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Identification of Bull Semen Microbiome by 16S Sequencing and Possible Relationships with Fertility. Microorganisms 2021; 9:microorganisms9122431. [PMID: 34946031 PMCID: PMC8705814 DOI: 10.3390/microorganisms9122431] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 01/04/2023] Open
Abstract
Reports on the use of 16S sequencing for the identification of bacteria in healthy animals are lacking. Bacterial contamination of bull semen can have a negative effect on the sperm quality. The aims of this study were threefold: to identify bacteria in the semen of healthy bulls using 16S sequencing; to investigate the differences in the bacterial community between individual bulls; and to establish if there was a relationship between the bacteria isolated and bull fertility. Semen from 18 bulls of known fertility was used for the DNA extraction and 16S sequencing; 107 bacterial genera were identified. The differences in the amplicon sequence variants (ASVs) and the numbers of genera between bulls were noted. Negative correlations (p < 0.05) between several bacterial genera with Curvibacter, Rikenellaceae RC9-gut-group and Dyella spp. were seen. Other negatively correlated bacteria were Cutibacterium, Ruminococcaceae UCG-005, Ruminococcaceae UCG-010 and Staphylococcus, all within the top 20 genera. Two genera, W5053 and Lawsonella, were enriched in bulls of low fertility; this is the first time that these bacteria have been reported in bull semen samples. The majority of the bacteria were environmental organisms or were species originating from the mucous membranes of animals and humans. The results of this study indicate that differences in the seminal microbiota of healthy bulls occur and might be correlated with fertility.
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Chirathanamettu TR, Pawar PD. Quorum sensing-induced phenotypic switching as a regulatory nutritional stress response in a competitive two-species biofilm: An individual-based cellular automata model. J Biosci 2020. [DOI: 10.1007/s12038-020-00092-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Kenna DTD, Fuller A, Martin K, Perry C, Pike R, Burns PJ, Narayan O, Wilkinson S, Hill R, Woodford N, Logan JMJ, Turton JF. rpoB gene sequencing highlights the prevalence of an E. miricola cluster over other Elizabethkingia species among UK cystic fibrosis patients. Diagn Microbiol Infect Dis 2017; 90:109-114. [PMID: 29174734 DOI: 10.1016/j.diagmicrobio.2017.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 11/26/2022]
Abstract
Difficulties in distinguishing species of the Elizabethkingia genus by MALDI-TOF prompted use of rpoB sequencing to investigate species distribution among 44 isolates from cystic fibrosis (CF) patients. Forty-three isolates from 38 patients formed a cluster comprising E. miricola and proposed novel species E. bruuniana sp. nov., the exception clustering with proposed species E. ursingii sp. nov., also part of this wider cluster. All 44 isolates were PCR-positive for urease gene ureG, whereas only one of 23 E. anophelis isolates from non-CF patients was positive, suggesting that this gene is largely associated with the E. miricola cluster. Antibiotic susceptibilities of 12 CF isolates revealed all were resistant to beta-lactams with the exception of piperacillin-tazobactam, and were only susceptible to minocycline and co-trimoxazole. Pulsed-field gel electrophoresis analysis revealed 4 shared strains among 17 CF patients in one pediatric clinic, but epidemiological investigations did not support patient-to-patient transmission except between one sibling pair.
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Affiliation(s)
- Dervla T D Kenna
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK.
| | - Alice Fuller
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Kate Martin
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Claire Perry
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Rachel Pike
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Phillipa J Burns
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust M13 9WL, UK
| | - Omendra Narayan
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust M13 9WL, UK
| | - Stuart Wilkinson
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust M13 9WL, UK
| | - Robert Hill
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Julie M J Logan
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Jane F Turton
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
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Høiby N, Bjarnsholt T, Moser C, Jensen PØ, Kolpen M, Qvist T, Aanaes K, Pressler T, Skov M, Ciofu O. Diagnosis of biofilm infections in cystic fibrosis patients. APMIS 2017; 125:339-343. [PMID: 28407432 DOI: 10.1111/apm.12689] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/03/2017] [Indexed: 12/22/2022]
Abstract
Chronic Pseudomonas aeruginosa biofilm lung infection in cystic fibrosis patients is the best described biofilm infection in medicine. The initial focus can be the paranasal sinuses and then follows repeated colonization and infection of the lungs by aspiration. The matrix of the biofilms is dominated by alginate and the pathogenesis of tissue damage is immune complex-mediated chronic inflammation dominated by polymorphonuclear leukocytes and their products (DNA, oxygen radicals and proteases). The P. aeruginosa biofilm infection can be diagnosed by microscopy of lung tissue, sputum and mucus from the paranasal sinuses, where aggregates of the bacteria are found surrounded by the abundant alginate matrix. Specific PNA-FISH probes can be used to identify P. aeruginosa and other pathogens in situ in the biofilms. Growth of mucoid colonies from the locations mentioned above is also diagnostic for biofilm infection. Rise of specific anti-P. aeruginosa antibodies is likewise diagnostic, IgG in serum in case of lung infection, sIgA in saliva or nasal secretions in case of paranasal sinus infection. Similar approaches have been developed to diagnose chronic biofilm infections in cystic fibrosis caused by other pathogens e.g., Stenotrophomonas, Burkholderia multivorans, Achromobacter xylosoxidans and Mycobacterium abscessus complex.
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Affiliation(s)
- Niels Høiby
- Department of Clinical Microbiology, University of Copenhagen, Copenhagen, Denmark.,Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Clinical Microbiology, University of Copenhagen, Copenhagen, Denmark.,Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Claus Moser
- Department of Clinical Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Clinical Microbiology, University of Copenhagen, Copenhagen, Denmark.,Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, University of Copenhagen, Copenhagen, Denmark.,Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tavs Qvist
- Copenhagen Cystic Fibrosis Centre, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Aanaes
- Department of Otorhinology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tanja Pressler
- Copenhagen Cystic Fibrosis Centre, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Skov
- Copenhagen Cystic Fibrosis Centre, University of Copenhagen, Copenhagen, Denmark
| | - Oana Ciofu
- Costerton Biofilm Center, Institute for Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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Hakima N, Bidet P, Lopez M, Rioualen S, Carol A, Bonacorsi S. First case of neonatal bacteremia due to Dyella genus. Diagn Microbiol Infect Dis 2017; 87:199-201. [PMID: 27856045 DOI: 10.1016/j.diagmicrobio.2016.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/23/2016] [Accepted: 03/01/2016] [Indexed: 11/20/2022]
Abstract
We describe the first case of sepsis due to a yet unnamed species of Dyella genus associated to gastrointestinal perforation in a premature newborn. The rarity of such environmental bacteria in human infection, their misidentification with classical methods and their antibiotic resistance represent real challenges for both microbiologists and clinicians.
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MESH Headings
- Humans
- Male
- Anti-Bacterial Agents/pharmacology
- Bacteremia/diagnosis
- Bacteremia/microbiology
- Bacterial Typing Techniques
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Drug Resistance, Multiple, Bacterial
- Gammaproteobacteria/classification
- Gammaproteobacteria/drug effects
- Gammaproteobacteria/genetics
- Gammaproteobacteria/isolation & purification
- Gram-Negative Bacterial Infections/diagnosis
- Gram-Negative Bacterial Infections/microbiology
- Infant, Premature
- Intestinal Perforation/complications
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Infant, Newborn
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Affiliation(s)
- Nesrine Hakima
- AP-HP, Laboratoire de Microbiologie, Hôpital Robert-Debré, F-75019 Paris, France
| | - Philippe Bidet
- AP-HP, Laboratoire de Microbiologie, Hôpital Robert-Debré, F-75019 Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, IAME, UMR 1137, F-75018 Paris, France
| | - Maureen Lopez
- AP-HP, Laboratoire de Microbiologie, Hôpital Robert-Debré, F-75019 Paris, France
| | - Stéphane Rioualen
- AP-HP, Service de Néonatologie, Hôpital Robert-Debré, F-75019 Paris, France
| | - Agnès Carol
- AP-HP, Laboratoire de Microbiologie, Hôpital Robert-Debré, F-75019 Paris, France
| | - Stéphane Bonacorsi
- AP-HP, Laboratoire de Microbiologie, Hôpital Robert-Debré, F-75019 Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, IAME, UMR 1137, F-75018 Paris, France.
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An exploratory study of microbial diversity in sinus infections of cystic fibrosis patients by molecular methods. J Cyst Fibros 2014; 13:645-52. [DOI: 10.1016/j.jcf.2014.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 01/16/2014] [Accepted: 02/14/2014] [Indexed: 01/31/2023]
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