-AP, 4-aminophenol
- APAP, N-acetyl-p-aminophenol or paracetamol
- Amidase evolution
- Deaminase
- Dioxygenase
- GAC, granular activated carbon
- HGT, horizontal gene transfer
- HQ, hydroquinone
- HRT, hydraulic retention time
- MAG, metagenome-assembled genome
- MBR, membrane bioreactor
- Metagenomics
- Mobile genetic elements
- Pfast, Pseudomonas sp. isolate growing fast on APAP as sole carbon source
- Pseudomonas
- Pslow, Pseudomonas sp. isolate growing slow on APAP as sole carbon source
- SRT, solid retention time
- TPM, transcripts per million
- WWTP, wastewater treatment plant
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Affiliation(s)
- Ana B. Rios-Miguel
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Garrett J. Smith
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Mike S.M. Jetten
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Huub J.M. Op den Camp
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
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Kumar S, Anwer R, Azzi A. Virulence Potential and Treatment Options of Multidrug-Resistant (MDR) Acinetobacter baumannii. Microorganisms 2021; 9:microorganisms9102104. [PMID: 34683425 PMCID: PMC8541637 DOI: 10.3390/microorganisms9102104] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/18/2021] [Accepted: 09/21/2021] [Indexed: 12/12/2022] Open
Abstract
Acinetobacter baumannii is an opportunistic pathogen which is undoubtedly known for a high rate of morbidity and mortality in hospital-acquired infections. A. baumannii causes life-threatening infections, including; ventilator-associated pneumonia (VAP), meningitis, bacteremia, and wound and urinary tract infections (UTI). In 2017, the World Health Organization listed A. baumannii as a priority-1 pathogen. The prevalence of A. baumannii infections and outbreaks emphasizes the direct need for the use of effective therapeutic agents for treating such infections. Available antimicrobials, such as; carbapenems, tigecycline, and colistins have insufficient effectiveness due to the appearance of multidrug-resistant strains, accentuating the need for alternative and novel therapeutic remedies. To understand and overcome this menace, the knowledge of recent discoveries on the virulence factors of A. baumannii is needed. Herein, we summarized the role of various virulence factors, including; outer membrane proteins, efflux pumps, biofilm, penicillin-binding proteins, and siderophores/iron acquisition systems. We reviewed the recent scientific literature on different A. baumannii virulence factors and the effective antimicrobial agents for the treatment and management of bacterial infections.
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Affiliation(s)
- Sunil Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to Be University), Mullana, Ambala 133207, India;
| | - Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia;
| | - Arezki Azzi
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia
- Correspondence:
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Peng Z, Dottorini T, Hu Y, Li M, Yan S, Fanning S, Baker M, Xu J, Li F. Comparative Genomic Analysis of the Foodborne Pathogen Burkholderia gladioli pv. cocovenenans Harboring a Bongkrekic Acid Biosynthesis Gene Cluster. Front Microbiol 2021; 12:628538. [PMID: 34079526 PMCID: PMC8166232 DOI: 10.3389/fmicb.2021.628538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
The environmental bacterium Burkholderia gladioli pv. cocovenenans (B. cocovenenans) has been linked to fatal food poisoning cases in Asia and Africa. Bongkrekic acid (BA), a mitochondrial toxin produced by B. cocovenenans, is thought to be responsible for these outbreaks. While there are over 80 species in the Burkholderia genus, B. cocovenenans is the only pathovar capable of producing BA and causing human death. However, the genomic features of B. gladioli and the evolution of the BA biosynthesis gene cluster, bon, in B. cocovenenans remain elusive. In this study, 239 whole genome sequences (WGSs) of B. gladioli, isolated from 12 countries collected over 100 years, were used to analyze the intra-species genomic diversity and phylogenetic relationships of B. gladioli and to explore the origin and evolution of the bon gene cluster. Our results showed that the genome-wide average nucleotide identity (ANI) values were above 97.29% for pairs of B. gladioli genomes. Thirty-six of the 239 (15.06%) B. gladioli genomes, isolated from corn, rice, fruits, soil, and patients from Asia, Europe, North America, and South America, contained the bon gene cluster and formed three clades within the phylogenetic tree. Pan- and core-genome analysis suggested that the BA biosynthesis genes were recently acquired. Comparative genome analysis of the bon gene cluster showed that complex recombination events contributed to this toxin biosynthesis gene cluster's evolution and formation. This study suggests that a better understanding of the genomic diversity and evolution of this lethal foodborne pathovar will potentially contribute to B. cocovenenans food poisoning outbreak prevention.
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Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
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Wallner A, King E, Ngonkeu ELM, Moulin L, Béna G. Genomic analyses of Burkholderia cenocepacia reveal multiple species with differential host-adaptation to plants and humans. BMC Genomics 2019; 20:803. [PMID: 31684866 PMCID: PMC6829993 DOI: 10.1186/s12864-019-6186-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Background Burkholderia cenocepacia is a human opportunistic pathogen causing devastating symptoms in patients suffering from immunodeficiency and cystic fibrosis. Out of the 303 B. cenocepacia strains with available genomes, the large majority were isolated from a clinical context. However, several isolates originate from other environmental sources ranging from aerosols to plant endosphere. Plants can represent reservoirs for human infections as some pathogens can survive and sometimes proliferate in the rhizosphere. We therefore investigated if B. cenocepacia had the same potential. Results We selected genome sequences from 31 different strains, representative of the diversity of ecological niches of B. cenocepacia, and conducted comparative genomic analyses in the aim of finding specific niche or host-related genetic determinants. Phylogenetic analyses and whole genome average nucleotide identity suggest that strains, registered as B. cenocepacia, belong to at least two different species. Core-genome analyses show that the clade enriched in environmental isolates lacks multiple key virulence factors, which are conserved in the sister clade where most clinical isolates fall, including the highly virulent ET12 lineage. Similarly, several plant associated genes display an opposite distribution between the two clades. Finally, we suggest that B. cenocepacia underwent a host jump from plants/environment to animals, as supported by the phylogenetic analysis. We eventually propose a name for the new species that lacks several genetic traits involved in human virulence. Conclusion Regardless of the method used, our studies resulted in a disunited perspective of the B. cenocepacia species. Strains currently affiliated to this taxon belong to at least two distinct species, one having lost several determining animal virulence factors.
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Affiliation(s)
- Adrian Wallner
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
| | - Eoghan King
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
| | - Eddy L M Ngonkeu
- Institute of Agronomic Research for Development (IRAD), PO Box 2123, Yaoundé, Cameroon
| | - Lionel Moulin
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
| | - Gilles Béna
- IRD, CIRAD, University of Montpellier, IPME; 911 avenue Agropolis, BP 64501, 34394, Montpellier, France.
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Alex A, Antunes A. Whole-Genome Comparisons Among the Genus Shewanella Reveal the Enrichment of Genes Encoding Ankyrin-Repeats Containing Proteins in Sponge-Associated Bacteria. Front Microbiol 2019; 10:5. [PMID: 30787909 PMCID: PMC6372511 DOI: 10.3389/fmicb.2019.00005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 01/07/2019] [Indexed: 11/13/2022] Open
Abstract
The bacterial members of the genus Shewanella are widely distributed and inhabit both freshwater and marine environments. Some members of Shewanella have gained considerable attention due to its ability to survive in redox-stratified environments. However, a gap of knowledge exists on the key genomic features of the sponge-associated Shewanella sp. involving the successful host-bacteria interaction, as sponge-symbiotic Shewanella are largely underrepresented in the public repositories. With the aim of identifying the genomic signatures of sponge-Shewanella association, we generated a high-quality genome data of a sponge-associated, Shewanella sp. OPT22, isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative analyses of 68 genome strains of the genus Shewanella including two previously reported genomes of sponge-associated bacteria, Shewanella spongiae KCTC 22492 and Shewanella sp. Alg231_23. The 16S rRNA-based phylogenetic reconstruction showed the well-supported affiliation of OPT22 and KCTC 22492 with previously reported sponge-associated bacteria, affirming the “sponge-specific” nature of these two bacterial strains isolated from different marine sponge species from the Atlantic and Pacific (East Sea) Oceans, respectively. The genome comparison of the 68 strains of Shewanella inhabiting different habitats revealed the unusual/previously unreported abundance of genes encoding for ankyrin-repeat containing proteins (ANKs) in the genomes of the two sponge-associated strains, OPT22 (ANKs; n = 45) and KCTC 22492 (ANKs; n = 52), which might be involved in sponge-Shewanella interactions. Focused analyses detected the syntenic organization of the gene cluster encoding major secretion system (type III/IV/VI) components and the presence of effector homologs in OPT22 and KCTC 22492 that seem to play a role in the virulence of the sponge bacteria. The genomic island (GI) of Shewanella sp. OPT22 was identified to localize a gene cluster encoding T4SS components and ANK (n = 1), whereas S. spongiae KCTC 22492 harbored a total of seven ANKs within multiple GIs. GIs may play a pivotal role in the dissemination of symbioses-related genes (ANKs) through the horizontal gene transfer, contributing to the diversification and adaptation of sponge-associated Shewanella. Overall, the genome analyses of Shewanella isolates from marine sponges revealed genomic repertoires that might be involved in establishing successful symbiotic relationships with the sponge hosts.
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Affiliation(s)
- Anoop Alex
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
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Salloum T, Nassour E, Araj GF, Abboud E, Tokajian S. Insights into the genome diversity and virulence of two clinical isolates of Burkholderia cenocepacia. J Med Microbiol 2018; 67:1157-1167. [PMID: 29897328 DOI: 10.1099/jmm.0.000759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
PURPOSE Burkholderia cenocepacia is among the most common members of the Burkholderia cepacia complex (Bcc) isolated from patients with cystic fibrosis (CF). The factors triggering the high rates of morbidity and mortality in CF patients are not well elucidated. In this study, we aim to highlight the genome diversity of two clinical isolates of B. cenocepacia through comparative genome analysis. METHODOLOGY The repertoire of virulence factors and resistance genes compared to reference strains J2315 and K56-2 was elucidated. The isolates were screened for the presence of phages and insertion sequences. Two methods were combined to obtain an accurate prediction of genomic islands (GIs): the cumulative GC profile and the IslandViewer web tool. To study evolutionary relatedness, whole genome-based single-nucleotide polymorphism (wgSNP) analysis was also performed with 43 publically available strains of the Bcc of various sequence types.Results/Key findings. Genome-based species identification of the two isolates BC-AUH and BC-BMEH confirmed the species as B. cenocepacia. Both belonged to ST-602, a double-locus variant of ST-32 (CC31), genomovar IIIA, and carried a large number of antibiotic resistance genes. Eighteen GIs were predicted in BC-AUH and BC-BMEH, occupying 9.3 and 6.1 % of the respective genomes. Comparison to J2315 revealed 89 and 85 genes unique to BC-BMEH and BC-AUH, respectively. Additionally, 1823 intergenic SNPs were detected between BC-BMEH and BC-AUH. CONCLUSION This study mapped existing genetic variations in B. cenocepacia associated with notorious outcomes in CF patients, and the data obtained provide comprehensive, genome-inferred insights and multifactorial examination of an important human pathogen.
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Affiliation(s)
- Tamara Salloum
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Elie Nassour
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - George F Araj
- 2Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Edmond Abboud
- 3Laboratory Department, the Middle East Institute of Health University Center, Bsalim, Lebanon
| | - Sima Tokajian
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
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Scoffone VC, Chiarelli LR, Trespidi G, Mentasti M, Riccardi G, Buroni S. Burkholderia cenocepacia Infections in Cystic Fibrosis Patients: Drug Resistance and Therapeutic Approaches. Front Microbiol 2017; 8:1592. [PMID: 28878751 PMCID: PMC5572248 DOI: 10.3389/fmicb.2017.01592] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/04/2017] [Indexed: 12/29/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen particularly dangerous for cystic fibrosis (CF) patients. It can cause a severe decline in CF lung function possibly developing into a life-threatening systemic infection known as cepacia syndrome. Antibiotic resistance and presence of numerous virulence determinants in the genome make B. cenocepacia extremely difficult to treat. Better understanding of its resistance profiles and mechanisms is crucial to improve management of these infections. Here, we present the clinical distribution of B. cenocepacia described in the last 6 years and methods for identification and classification of epidemic strains. We also detail new antibiotics, clinical trials, and alternative approaches reported in the literature in the last 5 years to tackle B. cenocepacia resistance issue. All together these findings point out the urgent need of new and alternative therapies to improve CF patients’ life expectancy.
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Affiliation(s)
- Viola C Scoffone
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | | | - Gabriele Trespidi
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Massimo Mentasti
- Respiratory and Vaccine Preventable Bacteria Reference Unit, Public Health EnglandLondon, United Kingdom.,Department of Microbiology, Royal Cornwall HospitalTruro, United Kingdom
| | - Giovanna Riccardi
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
| | - Silvia Buroni
- Department of Biology and Biotechnology, University of PaviaPavia, Italy
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Teng JLL, Yeung ML, Chan E, Jia L, Lin CH, Huang Y, Tse H, Wong SSY, Sham PC, Lau SKP, Woo PCY. PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome. Front Microbiol 2017; 8:1448. [PMID: 28824579 PMCID: PMC5539568 DOI: 10.3389/fmicb.2017.01448] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/17/2017] [Indexed: 12/19/2022] Open
Abstract
Although PacBio third-generation sequencers have improved the read lengths of genome sequencing which facilitates the assembly of complete genomes, no study has reported success in using PacBio data alone to completely sequence a two-chromosome bacterial genome from a single library in a single run. Previous studies using earlier versions of sequencing chemistries have at most been able to finish bacterial genomes containing only one chromosome with de novo assembly. In this study, we compared the robustness of PacBio RS II, using one SMRT cell and the latest P6-C4 chemistry, with Illumina HiSeq 1500 in sequencing the genome of Burkholderia pseudomallei, a bacterium which contains two large circular chromosomes, very high G+C content of 68–69%, highly repetitive regions and substantial genomic diversity, and represents one of the largest and most complex bacterial genomes sequenced, using a reference genome generated by hybrid assembly using PacBio and Illumina datasets with subsequent manual validation. Results showed that PacBio data with de novo assembly, but not Illumina, was able to completely sequence the B. pseudomallei genome without any gaps or mis-assemblies. The two large contigs of the PacBio assembly aligned unambiguously to the reference genome, sharing >99.9% nucleotide identities. Conversely, Illumina data assembled using three different assemblers resulted in fragmented assemblies (201–366 contigs), sharing only 92.2–100% and 92.0–100% nucleotide identities to chromosomes I and II reference sequences, respectively, with no indication that the B. pseudomallei genome consisted of two chromosomes with four copies of ribosomal operons. Among all assemblies, the PacBio assembly recovered the highest number of core and virulence proteins, and housekeeping genes based on whole-genome multilocus sequence typing (wgMLST). Most notably, assembly solely based on PacBio outperformed even hybrid assembly using both PacBio and Illumina datasets. Hybrid approach generated only 74 contigs, while the PacBio data alone with de novo assembly achieved complete closure of the two-chromosome B. pseudomallei genome without additional costly bench work and further sequencing. PacBio RS II using P6-C4 chemistry is highly robust and cost-effective and should be the platform of choice in sequencing bacterial genomes, particularly for those that are well-known to be difficult-to-sequence.
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Affiliation(s)
- Jade L L Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Elaine Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Lilong Jia
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Chi Ho Lin
- Centre for Genomic Sciences, The University of Hong KongHong Kong, Hong Kong
| | - Yi Huang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong
| | - Herman Tse
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Samson S Y Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong
| | - Pak Chung Sham
- Centre for Genomic Sciences, The University of Hong KongHong Kong, Hong Kong.,Department of Psychiatry, The University of Hong KongHong Kong, Hong Kong
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, Hong Kong
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, Department of MicrobiologyThe University of Hong Kong, Hong Kong, Hong Kong.,Research Centre of Infection and ImmunologyThe University of Hong Kong, Hong Kong, Hong Kong.,Carol Yu Centre for Infection, The University of Hong KongHong Kong, Hong Kong.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong KongHong Kong, Hong Kong
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