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Rasaruck U, Kasetsuwan N, Kittipibul T, Pongchaikul P, Chatsuwan T. Composition and diversity of meibum microbiota in meibomian gland dysfunction and the correlation with tear cytokine levels. PLoS One 2023; 18:e0296296. [PMID: 38134040 PMCID: PMC10745150 DOI: 10.1371/journal.pone.0296296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
Meibomian gland dysfunction (MGD) leads to meibum stasis and pathogenic bacteria proliferation. We determined meibum microbiota via next-generation sequencing (NGS) and examined their association with tear cytokine levels in patients with MGD. This cross-sectional study included 44 moderate-severe patients with MGD and 44 healthy controls (HCs). All volunteers underwent assessment with the ocular surface disease index questionnaire, Schirmer without anesthesia, tear break-up time, Oxford grading of ocular surface staining, and lid and meibum features. Sample collection included tears for cytokine detection and meibum for 16S rRNA NGS. No significant differences were observed in the α-diversity of patients with MGD compared with that in HCs. However, Simpson's index showed significantly decreased α-diversity for severe MGD than for moderate MGD (p = 0.045). Principal coordinate analysis showed no significant differences in β-diversity in meibum samples from patients with MGD and HCs. Patients with MGD had significantly higher relative abundances of Bacteroides (8.54% vs. 6.00%, p = 0.015) and Novosphingobium (0.14% vs. 0.004%, p = 0.012) than the HCs. Significantly higher interleukin (IL)-17A was detected in the MGD group than in the HC group, particularly for severe MGD (p = 0.008). Although Bacteroides was more abundant in the MGD group than in the HC group, it was not positively correlated with IL-17A. The relationship between core meibum microbiota and tear cytokine levels remains unclear. However, increased Bacteroides and Novosphingobium abundance may be critical in MGD pathophysiology.
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Affiliation(s)
- Ubonwan Rasaruck
- Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ngamjit Kasetsuwan
- Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center of Cornea and Limbal Stem Cell Transplantation, Department of Ophthalmology, King Chulalongkorn Memorial Hospital and Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thanachaporn Kittipibul
- Department of Ophthalmology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center of Cornea and Limbal Stem Cell Transplantation, Department of Ophthalmology, King Chulalongkorn Memorial Hospital and Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pisut Pongchaikul
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital Mahidol University, Samut Prakarn, Thailand
- Integrative Computational Bioscience (ICBS) Center, Mahidol University, Nakorn Pathom, Thailand
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Comprehensive investigation of antibiotic resistance gene content in cfiA-harboring Bacteroides fragilis isolates of human and animal origins by whole genome sequencing. Int J Med Microbiol 2022; 312:151559. [PMID: 35961233 DOI: 10.1016/j.ijmm.2022.151559] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 06/18/2022] [Accepted: 08/07/2022] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION The emergence of multidrug resistance in Bacteroides fragilis, especially the phylogenetic lineage carrying the carbapenemase gene cfiA, represents an increasing threat to human health. However, knowledge on the diversity of the multidrug-resistant strains and the genetic elements carrying the antibiotic resistance genes (ARGs) remains limited. AIM The objective of the study was to describe the resistome in cfiA-positive B. fragilis. METHODS A collection of cfiA-positive B. fragilis from diverse human (8 bacteremias, 15 wound infections) and animal (2 chickens, 2 pigs, 6 dogs, 3 cats) sources in Hong Kong, 2015-2017 was analysed by whole genome sequencing. RESULTS In the 36 isolates, 13 distinct ARGs (total number 83, median 2, range 0-7 per isolate) other than cfiA were detected. ARGs encoding resistance to aminoglycosides, β-lactams, macrolides, sulphonamides and tetracyclines were carried by CTn341-like, CTnHyb-like, Tn5220-like, Tn4555-like and Tn613-like transposons and were detected in phylogenetically diverse isolates of different host sources. Only few ARGs encoding resistance to metronidazole and tetracyclines were localized on plasmids. In two chicken isolates, a novel transposon (designated as Tn6994) was found to be involved in the dissemination of multiple ARGs mediating resistance to multiple antibiotics, including metronidazole and linezolid that are critically important for treatment of anaerobic infections. In mating experiments, Tn6994 and the associated phenotypic resistance could be transferred to Bacteroides nordii recipient. CONCLUSION This study illustrates the importance of transposons in the dissemination of ARGs in the cfiA-positive division of B. fragilis. One Health approach is necessary to track the dissemination of ARGs.
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Stankeviciute G, Tang P, Ashley B, Chamberlain JD, Hansen ME, Coleman A, D’Emilia R, Fu L, Mohan EC, Nguyen H, Guan Z, Campopiano DJ, Klein EA. Convergent evolution of bacterial ceramide synthesis. Nat Chem Biol 2022; 18:305-312. [PMID: 34969973 PMCID: PMC8891067 DOI: 10.1038/s41589-021-00948-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 10/29/2021] [Indexed: 12/20/2022]
Abstract
The bacterial domain produces numerous types of sphingolipids with various physiological functions. In the human microbiome, commensal and pathogenic bacteria use these lipids to modulate the host inflammatory system. Despite their growing importance, their biosynthetic pathway remains undefined since several key eukaryotic ceramide synthesis enzymes have no bacterial homolog. Here we used genomic and biochemical approaches to identify six proteins comprising the complete pathway for bacterial ceramide synthesis. Bioinformatic analyses revealed the widespread potential for bacterial ceramide synthesis leading to our discovery of a Gram-positive species that produces ceramides. Biochemical evidence demonstrated that the bacterial pathway operates in a different order from that in eukaryotes. Furthermore, phylogenetic analyses support the hypothesis that the bacterial and eukaryotic ceramide pathways evolved independently.
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Affiliation(s)
- Gabriele Stankeviciute
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA
| | - Peijun Tang
- East Chem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Ben Ashley
- East Chem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Joshua D. Chamberlain
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Matthew E.B. Hansen
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aimiyah Coleman
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Rachel D’Emilia
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Larina Fu
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Eric C. Mohan
- East Chem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom
| | - Hung Nguyen
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.
| | - Dominic J. Campopiano
- East Chem School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, United Kingdom,Correspondence to: , , and
| | - Eric A. Klein
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ 08102, USA,Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901, USA,Biology Department, Rutgers University-Camden, Camden, NJ 08102, USA.,Correspondence to: , , and
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Matos J, Matos I, Calha M, Santos P, Duarte I, Cardoso Y, Faleiro ML. Insights from Bacteroides Species in Children with Type 1 Diabetes. Microorganisms 2021; 9:1436. [PMID: 34361871 PMCID: PMC8306409 DOI: 10.3390/microorganisms9071436] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/24/2021] [Accepted: 06/29/2021] [Indexed: 12/11/2022] Open
Abstract
In our previous study the enrichment of the intestinal proteome of type 1 diabetes (T1D) children with Bacteroides proteins was observed, which led us to our current study that aimed to isolate and characterize Bacteroides species from fecal samples of T1D and control children. Repetitive sequence-based PCR (rep-PCR) was used for typing the isolated Bacteroides species. The antibiotic susceptibility and mucinolytic activity of the isolates was determined. The quantification of specific bacterial groups in the fecal samples was determined by qPCR. The ability to adhere and invade the human colonic cell line HT29-MTX-E12 of strains of P. dorei, B. uniformis and P. distasonis was determined and their whole genome sequencing was performed. The results showed similar numbers of Bacteroides species in T1D and control samples, but unique Bacteroides species and a higher recovery of P. distasonis from T1D samples was observed. Rep-PCR grouped the different Bacteroides species, but no discrimination by origin was achieved. T1D children showed a significant increase in Proteobacteria and a depletion in Lactobacillus sp. All tested P. dorei, B. uniformis and P. distasonis were able to adhere to HT29-MTX-E12 cells but significant differences (p < 0.05) in the ability to invade was observed. The highest ability to invade was exhibited by P. distasonis PtF D14MH1 and P. dorei PtFD16P1, while B. uniformis strains were unable to invade. The damage to tight junctions was also observed. The presence of Lactobacillus sp. inhibited the invasion ability of P. distasonis PtF D14MH1 but not P. dorei PtFD16P1. Sequences of agonist peptides of the human natural preproinsulin and the insulin B chain insB:9-23 peptide mimics were identified. The results reported in our study stresses the continued efforts required to clarify the link between T1D and gut microbiota.
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Affiliation(s)
- José Matos
- Faculdade de Ciências e Tecnologia, C8, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal; (J.M.); (I.M.); (P.S.); (Y.C.)
- Algarve Biomedical Center, Research Institute, 8005-139 Faro, Portugal
| | - Isabel Matos
- Faculdade de Ciências e Tecnologia, C8, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal; (J.M.); (I.M.); (P.S.); (Y.C.)
- Algarve Biomedical Center, Research Institute, 8005-139 Faro, Portugal
| | - Manuela Calha
- Unidade de Diabetologia, Centro Hospitalar Universitário do Algarve, 8000-386 Faro, Portugal;
| | - Pedro Santos
- Faculdade de Ciências e Tecnologia, C8, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal; (J.M.); (I.M.); (P.S.); (Y.C.)
- Algarve Biomedical Center, Research Institute, 8005-139 Faro, Portugal
| | - Isabel Duarte
- CINTESIS—Center for Health Technology and Services Research, Universidade do Algarve, 8005-139 Faro, Portugal;
| | - Yameric Cardoso
- Faculdade de Ciências e Tecnologia, C8, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal; (J.M.); (I.M.); (P.S.); (Y.C.)
| | - Maria Leonor Faleiro
- Faculdade de Ciências e Tecnologia, C8, Campus de Gambelas, Universidade do Algarve, 8005-139 Faro, Portugal; (J.M.); (I.M.); (P.S.); (Y.C.)
- Algarve Biomedical Center, Research Institute, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal
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5
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Bhat AH. Bacterial zoonoses transmitted by household pets and as reservoirs of antimicrobial resistant bacteria. Microb Pathog 2021; 155:104891. [PMID: 33878397 DOI: 10.1016/j.micpath.2021.104891] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 12/27/2022]
Abstract
Numerous individuals are committed to growing pet creatures like cats, dogs, and rats etc., pay care for them and as a result of this, there's a boost of their populace in advanced culture. The close interaction between family pets and individuals offers ideal conditions for bacterial transmission. Distinctive sorts of antimicrobial agents are exploited for animal husbandry and studies have revealed that many bacteria have attained confrontation against them viz., Staphylococcus intermedius, Escherichia coli, methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococci and multidrug-resistant Salmonella typhi etc. and a few of these are a prospective for zoonotic transmission. In the current review, the attention has been paid on how household pets, especially dogs disperse the antimicrobial resistance in contrast to that of food animals. A lot of evidences are accessible on food animals and nation-wide scrutiny programmes solely hub on food animals; therefore, for steerage antimicrobial use policy in small animal veterinary exercise as well as for gauging the chance of transmission of antimicrobial resistance to humans' statistics on pet animals are sincerely needed. Transmission of such organisms, especially pathogenic staphylococci, occurs between pets, owners, and veterinary staff, and pets can act as reservoirs of such bacteria; this may additionally have an impact on the use of antimicrobials in human medicine. There is a need to generate statistics concerning each the levels of carriage of such microorganism in pets and the risk factors associated with the switch of the microorganism to human beings who have contact with infected pets, as nicely as to improve hygiene measures in veterinary practice.
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Affiliation(s)
- Aashaq Hussain Bhat
- Department of Zoology, Government Degree College, Billawar, 184204, Kathua, Jammu and Kashmir, India.
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Valdezate S, Cobo F, Monzón S, Medina-Pascual MJ, Zaballos Á, Cuesta I, Pino-Rosa S, Villalón P. Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA. Antibiotics (Basel) 2021; 10:antibiotics10030304. [PMID: 33809460 PMCID: PMC8001070 DOI: 10.3390/antibiotics10030304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/09/2021] [Accepted: 03/13/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Bacteroides fragilis shows high antimicrobial resistance (AMR) rates and possesses numerous AMR mechanisms. Its carbapenem-resistant strains (metallo-β-lactamase cfiA-positive) appear as an emergent, evolving clade. Methods: This work examines the genomes, taxonomy, and phylogenetic relationships with respect to other B. fragilis genomes of two B. fragilis strains (CNM20180471 and CNM20200206) resistant to meropenem+EDTA and other antimicrobial agents. Results: Both strains possessed cfiA genes (cfiA14b and the new cfiA28), along with other AMR mechanisms. The presence of other efflux-pump genes, mexAB/mexJK/mexXY-oprM, acrEF/mdtEF-tolC, and especially cusR, which reduces the entry of carbapenem via the repression of porin OprD, may be related to meropenem–EDTA resistance. None of the detected insertion sequences were located upstream of cfiA. The genomes of these and other B. fragilis strains that clustered together in phylogenetic analyses did not meet the condition of >95% average nucleotide/amino acid identity, or >70% in silico genome-to-genome hybridization similarity, to be deemed members of the same species, although <1% difference in the genomic G+C content was seen with respect to the reference genome B. fragilis NCTC 9343T. Conclusions: Carbapenem-resistant strains may be considered a distinct clonal entity, and their surveillance is recommended given the ease with which they appear to acquire AMR.
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Affiliation(s)
- Sylvia Valdezate
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
- Correspondence: ; Tel.: +34-91-822-3734; Fax: +34-91-509-7966
| | - Fernando Cobo
- Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain; (F.C.); (S.M.); (I.C.)
| | - Sara Monzón
- Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain; (F.C.); (S.M.); (I.C.)
| | - María J. Medina-Pascual
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
| | - Ángel Zaballos
- Bionformatics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain;
- Genomics Unit, Applied Services, Training and Research, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain
| | - Isabel Cuesta
- Department of Microbiology, Instituto Biosanitario de Granada, University Hospital of Virgen de las Nieves, Avda. Fuerzas Armadas s/n, 18014 Granada, Spain; (F.C.); (S.M.); (I.C.)
| | - Silvia Pino-Rosa
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
| | - Pilar Villalón
- National Centre of Microbiology, Reference and Research Laboratory for Taxonomy, Instituto de Salud Carlos III, Majadahonda, 280220 Madrid, Spain; (M.J.M.-P.); (S.P.-R.); (P.V.)
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Affiliation(s)
- Hannah C. Carrow
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Lakshmi E. Batachari
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Hiutung Chu
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccine, La Jolla, California, United States of America
- Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada
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8
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Kim JA, Jung MY, Kim DH, Kim Y. Genome analysis of Bacteroides sp.CACC 737 isolated from feline for its potential application. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2020; 62:952-955. [PMID: 33987575 PMCID: PMC7721585 DOI: 10.5187/jast.2020.62.6.952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/21/2020] [Accepted: 10/15/2020] [Indexed: 11/20/2022]
Abstract
Bacteroides sp. CACC 737 was isolated from a feline, and its
potential probiotic properties were characterized using functional genome
analysis. Whole-genome sequencing was performed using the PacBio RSII and
Illumina HiSeq platforms. The complete genome of strain CACC 737 contained 4.6
Mb, with a guanine (G) + cytosine (C) content of 45.8%, six cryptic plasmids,
and extracellular polysaccharide gene as unique features. The strain was
beneficial to animal health when consumed as feed, for example, for ameliorating
immunological dysfunctions and metabolic disorders. The genome information adds
to the comprehensive understanding of Bacteroides sp. and
suggests potential animal-related industrial applications for this strain.
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Affiliation(s)
- Jung-Ae Kim
- Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea.,Department of Bioactive Material Sciences, Jeonbuk National University, Jeonju 54896, Korea
| | - Min Young Jung
- Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea
| | - Dae-Hyuk Kim
- Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea.,Department of Molecular Biology, Jeonbuk National University, Jeonju 54896, Korea
| | - Yangseon Kim
- Department of Research and Development, Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup 56212, Korea
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Mohsin M, Tanaka K, Kawahara R, Kondo S, Noguchi H, Motooka D, Nakamura S, Khong DT, Nguyen TN, Hoang TN, Yamamoto Y. Whole-genome sequencing and comparative analysis of the genomes of Bacteroides thetaiotaomicron and Escherichia coli isolated from a healthy resident in Vietnam. J Glob Antimicrob Resist 2020; 21:65-67. [PMID: 32200128 DOI: 10.1016/j.jgar.2020.02.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 02/25/2020] [Accepted: 02/29/2020] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES The aim of this study was to report the draft genome sequences of two multidrug-resistant bacteria (Bacteroides thetaiotaomicron F9-2 and Escherichia coli 09-02E) isolated from stool samples of a healthy resident in Vietnam. METHODS Genome sequences were determined using MiSeq and MinION platforms. Genome assembly was performed using Platanus Assembler v.1.2.4 and Canu v.1.7. The DDBJ Fast Annotation and Submission Tool were used for genome annotation. RESULTS The genome of B. thetaiotaomicron F9-2 comprised 6 283 774 bp with a GC content of 42.7% and 4802 protein coding sequences (CDS), whereas the genome of E. coli 09-02E comprised 5 246 320 bp with a GC content of 50.6% and 4991 protein CDS. Both strains harboured common antimicrobial resistance genes, such as those for sulfonamides (sul2) and aminoglycosides (strA, strB). However, the sul2-strA-strB cassette was located on the chromosome of B. thetaiotaomicron F9-2, whereas it was located on a plasmid in E. coli 09-02E. These genes were flanked by different insertion sequences. CONCLUSION Considering their diversities in the human gut resistome, these strains would be of considerable interest for detailed comparative genomic analysis. Notably, the same sul2 cassette was found in facultative and obligate anaerobic bacterial isolates (resident in humans). However, the different location of the cassette indicates a possible mechanism of gene transfer among gut microbes.
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Affiliation(s)
- Mashkoor Mohsin
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Japan; Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Kaori Tanaka
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Ryuji Kawahara
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Shinji Kondo
- Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
| | - Hideki Noguchi
- Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Diep Thi Khong
- Center of Medical-Pharmaceutical Science and Technology Services, Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Thang Nam Nguyen
- Center of Medical-Pharmaceutical Science and Technology Services, Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Trong Nang Hoang
- Center of Medical-Pharmaceutical Science and Technology Services, Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Yoshimasa Yamamoto
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan.
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10
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Sydenham TV, Overballe-Petersen S, Hasman H, Wexler H, Kemp M, Justesen US. Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids. Microb Genom 2019; 5:e000312. [PMID: 31697231 PMCID: PMC6927303 DOI: 10.1099/mgen.0.000312] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/17/2019] [Indexed: 02/06/2023] Open
Abstract
Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen. Antimicrobial resistance (AMR) and the prevalence of AMR genes are increasing, and prediction of antimicrobial susceptibility based on sequence information could support targeted antimicrobial therapy in a clinical setting. Complete identification of insertion sequence (IS) elements carrying promoter sequences upstream of resistance genes is necessary for prediction of AMR. However, de novo assemblies from short reads alone are often fractured due to repeat regions and the presence of multiple copies of identical IS elements. Identification of plasmids in clinical isolates can aid in the surveillance of the dissemination of AMR, and comprehensive sequence databases support microbiome and metagenomic studies. We tested several short-read, hybrid and long-lead assembly pipelines by assembling the type strain B. fragilis CCUG4856T (=ATCC25285=NCTC9343) with Illumina short reads and long reads generated by Oxford Nanopore Technologies (ONT) MinION sequencing. Hybrid assembly with Unicycler, using quality filtered Illumina reads and Filtlong filtered and Canu-corrected ONT reads, produced the assembly of highest quality. This approach was then applied to six clinical multidrug-resistant B. fragilis isolates and, with minimal manual finishing of chromosomal assemblies of three isolates, complete, circular assemblies of all isolates were produced. Eleven circular, putative plasmids were identified in the six assemblies, of which only three corresponded to a known cultured Bacteroides plasmid. Complete IS elements could be identified upstream of AMR genes; however, there was not complete correlation between the absence of IS elements and antimicrobial susceptibility. As our knowledge on factors that increase expression of resistance genes in the absence of IS elements is limited, further research is needed prior to implementing AMR prediction for B. fragilis from whole-genome sequencing.
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Affiliation(s)
- Thomas V. Sydenham
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
- Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark
| | | | - Henrik Hasman
- Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hannah Wexler
- GLAVA Health Care System and David Geffen School of Medicine, UCLA (University of California, Los Angeles), Los Angeles, CA, USA
| | - Michael Kemp
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Ulrik S. Justesen
- Research Unit of Clinical Microbiology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
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Zhu D, Wan J, Yang Z, Xu J, Wang M, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, Chen X, Cheng A. First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China. Front Vet Sci 2019; 6:128. [PMID: 31069241 PMCID: PMC6491836 DOI: 10.3389/fvets.2019.00128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
We report for the first time the occurrence of integrative conjugative elements (ICEs) in Riemerella anatipestifer (R.anatipestifer) isolated from diseased ducks in China. For this purpose, a total of 48 genome sequences were investigated, which comprised 30 publicly available R. anatipestifer genome sequences, and 18 clinical isolates genomes sequences. Two ICEs, named ICERanRCAD0133-1 and ICERanRCAD0179-1 following the classic nomenclature system, were identified in R. anatipestifer through the use of bioinformatics tools. Comparative analysis revealed that three ICEs in Ornithobacterium rhinotracheale showed a high degree of conservation with the core genes of ICERanRCAD0133-1, while 13 ICEs with high similarity to ICERanRCAD0179-1 were found in Bacteroidetes. Based on the definition of ICE family, ICERanRCAD0179-1 was grouped in CTnDOT/ERL family; however, ICERanRCAD0133-1, which had no significant similarity with known ICEs, might be classified into a novel ICE family. The sequences of ICERanRCAD0133-1 and ICERanRCAD0179-1 were 70890 bp and 49166 bp in length, had 33.14 and 50.34% GC content, and contained 77 CDSs and 51 CDSs, respectively. Cargo genes carried by these two ICEs were predicted to encode: R-M systems, IS elements, a putative TonB-dependent receptor, a bacteriocin/lantibiotic efflux ABC transporter, a tetracycline resistance gene and more. In addition, phylogenetic analyses revealed that ICERanRCAD0179-1 and related ICEs were derived from a common ancestor, which may have undergone divergence prior to integartation into the host bacterial chromosome, and that the core genes co-evolved via a related evolutionary process or experienced only a low degree of recombination events during spread from a common CTnDOT/ERL family ancestor. Collectively, this study is the first identification and characterization of ICEs in R. anatipestifer; and provides new insights into the genetic diversity, evolution, adaptation, antimicrobial resistance, and virulence of R. anatipestifer.
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Affiliation(s)
- Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Jianbang Wan
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China
| | - Zhishuang Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Jinge Xu
- Guizhou Animal Husbandry and Veterinary Research Institute, Guiyang, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunya Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Ling Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yanling Yu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiaoyue Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World. mSphere 2019; 4:4/2/e00040-19. [PMID: 30944210 PMCID: PMC6449604 DOI: 10.1128/msphere.00040-19] [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] [Indexed: 01/14/2023] Open
Abstract
Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE. Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis strains derived from various environmental settings and human infections from different geographic regions around the world from 1950s to the present. Putative integrative and conjugative elements (ICEs) were identified in 31/36 (86.1%) strains in the study. A total of 52 putative ICEs (including eight degenerated elements lacking integrases) were identified and categorized into three types based on the architecture of the conjugation module and the phylogeny of the relaxase, coupling protein, TraG, and TraJ protein sequences. The type II and III ICEs were found to integrate adjacent to tRNA genes, while type I ICEs integrate into intergenic regions or into a gene. The ICEs carry various cargo genes, including transcription regulator genes and genes conferring antibiotic resistance. The adaptive immune CRISPR-Cas system was found in nine strains, including five strains in which CRISPR-Cas machinery and ICEs coexist at different locations on the same chromosome. One ICE-derived spacer was present in the CRISPR locus in one strain. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in E. anophelis differ in architecture and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. The categorization of ICEs will facilitate further investigations of the impact of ICE on virulence, genome epidemiology, and adaptive genomics of E. anophelis. IMPORTANCEElizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE.
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Bacteroides Spp. Blebitis, Keratitis, and Endophthalmitis Following Uncomplicated Trabeculectomy. J Glaucoma 2019; 28:e118-e120. [PMID: 30855413 DOI: 10.1097/ijg.0000000000001235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE To describe the first known case of Bacteroides spp. related blebitis, keratitis, and endophthalmitis following uncomplicated trabeculectomy. METHODS This was a case report and literature review. CASE A 63-year-old immunocompetent white male underwent uncomplicated trabeculectomy of his right eye. Two weeks later, a blebitis with adjacent keratitis was diagnosed, progressing over several days to endophthalmitis despite hourly topical fortified antibiotic therapy. Although gram stain and culture of the bleb surface, a conjunctival suture, the aqueous humor, and the vitreous were negative, topical real-time quantitative polymerase chain reaction testing disclosed the presence of Bacteroides spp. Following treatment with topical and intravitreal clindamycin and intravenous meropenem, all clinical evidence of infection resolved. Best spectacle-corrected visual acuity improved to 20/25 (0.8) subsequent to combined cataract extraction, intraocular lens implantation, and pars plana vitrectomy for persistent vitreous debris. CONCLUSIONS Bacteroides may be a rare cause of postoperative blebitis, keratitis, and endophthalmitis. A favorable outcome may be attained, provided that an accurate diagnosis and effective treatment can be provided, which may be facilitated by real-time quantitative polymerase chain reaction in select cases.
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Husain F, Tang K, Veeranagouda Y, Boente R, Patrick S, Blakely G, Wexler HM. Novel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation. Microb Genom 2019; 3. [PMID: 29208130 PMCID: PMC5729914 DOI: 10.1099/mgen.0.000136] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems. Conjugative transposon-like genes within a transferred segment and within a putative integrative conjugative element (ICE5) ~45 kb downstream from the transferred segment both encode proteins that may be involved in the observed transfer. These data indicate that chromosomal transfer is a driver of antigenic diversity and nutrient adaptation in Bacteroides that (1) contributes to the dissemination of the extensive B. fragilis pan-genome, (2) allows rapid adaptation to a changing environment and (3) can confer pathogenic characteristics to host symbionts.
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Affiliation(s)
- Fasahath Husain
- Brentwood Biomedical Research Institute, Los Angeles, CA, USA
| | | | | | | | | | | | - Hannah M. Wexler
- Research, GLAVAHCS, 11301 Wilshire Blvd., 691/151J Bldg. 115, Room 312, Los Angeles, CA, USA
- *Correspondence: Hannah M. Wexler,
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15
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Pan Z, Liu J, Zhang Y, Chen S, Ma J, Dong W, Wu Z, Yao H. A novel integrative conjugative element mediates transfer of multi-drug resistance between Streptococcus suis strains of different serotypes. Vet Microbiol 2019; 229:110-116. [DOI: 10.1016/j.vetmic.2018.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 10/27/2022]
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16
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Ghotaslou R, Bannazadeh Baghi H, Alizadeh N, Yekani M, Arbabi S, Memar MY. Mechanisms of Bacteroides fragilis resistance to metronidazole. INFECTION GENETICS AND EVOLUTION 2018; 64:156-163. [PMID: 29936037 DOI: 10.1016/j.meegid.2018.06.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/09/2018] [Accepted: 06/16/2018] [Indexed: 01/01/2023]
Abstract
Metronidazole-resistant Bacteroides fragilis (B. fragilis) have been reported worldwide. Several mechanisms contribute to B. fragilis resistance to metronidazole. In some cases, the mechanisms of metronidazole resistance are unknown. Understanding the mechanisms of resistance is important for therapy, the design of new alternative drugs, and control of resistant strains. In this study, a comprehensive review of the B. fragilis resistance mechanisms to metronidazole was prepared. The rate of metronidazole-resistant B. fragilis has been reported as ranging from 0.5% to 7.8% in many surveys. According to CLSI, isolates with MICs ≥32 μg/mL are considered to be metronidazole-resistant. In the majority of cases, metronidazole resistance in B. fragilis is coupled with the existence of nim genes. Metronidazole resistance could be induced in nim-negative strains by exposure to sub-MIC levels of metronidazole. There are multi-drug efflux pumps in B. fragilis which can pump out a variety of substrates such as metronidazole. The recA overexpression and deficiency of feoAB are other reported metronidazole resistance mechanisms in this bacterium.
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Affiliation(s)
- Reza Ghotaslou
- The Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Bannazadeh Baghi
- Department of Microbiology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Naser Alizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mina Yekani
- Department of Microbiology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahram Arbabi
- The Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Microbiology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Yousef Memar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
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17
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Lange A, Beier S, Steimle A, Autenrieth IB, Huson DH, Frick JS. Extensive Mobilome-Driven Genome Diversification in Mouse Gut-Associated Bacteroides vulgatus mpk. Genome Biol Evol 2016; 8:1197-207. [PMID: 27071651 PMCID: PMC4860699 DOI: 10.1093/gbe/evw070] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Like many other Bacteroides species, Bacteroides vulgatus strain mpk, a mouse fecal isolate which was shown to promote intestinal homeostasis, utilizes a variety of mobile elements for genome evolution. Based on sequences collected by Pacific Biosciences SMRT sequencing technology, we discuss the challenges of assembling and studying a bacterial genome of high plasticity. Additionally, we conducted comparative genomics comparing this commensal strain with the B. vulgatus type strain ATCC 8482 as well as multiple other Bacteroides and Parabacteroides strains to reveal the most important differences and identify the unique features of B. vulgatus mpk. The genome of B. vulgatus mpk harbors a large and diverse set of mobile element proteins compared with other sequenced Bacteroides strains. We found evidence of a number of different horizontal gene transfer events and a genome landscape that has been extensively altered by different mobilization events. A CRISPR/Cas system could be identified that provides a possible mechanism for preventing the integration of invading external DNA. We propose that the high genome plasticity and the introduced genome instabilities of B. vulgatus mpk arising from the various mobilization events might play an important role not only in its adaptation to the challenging intestinal environment in general, but also in its ability to interact with the gut microbiota.
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Affiliation(s)
- Anna Lange
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Sina Beier
- Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Alex Steimle
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Ingo B Autenrieth
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Daniel H Huson
- Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Tübingen, Germany
| | - Julia-Stefanie Frick
- Interfacultary Institute for Microbiology and Infection Medicine, Department for Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
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18
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Husain F, Veeranagouda Y, Boente R, Tang K, Mulato G, Wexler HM. The Ellis Island Effect: A novel mobile element in a multi-drug resistant Bacteroides fragilis clinical isolate includes a mosaic of resistance genes from Gram-positive bacteria. Mob Genet Elements 2014; 4:e29801. [PMID: 25165618 PMCID: PMC4145004 DOI: 10.4161/mge.29801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/29/2014] [Accepted: 07/01/2014] [Indexed: 01/13/2023] Open
Abstract
Objectives: Bacteroides fragilis, a Gram-negative anaerobic bacterium, is alternately a gut commensal or virulent pathogen and is an important reservoir for horizontal gene transfer (HGT) of bacterial resistance and virulence genes in the human gastrointestinal tract. We identified a unique conjugative transposon (CTn) in a multidrug resistant clinical isolate of B. fragilis (BF-HMW615); we named this element CTnHyb because it included a hybrid mosaic of foreign elements. This study reports the characterization of CTnHyb and discusses the potential impact on horizontal spread of resistance genes. Results: CTnHyb contains several efflux pump genes and several genes that confer or may confer antibiotic resistance to tetracycline, kanamycin, metronidazole and spectinomycin (truncated gene). CTnHyb also contains a mosaic of mobile elements from Gram-positive organisms. CTnHyb is easily transferred from BF-HMW615 (the original isolate) to BF638R (lab strain) and integrated into the BF638R chromosome. The "foreign" (from Gram-positive bacteria) nucleotide sequences within CTnHyb were > 99% preserved indicating that the gene acquisition from the Gram-positive bacteria was very recent. Conclusion: CTnHyb is a novel CTn residing in a multidrug resistant strain of B. fragilis. The global nature and wide phylogenetic reach of HGT means that any gene in any bacterium can potentially be mobilized. Understanding the mechanisms that drive the formation and transfer of these elements and, potentially, ways to limit the transfer are necessary to prevent a devastating spread of resistance elements.
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Affiliation(s)
| | - Yaligara Veeranagouda
- GLAVAHCS; Los Angeles, CA USA ; David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
| | | | - Kevin Tang
- David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
| | - Gabriela Mulato
- David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
| | - Hannah M Wexler
- GLAVAHCS; Los Angeles, CA USA ; David Geffen School of Medicine; University of California Los Angeles; Los Angeles, CA USA
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Abstract
UNLABELLED CTnDOT is a 65-kb conjugative transposon that is found in Bacteroides spp., which are one of the more abundant members within the lower human gastrointestinal tract. CTnDOT encodes resistance to the antibiotics erythromycin and tetracycline (Tc). An interesting feature of CTnDOT is that exposure to low levels of Tc induces a cascade of events that ultimately results in CTnDOT conjugative transfer. However, Tc is apparently not a switch that activates transfer but rather a signal that appears to override a series of negative regulators that inhibit premature excision and transfer of CTnDOT. In this minireview, we summarize over 20 years of research that focused on elucidating the highly coordinated regulation of excision, mobilization, and transfer of CTnDOT. IMPORTANCE Bacteroides spp. are abundant commensals in the human colon, but they are also considered opportunistic pathogens, as they can cause life-threatening infections if they should escape the colon. Bacteroides spp. are the most common cause of anaerobic infections and are rather difficult to treat due to the prevalence of antibiotic resistance within this genus. Today over 80% of Bacteroides are resistant to tetracycline (Tc), and a study looking at both clinical and community isolates demonstrated that this resistance was specifically due to the conjugative transposon CTnDOT.
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20
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Tetracycline-related transcriptional regulation of the CTnDOT mobilization region. J Bacteriol 2013; 195:5431-8. [PMID: 24078614 DOI: 10.1128/jb.00691-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
CTnDOT is a 65-kb conjugative transposon (CTn) in Bacteroides spp. that confers resistance to the antibiotics erythromycin and tetracycline (Tc). Conjugative transfer of CTnDOT is regulated upon exposure of cells to Tc. In the absence of Tc, no transfer is detectable; however, a cascade of regulatory events results in the conjugative transfer of CTnDOT upon Tc induction. Previous studies addressing regulation of CTnDOT conjugative transfer focused primarily on the 13-kb transfer (tra) operon, which encodes the proteins required for assembly of the mating apparatus. We report here that the mob operon that encodes the relaxase and coupling proteins required for mobilization of CTnDOT are regulated at the transcriptional level upon Tc induction. The Xis2d and Exc excision proteins are required for the upregulation of mob transcription upon Tc induction, and yet a deletion of xis2c has no effect. We also show preliminary evidence suggesting that the integrase, IntDOT, may play a regulatory role, as pLYL72 transfer is not detectable when intDOT is provided in trans.
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Veeranagouda Y, Husain F, Wexler HM. Transposon mutagenesis of Bacteroides fragilis using a mariner transposon vector. Anaerobe 2013; 22:126-9. [PMID: 23664906 DOI: 10.1016/j.anaerobe.2013.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 04/24/2013] [Accepted: 04/26/2013] [Indexed: 11/17/2022]
Abstract
The mariner transposon vector pYV07 was tested for use in the mutagenesis of Bacteroides fragilis 638R. The transposon vector efficiently generated mutants in B. fragilis 638R. The transposon disrupted genes were scattered throughout the genome of B. fragilis 638R. This method serves as a powerful tool to study B. fragilis.
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Schillinger T, Lisfi M, Chi J, Cullum J, Zingler N. Analysis of a comprehensive dataset of diversity generating retroelements generated by the program DiGReF. BMC Genomics 2012; 13:430. [PMID: 22928525 PMCID: PMC3521204 DOI: 10.1186/1471-2164-13-430] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/18/2012] [Indexed: 12/01/2022] Open
Abstract
Background Diversity Generating Retroelements (DGRs) are genetic cassettes that can introduce tremendous diversity into a short, defined region of the genome. They achieve hypermutation through replacement of the variable region with a strongly mutated cDNA copy generated by the element-encoded reverse transcriptase. In contrast to “selfish” retroelements such as group II introns and retrotransposons, DGRs impart an advantage to their host by increasing its adaptive potential. DGRs were discovered in a bacteriophage, but since then additional examples have been identified in some bacterial genomes. Results Here we present the program DiGReF that allowed us to comprehensively screen available databases for DGRs. We identified 155 DGRs which are found in all major classes of bacteria, though exhibiting sporadic distribution across species. Phylogenetic analysis and sequence comparison showed that DGRs move between genomes by associating with various mobile elements such as phages, transposons and plasmids. The DGR cassettes exhibit high flexibility in the arrangement of their components and easily acquire additional paralogous target genes. Surprisingly, the genomic data alone provide new insights into the molecular mechanism of DGRs. Most notably, our data suggest that the template RNA is transcribed separately from the rest of the element. Conclusions DiGReF is a valuable tool to detect DGRs in genome data. Its output allows comprehensive analysis of various aspects of DGR biology, thus deepening our understanding of the role DGRs play in prokaryotic genome plasticity, from the global down to the molecular level.
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Affiliation(s)
- Thomas Schillinger
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
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