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Amison RT, Faure ME, O'Shaughnessy BG, Bruce KD, Hu Y, Coates A, Page CP. The small quinolone derived compound HT61 enhances the effect of tobramycin against Pseudomonas aeruginosa in vitro and in vivo. Pulm Pharmacol Ther 2019; 61:101884. [PMID: 31887372 DOI: 10.1016/j.pupt.2019.101884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 12/25/2019] [Indexed: 11/26/2022]
Abstract
HT61 is a small quinolone-derived compound previously demonstrated to exhibit bactericidal activity against gram-positive bacteria including methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA). When combined with the classical antibiotics and antiseptics neomycin, gentamicin, mupirocin and chlorhexidine, HT61 demonstrated synergistic bactericidal activity against both MSSA and MRSA infections in vitro. In this study, we investigated the individual antimicrobial activity of HT61 alongside its capability to potentiate the efficacy of tobramycin against both a tobramycin sensitive laboratory reference strain (PAO1) and tobramycin resistant clinical isolates (RP73, NN2) of the gram-negative bacteria Pseudomonas aeruginosa (P. aeruginosa). Using broth microdilution methods, the MICs of HT61 were assessed against all strains, as well as the effect of HT61 in combination with tobramycin using both the chequerboard method and bacterial time-kill assays. A murine model of pulmonary infection was also used to evaluate the combination therapy of tobramycin and HT61 in vivo. In these studies, we demonstrated significant synergism between HT61 and tobramycin against the tobramycin resistant P. aeruginosa strains RP73 and NN2, whilst an additive/intermediate effect was observed for P. aeruginosa strain PA01 which was further confirmed using bacterial time kill analysis. In addition, the enhancement of tobramycin by HT61 was also evident in in vitro assays of biofilm eradication. Finally, in vivo studies revealed analogous effects to those observed in vitro with HT61 significantly reducing bacterial load when administered in combination with tobramycin against each of the three P. aeruginosa strains at the highest tested dose (10 mg/kg).
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Affiliation(s)
- R T Amison
- Sackler Institute of Pulmonary Pharmacology, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK.
| | - M-E Faure
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
| | - B G O'Shaughnessy
- Sackler Institute of Pulmonary Pharmacology, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
| | - K D Bruce
- School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
| | - Y Hu
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 ORE, UK
| | - A Coates
- Institute of Infection and Immunity, St George's, University of London, Cranmer Terrace, London, SW17 ORE, UK
| | - C P Page
- Sackler Institute of Pulmonary Pharmacology, School of Cancer and Pharmaceutical Sciences, King's College London, London, SE1 9NH, UK
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Rogers GB, Bruce KD, Martin ML, Burr LD, Serisier DJ. Corrections. The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial. Lancet Respir Med 2015; 3:e15. [PMID: 25890660 DOI: 10.1016/s2213-2600(15)00102-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Rogers GB, Kozlowska J, Keeble J, Metcalfe K, Fao M, Dowd SE, Mason AJ, McGuckin MA, Bruce KD. Functional divergence in gastrointestinal microbiota in physically-separated genetically identical mice. Sci Rep 2014; 4:5437. [PMID: 24961643 PMCID: PMC4069701 DOI: 10.1038/srep05437] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 06/05/2014] [Indexed: 12/20/2022] Open
Abstract
Despite the fundamental contribution of the gut microbiota to host physiology, the extent of its variation in genetically-identical animals used in research is not known. We report significant divergence in both the composition and metabolism of gut microbiota in genetically-identical adult C57BL/6 mice housed in separate controlled units within a single commercial production facility. The reported divergence in gut microbiota has the potential to confound experimental studies using mammalian models.
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Affiliation(s)
- G. B. Rogers
- Immunity, Infection, and Inflammation Program, Mater Research Institute – University of Queensland, Translational Research Institute, Woolloongabba, Australia
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Bedford Park, Adelaide, Australia
| | - J. Kozlowska
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
| | - J. Keeble
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
| | - K. Metcalfe
- Charles River UK, Manston Rd. Margate, Kent CT9 4LT UK
| | - M. Fao
- Charles River UK, Manston Rd. Margate, Kent CT9 4LT UK
| | - S. E. Dowd
- Molecular Research MR DNA, Shallowater, TX 79363, USA
| | - A. J. Mason
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
| | - M. A. McGuckin
- Immunity, Infection, and Inflammation Program, Mater Research Institute – University of Queensland, Translational Research Institute, Woolloongabba, Australia
| | - K. D. Bruce
- King's College London, Institute of Pharmaceutical Science, London, SE1 9NH, UK
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Sobey AJ, Townsend NC, Metcalf CD, Bruce KD, Fazi FM. Incorporation of Early Career Researchers within multidisciplinary research at academic institutions. Research Evaluation 2013. [DOI: 10.1093/reseval/rvt004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Hafiz TH, Cuthbertson LC, Oliver AO, Rogers GB, Bruce KD, Carroll MP, Gast CVVD. P89 The Effect of Sample Handling on Viable Bacterial Community Profiles from Cystic Fibrosis Sputum Samples. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Daniels TWV, Rogers GB, Stressmann FA, van der Gast CJ, Bruce KD, Jones GR, Connett GJ, Legg JP, Carroll MP. Impact of antibiotic treatment for pulmonary exacerbations on bacterial diversity in cystic fibrosis. J Cyst Fibros 2012; 12:22-8. [PMID: 22717533 DOI: 10.1016/j.jcf.2012.05.008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/16/2012] [Accepted: 05/24/2012] [Indexed: 11/27/2022]
Abstract
BACKGROUND A diverse array of bacterial species is present in the CF airways, in addition to those recognised as clinically important. Here, we investigated the relative impact of antibiotics, used predominantly to target Pseudomonas aeruginosa during acute exacerbations, on other non-pseudomonal species. METHODS The relative abundance of viable P. aeruginosa and non-pseudomonal species was determined in sputa from 12 adult CF subjects 21, 14, and 7 days prior to antibiotics, day 3 of treatment, the final day of treatment, and 10-14 days afterwards, by T-RFLP profiling. RESULTS Overall, relative P. aeruginosa abundance increased during antibiotic therapy compared to other bacterial species; mean abundance pre-antibiotic 51.0±36.0% increasing to 71.3±30.4% during antibiotic (ANOVA: F(1,54)=5.16; P<0.027). Further, the number of non-pseudomonal species detected fell; pre-antibiotic 6.0±3.3 decreasing to 3.7±3.3 during treatment (ANOVA: F(1,66)=5.11; P<0.027). CONCLUSIONS Antibiotic treatment directed at P. aeruginosa has an additional significant impact on non-pseudomonal, co-colonising species.
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Affiliation(s)
- T W V Daniels
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
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Sadek KH, Cagampang FR, Bruce KD, Shreeve N, Macklon N, Cheong Y. Variation in stability of housekeeping genes in endometrium of healthy and polycystic ovarian syndrome women. Hum Reprod 2011; 27:251-6. [PMID: 22052386 DOI: 10.1093/humrep/der363] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND The use of housekeeping genes (HKG) as internal controls for real-time qPCR studies of gene expression is based on the assumption of their inherent stability. However, it is unclear whether this stability is maintained in disease states. In order to test this, the present study investigated the expression of specific HKG in the endometrium of healthy and polycystic ovarian syndrome (PCOS) women. METHODS Endometrial tissue samples were taken from women with PCOS (n= 9) and controls (n= 10). The stability of nine candidate reference genes in the endometrial tissues were evaluated; four encode mitochondrial proteins [ATP5B, succinate dehydrogenase complex subunit A (SDHA), cytochrome c-1, glyceraldehyde-3-phosphatedehydrogenase], two encode ribosomal protein genes (18s ribosomal RNA, ribosomal protein L13A), one for cell structure (SDHA), one for cell signalling (beta actin, ACTB) and one involved in DNA repair (topoisomerase I, TOP1). The expression stability of these HKGs was calculated using geNORM qbasePLUS software, with stability defined by M-values, where higher M-value indicating less stability. In addition, changes in their cycle threshold values were analysed to determine direction of change between groups, and a Mann-Whitney U-test was used to determine statistical differences in expression. RESULTS The most stable HKGs observed across both PCOS endometrium were found to be YWHAZ, CYC1 and ACTB. Further TOP1 demonstrated higher gene expression in the endometrium from PCOS women compared with those from healthy women. CONCLUSIONS Of the nine HKGs examined, only YWHAZ, CYC1 and ACTB were stable in both control and PCOS endometrium: these should therefore be used as internal controls for quantitative reverse transcription-polymerase chain reaction analysis. Published discrepancies between endometrial gene expression studies may therefore be due in part to in the inappropriate HKG selection, and future gene expression studies should be based on HKG of known stability in both the disease and healthy states to avoid erroneous interpretation of results.
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Affiliation(s)
- K H Sadek
- Human Development and Health Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.
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Rogers GB, Marsh P, Stressmann AF, Allen CE, Daniels TVW, Carroll MP, Bruce KD. The exclusion of dead bacterial cells is essential for accurate molecular analysis of clinical samples. Clin Microbiol Infect 2011; 16:1656-8. [PMID: 20148918 DOI: 10.1111/j.1469-0691.2010.03189.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The DNA-based techniques used to detect bacteria in clinical samples are unable to discriminate between live bacteria, dead bacteria, and extracellular DNA. This failure to limit analysis to viable bacterial cells represents a significant problem, leading to false-positive results, as well as a failure to resolve the impact of antimicrobial therapy. The use of propidium monoazide treatment significantly reduces the contribution of dead cells and extracellular DNA to such culture-independent analyses. Here, the increased ability to resolve the impact of antibiotic therapy on Pseudomonas aeruginosa load in cystic fibrosis respiratory samples reveals statistically significant changes that would otherwise go undetected.
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Palial KK, Drury J, Heathcote L, Valentijin A, Farquharson RG, Gazvani R, Rudland PS, Hapangama DK, Celik N, Celik O, Aktan E, Ozerol E, Celik E, Bozkurt K, Paran H, Hascalik S, Ozerol I, Arase T, Maruyama T, Uchida H, Miyazaki K, Oda H, Uchida-Nishikawa S, Kagami M, Yamazaki A, Tamaki K, Yoshimura Y, De Vos M, Ortega C, Smitz J, Van Vaerenbergh I, Bourgain C, Devroey P, Luciano D, Exacoustos C, Zupi E, Luciano AA, Arduini D, Palomino WA, Argandona F, Kohen P, Azua R, Scarella A, Devoto L, McKinnon B, Bersinger NA, Mueller MD, Bonavita M, Mattila M, Ferreira FP, Maia-Filho V, Rocha AM, Serafini P, Motta ELA, Kim H, Kim CH, You RM, Nah HY, Lee JW, Kang HJ, Kang BM, Letur - Koenirsch H, Haouzi D, Olivennes F, Rouleau C, Cohen-Bacri P, Dechaud H, Hamamah S, D'Hooghe T, Hummelshoj L, Dunselman GAJ, Dirksen CD, EndoCost Consortium WERF, Simoens S, Novembri R, Luisi S, Carrarelli P, Rocha ALL, Toti P, Reis FM, Florio P, Petraglia F, Bruce KD, Sadek KH, Macklon N, Cagampang FR, Cheong Y, Goudakou M, Kalogeraki A, Matalliotakis I, Papatheodorou A, Pasadaki T, Karkanaki A, Prapas I, Prapas I, Kalogeraki A, Matalliotakis I, Panagiotidis I, Kasapi E, Karkanaki A, Goudakou M, Barlow D, Oliver J, Loumaye E, Khanmohammadi M, kazemnejad S, darzi S, Khanjani S, Zarnani A, Akhondi M, Tan CW, Ng CP, Loh SF, Tan HH, Choolani M, Griffith L, Chan J, Andersson KL, Sundqvist J, Scarselli G, Gemzell-Danielsson K, Lalitkumar PG, Jana S, Chattopadhyay R, Datta Ray C, Chaudhury K, Chakravarty BN, Hannan N, Evans J, Hincks C, Rombauts LJF, Salamonsen LA, Choi D, Lee J, Park J, Chang H, Kim M, Hwang K, Takeuchi K, Kurematsu T, Fukumoto Y, Yuki Y, Kuroki Y, Homan Y, Sata Y, Takeuchi M, Munoz Munoz E, Ortiz Olivera G, Fernandez Lopez I, Martinez Martinez B, Aguilar Prieto J, Portela Perez S, Pellicer Martinez A, Keltz M, Sauerbrun M, Breborowicz A, Gonzales E, Vicente-Munoz S, Puchades-Carrasco L, Morcillo I, Hidalgo JJ, Gilabert-Estelles J, Novella-Maestre E, Pellicer A, Pineda-Lucena A, Yavorovskaya KA, Okhtyrskaya TA, Demura TA, Faizulina NM, Ezhova LS, Kogan EA, Bilibio JP, Souza CAB, Rodini GP, Genro V, Andreoli CG, de Conto E, Cunha-Filho JSL, Saare M, Soritsa D, Jarva L, Vaidla K, Palta P, Laan M, Karro H, Soritsa A, Salumets A, Peters M, Miskova A, Pilmane M, Rezeberga D, Haouzi D, Dechaud H, Assou S, Letur H, Olivennes F, Hamamah S, Piomboni P, Stendardi A, Gambera L, De Leo V, Petraglia F, Focarelli R, Tamm K, Simm J, Salumets A, Metsis M, Vodolazkaia A, Fassbender A, Kyama CM, Bokor A, Schols D, Huskens D, Meuleman C, Peeraer K, Tomassetti C, D'Hooghe TM, Machens K, Afhuppe W, Schulz A, Diefenbach K, Schutt B, Faustmann T, Reischl J, Peters M, Altmae S, Reimand J, Laisk T, Saare M, Hovatta O, Kolde R, Vilo J, Stavreus-Evers A, Salumets A, Lee JH, Kim SG, Kim YY, Park IH, Sun HG, Lee KH, Ezoe K, Kawano H, Yabuuchi A, Ochiai K, Nagashima H, Osada H, Kagawa N, Kato O, Tamura I, Asada H, Taketani T, Tamura H, Sugino N, Garcia Velasco J, Prieto L, Quesada JF, Cambero O, Toribio M, Pellicer A, Hur CY, Lim KS, Lee WD, Lim JH, Germeyer A, Nelson L, Graham A, Jauckus J, Strowitzki T, Lessey B, Gyulmamedova I, Illina O, Illin I, Mogilevkina I, Chaika A, Nosenko O, Boykova I, Gulmamedova E, Isik H, Moraloglu O, Seven ALI, Kilic S, Erkayiran U, Caydere M, Batioglu S, Alhalabi M, Samawi S, Taha A, Kafri N, Modi S, Khatib A, Sharif J, Othman A, Lancuba S, Branzini C, Lopez M, Baricalla A, Cristina C, Chen J, Jiang Y, Zhen X, Hu Y, Yan G, Sun H, Mizumoto J, Ueno J, Carvalho FM, Casals G, Ordi J, Guimera M, Creus M, Fabregues F, Casamitjana R, Carmona F, Balasch J, Choi YS, Kim KC, Lee WD, Kim KH, Lee BS, Kim SH, Fassbender A, Overbergh L, Verdrengh E, Kyama C, Vodolazkaia A, Bokor A, Meuleman C, Peeraer K, Tomassetti C, Waelkens E, Mathieu C, D'Hooghe T, Iwasa T, Hatano K, Hasegawa E, Ito H, Isaka K, L. Rocha AL, Luisi S, Carrarelli P, Novembri R, Florio P, Reis F, Petraglia F, Lee KS, Joo JK, Son JB, Choi JR, Vidali A, Barad DH, Gleicher N, Jiang Y, Chen J, Zhen X, Hu Y, Sun H, Yan G, Sayyah-Melli M, Kazemi-Shishvan M. POSTER VIEWING SESSION - ENDOMETRIOSIS, ENDOMETRIUM, IMPLANTATION AND FALLOPIAN TUBE. Hum Reprod 2011. [DOI: 10.1093/humrep/26.s1.80] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bruce KD. Analysis of mer Gene Subclasses within Bacterial Communities in Soils and Sediments Resolved by Fluorescent-PCR-Restriction Fragment Length Polymorphism Profiling. Appl Environ Microbiol 2010; 63:4914-9. [PMID: 16535754 PMCID: PMC1389310 DOI: 10.1128/aem.63.12.4914-4919.1997] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial mer (mercury resistance) gene subclasses in mercury-polluted and pristine natural environments have been profiled by Fluorescent-PCR-restriction fragment length polymorphism (FluRFLP). For FluRFLP, PCR products were amplified from individual mer operons in mercury-resistant bacteria and from DNA isolated directly from bacteria in soil and sediment samples. The primers used to amplify DNA were designed from consensus sequences of the major subclasses of archetypal gram-negative mer operons within Tn501, Tn21, pDU1358, and pKLH2. Two independent PCRs were used to amplify two regions of different lengths (merRT(Delta)P [ca. 1 kb] and merR [ca. 0.4 kb]) starting at the same position in merR. The oligonucleotide primer common to both reactions (FluRX) was labelled at the 5(prm1) end with green (TET) fluorescent dye. Analysis of the mer sequences within databases indicated that the major subclasses could be differentiated on the basis of the length from FluRX to the first FokI restriction endonuclease site. The amplified PCR products were digested with FokI restriction endonuclease, with the restriction digest fragments resolved on an automated DNA sequencing machine which detected only those bands labelled with the fluorescent dye. For each of the individual mer operon sources examined, this single peak (in bases) position was observed in separate digests of either amplified region. These peak positions were as predicted on the basis of DNA sequence. mer PCR products amplified from DNA extracted directly from soil and sediment bacteria were studied in order to determine the profiles of the major mer subclasses present in each natural environment. In addition to peaks of the expected sizes, extra peaks were observed which were not predicted on the basis of DNA sequence. Those appearing in the restriction endonuclease digests of both study regions were presumed to be novel mer types. Genetic heterogeneity within and between mercury-polluted and pristine sites has been studied by this technique. Profiles generated were highly similar for samples taken within the same soil type. The profiles, however, changed markedly on crossing from one soil type to another, with gradients of the different groupings of mer genes identified.
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Rogers GB, Russell LE, Preston PG, Marsh P, Collins JE, Saunders J, Sutton J, Fine D, Bruce KD, Wright M. Characterisation of bacteria in ascites--reporting the potential of culture-independent, molecular analysis. Eur J Clin Microbiol Infect Dis 2010; 29:533-41. [PMID: 20238135 DOI: 10.1007/s10096-010-0891-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 02/15/2010] [Indexed: 02/07/2023]
Abstract
Spontaneous bacterial peritonitis (SBP) is a severe complication of liver disease. A significant proportion of patients have culture-negative ascites, despite having similar signs, symptoms and mortality to those with SBP. Therefore, empirical antibiotic treatment for infection is often started without knowledge of the causative organisms. Here, we investigated the potential of molecular techniques to provide rapid and accurate characterisation of the bacteria present in ascitic fluid. Ascites samples were obtained from 29 cirrhotic patients undergoing clinically indicated therapeutic paracentesis. Bacterial content was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis, quantitative polymerase chain reaction (PCR) and 16S ribosomal clone sequence analysis. Bacterial signal was detected in all samples, compared to three out of ten using standard methods. Bacterial loads ranged from 5.5 x 10(2) to 5.4 x 10(7) cfu/ml, with a mean value of 1.9 x 10(6) cfu/ml (standard deviation +/- 9.6 x 10(6) cfu/ml). In all but one instance, bacterial species identified by culture were also confirmed by molecular analyses. Preliminary data presented here suggests that culture-independent, molecular analyses could provide rapid characterisation of the bacterial content of ascites fluid, providing a basis for the investigation of SBP development and allowing early and targeted antibiotic intervention.
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Affiliation(s)
- G B Rogers
- Molecular Microbiology Research Group, PSD, King's College London, London, UK.
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Abstract
The metabolic syndrome (MetS) represents a combination of cardiometabolic risk determinants including obesity (central adiposity), insulin resistance, glucose intolerance, dyslipidaemia, non-alcoholic fatty liver disease and hypertension. MetS is rapidly increasing in prevalence worldwide as a consequence of the continued obesity "epidemic", and as a result will have a considerable impact on the global incidence of cardiovascular disease and type 2 diabetes. Currently, there is debate concerning whether the risk of cardiovascular disease is greater in patients diagnosed with MetS than that of the sum of the individual risk factors. At present, no unifying origin that can explain the pathogenesis of MetS has been identified and therefore no unique pharmacological treatment is available. This review summarises and critically evaluates the current clinical and scientific evidence supporting the existence of MetS as a multifactorial endocrine disease, for which maternal nutrition may be a common pathogenic mechanism. In addition, we suggest that ectopic fat accumulation (such as visceral and hepatic fat accumulation) and the proinflammatory state are central to the development of the MetS.
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Affiliation(s)
- K D Bruce
- Endocrinology and Metabolism Unit, DOHaD Division, Institute of Developmental Sciences, Southampton General Hospital, Southampton, UK
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Spasenovski T, Carroll MP, Lilley AK, Payne MS, Bruce KD. Modelling the bacterial communities associated with cystic fibrosis lung infections. Eur J Clin Microbiol Infect Dis 2010; 29:319-28. [PMID: 20099020 DOI: 10.1007/s10096-009-0861-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 12/11/2009] [Indexed: 12/24/2022]
Abstract
In many human diseases that cystic fibrosis (CF) patients suffer from, for example, lung infections, bacteria have been considered to grow as biofilms. The ability of key CF pathogens such as Pseudomonas aeruginosa to resist antibiotic therapies may be due to the poor drug penetration of these biofilms. The overall aim of this study was to develop biofilm models in vitro that resembled the bacterial species composition of CF sputa. Here, this was a step towards a longer term goal of forming multiple bacterial biofilm models in vitro that would serve, in turn, as better assays of antibiotic susceptibilities than conventionally grown cells. Biofilm models were constructed from 31 CF sputum samples, using a modified microtitre plate assay. Three forms of assessment of these biofilms were made, namely, the mass, microscopic analysis and species composition. Species composition in sputa and biofilms, characterised by terminal restriction fragment length polymorphism (T-RFLP) analysis of ribosomal gene polymerase chain reaction (PCR) products amplified from directly extracted nucleic acids, indicated that the bacterial community in sputa was well reproduced in the biofilm models. Typically, fresh sputa contained 4.6 +/- 2.3 bacterial species, with the species number decreasing to 4.0 +/- 1.6 over 5 days-this was not statistically significant (p = 0.29). This study outlines a novel methodology by which to generate and study bacterial biofilms communities. It is also hoped that the versatility of this in vitro approach, combined with its simplicity and high reproducibility, will make it an effective system to study CF sputum biofilm development and, in the longer term, serve as a means of assessing antibiotic susceptibilities.
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Affiliation(s)
- T Spasenovski
- Molecular Microbiology Research Laboratory, Pharmaceutical Science Division, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK
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Demirkan I, Williams HF, Dhawi A, Carter SD, Winstanley C, Bruce KD, Hart CA. Characterization of a spirochaete isolated from a case of bovine digital dermatitis. J Appl Microbiol 2007; 101:948-55. [PMID: 16968306 DOI: 10.1111/j.1365-2672.2006.02976.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The aim of the study was to characterize a spirochaete isolated from the lesions of a cow with digital dermatitis (DD). METHODS AND RESULTS The characterization was on the basis of its light and electron microscopic appearance, enzymic profile and DNA sequence analysis of its flagellin and 16S rRNA genes. The spirochaete was 6-8-microm long and 0.2-0.3 microm in diameter, and possessed seven to eight periplasmic flagella, with three to five helical turns. The enzymic profile of the bacterium resembles, but is not identical to that of Treponema brennaborense. Its flagellin gene sequence was identical to that of Treponema phagedenis but distinct from that of an ovine spirochaete. Analysis of a 1477-bp region of the 16S rRNA genes indicated that this is a Treponema species and that it is indistinguishable from some isolates made from cases of bovine DD in the United States. Finally, electron microscopy revealed the presence of myovirus-like bacteriophage particles in all cultures of the treponeme examined. CONCLUSIONS The spirochaete isolate was identified as a Treponema species closely related to some isolates from the United States (by 16S rDNA) and to T. phagedenis (by flagellin gene sequence) and is associated with bacteriophage particles. SIGNIFICANCE AND IMPACT OF THE STUDY The fact that the isolates with the same or very similar 16S rDNA sequences have been obtained from cases of bovine DD in cattle in different countries at different times, lends further support to the hypothesis that treponemes play a role in the pathogenesis of this disease.
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Affiliation(s)
- I Demirkan
- Department of Medical Microbiology, University of Liverpool, Liverpool, UK
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Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, Kehagia V, Connett GJ, Bruce KD. Use of 16S rRNA gene profiling by terminal restriction fragment length polymorphism analysis to compare bacterial communities in sputum and mouthwash samples from patients with cystic fibrosis. J Clin Microbiol 2006; 44:2601-4. [PMID: 16825392 PMCID: PMC1489498 DOI: 10.1128/jcm.02282-05] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial communities present in the oral cavity and the lungs of 19 adult cystic fibrosis (CF) patients were compared by using terminal restriction fragment length polymorphism analysis of 16S rRNA gene PCR products amplified from nucleic acids extracted directly from bacteria in clinical samples. Sputum samples were not found to be subject to profound contamination by oral cavity bacteria. Evidence of colonization of the CF lung by certain oral bacterial species was found.
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Affiliation(s)
- G B Rogers
- King's College London, Pharmaceutical Science Research Division, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, and Cystic Fibrosis Unit, Southampton University Hospital, United Kingdom
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16
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Green GL, Brostoff J, Hudspith B, Michael M, Mylonaki M, Rayment N, Staines N, Sanderson J, Rampton DS, Bruce KD. Molecular characterization of the bacteria adherent to human colorectal mucosa. J Appl Microbiol 2006; 100:460-9. [PMID: 16478485 DOI: 10.1111/j.1365-2672.2005.02783.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS To study large intestinal mucosal bacterial communities by Denaturing Gradient Gel Electrophoresis (DGGE) profiling and sequencing of 16S rRNA gene polymerase chain reaction (PCR) products amplified from DNA extracted from colorectal biopsies taken from healthy individuals. The specific aims were to determine how similar the mucosa-associated bacterial communities are within and between individuals and also to characterize the phylogenetic origin of isolated DGGE bands. METHODS AND RESULTS Human colorectal biopsies were taken at routine colonoscopy from 33 patients with normal looking mucosa. The DNA was extracted directly from single biopsies and the bacterial 16S rDNA PCR amplified. The PCR products were profiled using DGGE to generate a fingerprint of the dominant members of the bacterial community associated with the biopsy. The reproducibility of this method was high (>98%). Washed and unwashed biopsies gave similar DGGE banding patterns (Median Similarity Coefficient - MSC 96%, InterQuartile Range - IQR 3.0%, n = 5). Adjacent biopsies sampled from the same patient using different forceps gave similar DGGE profiles (MSC 94%, n = 2). Two colorectal biopsies sampled at locations 2-5 cm apart, from each of 18 patients, resulted in very similar profiles (MSC 100%, IQR 2.8%). Biopsies sampled from different locations within the large intestine of the same patient also gave similar DGGE profiles (MSC 98% IQR 3.3%n = 6). Although all patients (n = 33) gave different DGGE profiles, some similarity (c. 34%) was observed between profiles obtained from 15 patients arbitrarily selected. 35 DGGE bands were excised and sequenced. Many were found to be most closely related to uncultured bacterial sequence entries in the Genbank database. Others belonged to typical gut bacterial genera including Bacteroides, Ruminococcus, Faecalibacterium and Clostridium. CONCLUSIONS Bacterial communities adherent to colorectal mucosa within a normal patient show little variation; in contrast, mucosal bacterial communities sampled from different patients with normal colorectal mucosa show a high degree of variation. SIGNIFICANCE AND IMPACT OF THE STUDY This research demonstrates that DGGE profiling of 16S rRNA gene PCR products amplified from DNA extracted directly from mucosal samples offers fresh insight into the bacterial communities that are adherent to colorectal mucosa. These findings are important with respect to further studies on the gastrointestinal tract in health and disease.
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Affiliation(s)
- G L Green
- Life Sciences, King's College London, London, UK
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17
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Rogers GB, Carroll MP, Serisier DJ, Hockey PM, Jones G, Bruce KD. characterization of bacterial community diversity in cystic fibrosis lung infections by use of 16s ribosomal DNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol 2005; 42:5176-83. [PMID: 15528712 PMCID: PMC525137 DOI: 10.1128/jcm.42.11.5176-5183.2004] [Citation(s) in RCA: 235] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Progressive loss of lung function resulting from the inflammatory response to bacterial colonization is the leading cause of mortality in cystic fibrosis (CF) patients. A greater understanding of these bacterial infections is needed to improve lung disease management. As culture-based diagnoses are associated with fundamental drawbacks, we used terminal restriction fragment (T-RF) length polymorphism profiling and 16S rRNA clone data to characterize, without prior cultivation, the bacterial community in 71 sputa from 34 adult CF patients. Nineteen species from 15 genera were identified in 53 16S rRNA clones from three patients. Of these, 15 species have not previously been reported in CF lung infections and many were species requiring strict anaerobic conditions for growth. The species richness and evenness were determined from the T-RF length and volume for the 71 profiles. Species richness was on average 13.3 +/- 7.9 per sample and 13.4 +/- 6.7 per patient. On average, the T-RF bands of the lowest and highest volumes represented 0.6 and 59.2% of the total volume in each profile, respectively. The second through fifth most dominant T-RF bands represented 15.3, 7.5, 4.7, and 2.8% of the total profile volume, respectively. On average, the remaining T-RF bands represented 10.2% of the total profile volume. The T-RF band corresponding to Pseudomonas aeruginosa had the highest volume in 61.1% of the samples. However, 18 other T-RF band lengths were dominant in at least one sample. In conclusion, this reveals the enormous complexity of bacteria within the CF lung. Although their significance is yet to be determined, these findings alter our perception of CF lung infections.
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Affiliation(s)
- G B Rogers
- Division of Life Sciences, King's College London, London SE1 9NN, UK
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18
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Rogers GB, Hart CA, Mason JR, Hughes M, Walshaw MJ, Bruce KD. Bacterial diversity in cases of lung infection in cystic fibrosis patients: 16S ribosomal DNA (rDNA) length heterogeneity PCR and 16S rDNA terminal restriction fragment length polymorphism profiling. J Clin Microbiol 2003; 41:3548-58. [PMID: 12904354 PMCID: PMC179861 DOI: 10.1128/jcm.41.8.3548-3558.2003] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The leading cause of morbidity and mortality in cystic fibrosis (CF) patients stems from repeated bacterial respiratory infections. Many bacterial species have been cultured from CF specimens and so are associated with lung disease. Despite this, much remains to be determined. In the present study, we characterized without prior cultivation the total bacterial community present in specimens taken from adult CF patients, extracting DNA directly from 14 bronchoscopy or sputum samples. Bacterial 16S ribosomal DNA (rRNA) gene PCR products were amplified from extracted nucleic acids, with analyses by terminal restriction fragment length polymorphism (T-RFLP), length heterogeneity PCR (LH-PCR), and sequencing of individual cloned PCR products to characterize these communities. Using the same loading of PCR products, 12 distinct T-RFLP profiles were identified that had between 3 and 32 T-RFLP bands. Nine distinct LH-PCR profiles were identified containing between one and four bands. T-RFLP bands were detected in certain samples at positions that corresponded to pathogens cultured from CF samples, e.g., Burkholderia cepacia and Haemophilus influenzae. In every sample studied, one T-RFLP band was identified that corresponded to that produced by Pseudomonas aeruginosa. A total of 103 16S rRNA gene clones were examined from five patients. P. aeruginosa was the most commonly identified species (59% of clones). Stenotrophomonas species were also common, with eight other (typically anaerobic) bacterial species identified within the remaining 17 clones. In conclusion, T-RFLP analysis coupled with 16S rRNA gene sequencing is a powerful means of analyzing the composition and diversity of the bacterial community in specimens sampled from CF patients.
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Affiliation(s)
- G B Rogers
- Department of Life Sciences, King's College London, London SE1 9NN, United Kingdom
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19
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Demirkan I, Carter SD, Winstanley C, Bruce KD, McNAIR NM, Woodside M, Hart CA. Isolation and characterisation of a novel spirochaete from severe virulent ovine foot rot. J Med Microbiol 2001; 50:1061-1068. [PMID: 11761190 DOI: 10.1099/0022-1317-50-12-1061] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel spirochaete was isolated from a case of severe virulent ovine foot rot (SVOFR) by immunomagnetic separation with beads coated with polyclonal anti-treponemal antisera and prolonged anaerobic broth culture. The as yet unnamed treponeme differs considerably from the only other spirochaete isolated from ovine foot rot as regards morphology, enzymic profile and 16S rDNA sequence. On the basis of 16S rDNA, it was most closely related to another unnamed spirochaete isolated from cases of bovine digital dermatitis in the USA, raising the possibility of cross-species transmission. Further information is required to establish this novel ovine spirochaete as the cause of SVOFR.
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Affiliation(s)
| | | | - C Winstanley
- Departments of Veterinary Immunology and *Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool, †Division of Life Sciences, Franklin-Wilkins Building, Kings College, London, ‡Veterinary Research Laboratory, Belfast, Northern Ireland and §Clare Veterinary Group, Ballyclare, Northern Ireland
| | - K D Bruce
- Departments of Veterinary Immunology and *Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool, †Division of Life Sciences, Franklin-Wilkins Building, Kings College, London, ‡Veterinary Research Laboratory, Belfast, Northern Ireland and §Clare Veterinary Group, Ballyclare, Northern Ireland
| | - N M McNAIR
- Departments of Veterinary Immunology and *Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool, †Division of Life Sciences, Franklin-Wilkins Building, Kings College, London, ‡Veterinary Research Laboratory, Belfast, Northern Ireland and §Clare Veterinary Group, Ballyclare, Northern Ireland
| | - M Woodside
- Departments of Veterinary Immunology and *Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool, †Division of Life Sciences, Franklin-Wilkins Building, Kings College, London, ‡Veterinary Research Laboratory, Belfast, Northern Ireland and §Clare Veterinary Group, Ballyclare, Northern Ireland
| | - C A Hart
- Departments of Veterinary Immunology and *Medical Microbiology and Genitourinary Medicine, University of Liverpool, Liverpool, †Division of Life Sciences, Franklin-Wilkins Building, Kings College, London, ‡Veterinary Research Laboratory, Belfast, Northern Ireland and §Clare Veterinary Group, Ballyclare, Northern Ireland
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20
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Bruce KD, Hughes MR. Terminal restriction fragment length polymorphism monitoring of genes amplified directly from bacterial communities in soils and sediments. Mol Biotechnol 2000; 16:261-9. [PMID: 11252810 DOI: 10.1385/mb:16:3:261] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Terminal Restriction Fragment Length Polymorphism (T-RFLP) or Fluorescent Polymerase Chain Reaction/Restriction Fragment Length Polymorphism (FluRFLP) have made a significant impact on the way in which PCR products amplified from mixed community DNA extracts have been assessed. Technically, these approaches are essentially the same. PCR products are generated that contain at one 5' end label, typically a fluorescent moiety, that will be detected by a DNA sequencing machine. Upon digestion using a specific restriction endonuclease, labeled and unlabeled fragments are generated. This restriction endonuclease is chosen such that following this digestion, each labeled fragment corresponds to a different sequence variant. During electrophoretic separation, the DNA sequencing machine detects only these labeled fragments and therefore detects only the sequence variants. The aim of this article is to describe the protocols and demonstrate that this profiling can be performed using different DNA sequencing machines. The analysis and applications of this approach are also discussed.
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Affiliation(s)
- K D Bruce
- Division of Life Sciences, Franklin-Wilkins Building, 150 Stamford Street, King's College, London, SE1 8WA, UK.
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21
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Jones TH, Thompson LJ, Lawton JH, Bezemer TM, Bardgett RD, Blackburn TM, Bruce KD, Cannon PF, Hall GS, Hartley SE, Howson G, Jones CG, Kampichler C, Kandeler E, Ritchie DA. Impacts of rising atmospheric carbon dioxide on model terrestrial ecosystems. Science 1998; 280:441-3. [PMID: 9545223 DOI: 10.1126/science.280.5362.441] [Citation(s) in RCA: 162] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In model terrestrial ecosystems maintained for three plant generations at elevated concentrations of atmospheric carbon dioxide, increases in photosynthetically fixed carbon were allocated below ground, raising concentrations of dissolved organic carbon in soil. These effects were then transmitted up the decomposer food chain. Soil microbial biomass was unaffected, but the composition of soil fungal species changed, with increases in rates of cellulose decomposition. There were also changes in the abundance and species composition of Collembola, fungal-feeding arthropods. These results have implications for long-term feedback processes in soil ecosystems that are subject to rising global atmospheric carbon dioxide concentrations.
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Affiliation(s)
- TH Jones
- T. H. Jones, L. J. Thompson, J. H. Lawton, T. M. Bezemer, T. M. Blackburn, Natural Environment Research Council (NERC) Centre for Population Biology, Imperial College at Silwood Park, Ascot, Berkshire SL5 7PY, UK. R. D. Bardgett, School
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22
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Abstract
Mercury and its compounds are distributed widely across the earth. Many of the chemical forms of mercury are toxic to all living organisms. However, bacteria have evolved mechanisms of resistance to several of these different chemical forms, and play a major role in the global cycling of mercury in the natural environment. Five mechanisms of resistance to mercury compounds have been identified, of which resistance to inorganic mercury (HgR) is the best understood, both in terms of the mechanisms of resistance to mercury and of resistance to heavy metals in general. Resistance to inorganic mercury is encoded by the genes of the mer operon, and can be located on transposons, plasmids and the bacterial chromosome. Such systems have a worldwide geographical distribution, and furthermore, are found across a wide range of both Gram-negative and Gram-positive bacteria from both natural and clinical environments. The presence of mer genes in bacteria from sediment cores suggest that mer is an ancient system. Analysis of DNA sequences from mer operons and genes has revealed genetic variation both in operon structure and between individual genes from different mer operons, whilst analysis of bacteria which are sensitive to inorganic mercury has identified a number of vestigial non-functional operons. It is hypothesised that mer, due to its ubiquity with respect to geographical location, environment and species range, is an ancient system, and that ancient bacteria carried genes conferring resistance to mercury in response to increased levels of mercury in natural environments, perhaps resulting from volcanic activity. Models for the evolution of both a basic mer operon and for the Tn21-related family of mer operons and transposons are suggested. The study of evolution in bacteria has recently become dominated by the generation of phylogenies based on 16S rRNA genes. However, it is important not to underestimate the roles of horizontal gene transfer and recombinational events in evolution. In this respect mer is a suitable system for evaluating phylogenetic methods which incorporate the effects of horizontal gene transfer. In addition, the mer operon provides a model system in the study of environmental microbiology which is useful both as an example of a genotype which is responsive to environmental pressures and as a generic tool for the development of new methodology for the analysis of bacterial communities in natural environments.
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Affiliation(s)
- A M Osborn
- School of Biological Sciences, Donnan Laboratories, University of Liverpool, UK
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23
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Holt RJ, Strike P, Bruce KD. Phylogenetic analysis of tnpR genes in mercury resistant soil bacteria: the relationship between DNA sequencing and RFLP typing approaches. FEMS Microbiol Lett 1996; 144:95-102. [PMID: 8870257 DOI: 10.1111/j.1574-6968.1996.tb08514.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The diversity of resolvase (tnpR) genes carried by a number of mercury resistant soil bacteria has been investigated by DNA sequencing. The resulting DNA sequence information was compared to previously published tnpR DNA sequences and to previously published restriction fragment length polymorphism (RFLP) data, permitting the relationships between DNA sequencing and RFLP approaches to be studied by the use of phylogenetic trees. DNA maximum likelihood and DNA parsimony were used to construct a variety of phylogenetic trees. DNA sequencing confirmed the validity of RFLP analysis and highlighted the importance of restriction endonuclease choice upon the resulting RFLP patterns and dendrogram topology. The tnpR genes of two previously uncharacterised mercury resistant bacteria, T2-7 and T2-12 were also studied. DNA sequence data placed T2-7 in a previously described gene class, tnpR-D and T2-12 in a new gene class, tnpR-F. The significance of this data with respect to the recombination and evolution events occurring within bacterial populations are discussed.
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Affiliation(s)
- R J Holt
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, UK.
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24
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Pearson AJ, Bruce KD, Osborn AM, Ritchie DA, Strike P. Distribution of class II transposase and resolvase genes in soil bacteria and their association with mer genes. Appl Environ Microbiol 1996; 62:2961-5. [PMID: 8702289 PMCID: PMC168083 DOI: 10.1128/aem.62.8.2961-2965.1996] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Southern hybridization was performed on 30 gram-negative, mercury-resistant soil bacteria isolated from three terrestrail sites in Great Britain; two of these sites were mercury polluted (SO and SE), and one was pristine (SB). Most of the isolates (20 of 30) hybridized to probes encoding regions of the transposase (tnpA) and resolvase (tnpR) genes from Tn501 and Tn21. Isolates SE9 and SB3 hybridized to the Tn21 but not the Tn501 tnpA probe; however, they differed in that SB3 hybridized to both Tn501 and Tn21 tnpR probes while SE9 did not hybridize to either tnpR probe. The remaining isolates (7 of 30) did not hybridize to any of the transposon gene probes under the conditions used. tnpA and tnpR regions were PCR amplified from most of the hybridizing isolates and from Tn501 and Tn21, and variation was assessed by restriction fragment length polymorphism analysis. On the basis of these data, tnpA regions were divided into eight restriction fragment length polymorphism classes and tnpR regions were divided into five classes. Similarity coefficients were calculated between classes and used to construct dendrograms showing percent similarity. A compilation of the data from this study on tnpA and tnpR regions and a previous study on merRT delta P regions (A. M. Osborn, K. D. Bruce, P. Strike, and D. A. Ritchie, Appl. Environ. Microbiol. 59:4024-4030, 1993) indicates the presence of hybrid transposons and provides evidence for extensive recombination, both between transposon genes and between transposon and mer genes, within these natural populations of bacteria.
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Affiliation(s)
- A J Pearson
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, United Kingdom
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25
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Osborn AM, Bruce KD, Ritchie DA, Strike P. The sigA gene encoding the major sigma factor of RNA polymerase from the marine cyanobacterium Synechococcus sp. strain PCC 7002: cloning and characterization. Microbiology (Reading) 1996; 142 ( Pt 2):337-345. [PMID: 8932708 DOI: 10.1099/13500872-142-2-347] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The gene encoding the principal sigma factor from Synechococcus sp. strain PCC 7002 was isolated and characterized. The Synechococcus sp. strain PCC 7002 sigA gene encodes a protein of 375 amino acids (43 center dot 7 kDa) that is required for viability under normal growth conditions. The SigA protein was overproduced in Escherichia coli and the purified protein was used to raise polyclonal antiserum in rabbits. This antiserum was used in immunoblot analyses of partially purified RNA polymerase from Synechococcus sp. strain PR6000. The probable in vivo translational start site was identified by a comparison of amino acid sequencing results obtained with SigA proteins overproduced in E. coli with immunoblot analyses of SigA protein in crude preparations of RNA polymerase from the cyanobacterium. The sigA gene is encoded on a transcript of 1700 bases that initiates 496 nucleotides upstream from the probable in vivo translational start site. The abundance of sigA transcripts decreases rapidly after the removal of combined nitrogen from the growth medium.
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Affiliation(s)
- A M Osborn
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
| | - K D Bruce
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
| | - D A Ritchie
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
| | - P Strike
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
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26
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Osborn AM, Bruce KD, Ritchie DA, Strike P. The mercury resistance operon of the IncJ plasmid pMERPH exhibits structural and regulatory divergence from other Gram-negative mer operons. Microbiology (Reading) 1996; 142 ( Pt 2):337-345. [PMID: 8932707 DOI: 10.1099/13500872-142-2-337] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The bacterial mercury resistance determinant carried on the IncJ plasmid pMERPH has been characterized further by DNA sequence analysis. From the sequence of a 4097 bp Bg/II fragment which confers mercury resistance, it is predicted that the determinant consists of the genes merT, merP, merC and merA. The level of DNA sequence similarity between these genes and those of the mer determinant of Tn21 was between 56 center dot 4 and 62 center dot 4%. A neighbour-joining phylogenetic tree of merA gene sequences was constructed which suggested that pMERPH bears the most divergent Gram-negative mer determinant characterized to date. Although the determinant from pMERPH has been shown to be inducible, no regulatory genes have been found within the Bg/II fragment and it is suggested that a regulatory gene may be located elsewhere on the plasmid. The cloned determinant has been shown to express mercury resistance constitutively. Analysis of the pMERPH mer operator/promoter (O/P) region in vivo has shown constitutive expression from the mer PTCPA promoter, which could be partially repressed by the presence of a trans-acting MerR protein from a Tn21-like mer determinant. This incomplete repression of mer PTCPA promoter activity may be due to the presence of an extra base between the -35 and -10 sequences of the promoter and/or to variation in the MerR binding sites in the O/P region. Expression from the partially repressed mer PTCPA promoter could be restored by the addition of inducing levels of Hg2+ ions. Using the polymerase chain reaction with primers designed to amplify regions in the merP and merA genes, 1 center dot 37 kb pMERPH-like sequences have been amplified from the IncJ plasmid R391, the environmental isolate SE2 and from DNA isolated directly from non-cultivated bacteria in River Mersey sediment. This suggests that pMERPH-like sequences, although rare, are nevertheless persistent in natural environments.
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Affiliation(s)
- A M Osborn
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
| | - K D Bruce
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
| | - D A Ritchie
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
| | - P Strike
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, PO Box 147, Liverpool L69 3BX, UK
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27
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Bruce KD, Osborn AM, Pearson AJ, Strike P, Ritchie DA. Genetic diversity within mer genes directly amplified from communities of noncultivated soil and sediment bacteria. Mol Ecol 1995; 4:605-12. [PMID: 7582168 DOI: 10.1111/j.1365-294x.1995.tb00260.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Individual merRT delta P regions were amplified from DNA directly isolated from soil and sediment samples using consensus primers derived from the conserved mer sequences of Tn501, Tn21 and pMER419. Soil and sediment samples were taken from four sites in the British Isles; one 'pristine' (SB) and three polluted (SO, SE, T2) with respect to mercury. The sizes of the PCR products amplified (approximately 1 kb) were consistent with their generation from mer determinants related to the archetypal elements found in Gram negative bacteria. Forty-five individual clones of sequences obtained from these four sites were isolated which hybridized (> 70% homology) to a merRT delta P probe from Tn501. The diversity of these amplified mer genes was analysed using Restriction Fragment Length Polymorphism (RFLP) profiling. Fourteen RFLP classes were distinguished, 12 of which proved to be novel and only two of which had been identified in an earlier study of 40 Gram negative mercury resistant bacteria cultured from the same four sites. UPGMA analysis was used to examine the relationships between the 22 classes of determinant identified. The T2 site, which has the longest history of mercury exposure, was found to have the greatest level of diversity in terms of numbers of classes of determinant, while the SO site, which had the highest mercury levels showed relatively low variation. Variation of mer genes within and between the sequences from cultivated bacteria and from total bacterial DNA shows clearly that analysing only sequences from cultivated organisms results in a gross underestimation of genetic variation.
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Affiliation(s)
- K D Bruce
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, UK
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28
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Abstract
The proteins of nontypable and type b Haemophilus influenzae isolates were characterised using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). Coomassie Brilliant. Blue R-250 was used for protein detection. Two hundred and twenty eight proteins were resolved from whole cell lysates prepared from a standard nontypable H. influenzae strain (designated HI-64443) when isoelectric focusing was used for the first-dimensional separation of 2-D PAGE. When nonequilibrium pH gel electrophoresis (NEPHGE) was used to separate basic proteins in the first dimension, 50 proteins were detected for HI-64443; 20 of the basic proteins detected were considered to be unique for this separation protocol. The apparent molecular weights and isoelectric points were determined for 82 of the proteins resolved for HI-64443. The variation of the proteins from the standard bacterial strain (HI-64443) was determined for nontypable H. influenzae isolates. On the basis of their electrophoretic mobilities, 17.5% of the proteins of HI-64443 were shared by four other nontypable H. influenzae strains analysed. These data identified both conserved and variable proteins among the nontypable H. influenzae isolates analysed. The results obtained indicated that 2-D PAGE was able to discriminate nontypable H. influenzae into population clones identified by other procedures. The 2-D protein profiles obtained for type b H. influenzae strains were similar to those obtained for nontypable H. influenzae strains. The extent of the protein variation observed between type b and nontypable H. influenzae strain was similar to that observed among nontypable strains alone. These data are discussed in relation to the application of 2-D PAGE as a tool for studies on bacterial epidemiology and for the analysis of the genome structure and gene expression of Haemophilus influenzae.
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Affiliation(s)
- P Cash
- Department of Medical Microbiology, University of Aberdeen, Foresterhill, Scotland
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29
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Osborn AM, Bruce KD, Strike P, Ritchie DA. Polymerase chain reaction-restriction fragment length polymorphism analysis shows divergence among mer determinants from gram-negative soil bacteria indistinguishable by DNA-DNA hybridization. Appl Environ Microbiol 1993; 59:4024-30. [PMID: 7904439 PMCID: PMC195862 DOI: 10.1128/aem.59.12.4024-4030.1993] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Mercury resistant (Hgr) bacteria were isolated from four terrestrial sites: three containing high levels of mercury (sites T2, SE, and SO) and one uncontaminated site (SB). The frequencies of Hgr bacteria in the total cultivable populations were 0.05% (SB), 0.69% (SO), 4.8% (SE), and 25% (T2). Between 35 and 100% of the isolates from the four sites contained DNA sequences homologous to a DNA probe from the mercury resistance (mer) operon of the Tn501 Hgr determinant. The mer sequences of 10 Tn501-homologous Hgr determinants from each site were amplified by the polymerase chain reaction, with primers designed to consensus sequences of the mer determinants of Tn501, Tn21, and pMJ100, and were classified on the basis of the size of the amplified product and the restriction fragment length polymorphism pattern. Two main groups of amplification product were identified. The first, represented by the T2 and SB isolates and one SE isolate, gave an amplification product indistinguishable in size from that amplified from Tn501 (approximately 1,010 bp). The second group, represented by the SO isolates and the majority of the SE isolates, produced larger amplification products of 1,040 or 1,060 bp. Restriction fragment length polymorphism analysis revealed that each amplification product size group could be further subdivided into five subgroups.
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Affiliation(s)
- A M Osborn
- Department of Genetics and Microbiology, Donnan Laboratories, University of Liverpool, United Kingdom
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Abstract
Length variations of Haemophilus influenzae outer membrane porin protein P2 were found at the DNA and protein levels, notably in non-capsulate strains. Protein length, measured by SDS-polyacrylamide gel electrophoresis, was found to correlate with the length of the gene, measured by polymerase chain reaction amplification, and ranged from 35-42 kDa and 970-1090 nucleotides, respectively. This represents a length variation of some 15%. The genetic location of these variations was studied by restriction enzyme mapping 10 of the non-capsulate strains revealing further polymorphisms at the DNA level. All 10 strains were distinct and differed from a type b strain. The conservation and assortment of the different restriction sites in the alleles is discussed in relation to the very great diversity previously described for this protein and of the whole genome itself in non-capsulate strains. The roles of selection, horizontal gene transfer, and transformation in generating this diversity are discussed.
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Affiliation(s)
- K J Forbes
- Department of Medical Microbiology, University of Aberdeen, Foresterhill, UK
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Affiliation(s)
- K J Forbes
- Department of Medical Microbiology, University of Aberdeen, Foresterhill, AB9 2ZD, UK
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Bruce KD, Pennington TH. Clonal analysis of non-typable Haemophilus influenzae by sodium dodecyl sulphate-polyacrylamide gel electrophoresis of whole cell polypeptides. J Med Microbiol 1991; 34:277-83. [PMID: 2030503 DOI: 10.1099/00222615-34-5-277] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A collection of 223 strains of non-typable Haemophilus influenzae was assembled. Most strains were isolated from hospital in-patients in North East Scotland between 1984 and 1989. These isolates were examined by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole cell polypeptides. Variability was assessed in terms of apparent molecular weight differences between the protein profiles. Isolates were grouped on the basis of Dice coefficients of similarity and assigned to clones. Of the 223 strains, 147 were unique; the remaining strains were assigned to multi-member clones of which 13 clones had two members, one clone had three members, three clones had four members, three clones had five members, two clones had six members and one clone had eight members. The longest time interval between isolation of clonally related strains virtually equalled the limits of the study. Isolates from a childrens' hospital were significantly less diverse than those from patients in adult wards.
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Affiliation(s)
- K D Bruce
- Department of Medical Microbiology, University of Aberdeen Medical School, Foresterhill
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Bruce KD, Jordens JZ. Characterization of noncapsulate Haemophilus influenzae by whole-cell polypeptide profiles, restriction endonuclease analysis, and rRNA gene restriction patterns. J Clin Microbiol 1991; 29:291-6. [PMID: 1706727 PMCID: PMC269756 DOI: 10.1128/jcm.29.2.291-296.1991] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Thirty-four clinical isolates of noncapsulate Haemophilus influenzae representing isolates with either related or dissimilar patterns of whole-cell polypeptide profiles on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) were further characterized by restriction enzyme analysis (REA) and rRNA gene restriction patterns. Total cellular DNA was extracted by a rapid, microcentrifuge-scale method and digested with BamHI, which gave a pattern of about 18 discrete bands. This confirmed the five closely related groupings suggested by SDS-PAGE. Isolates dissimilar by SDS-PAGE were also distinguishable by REA. However, there was no correlation between the degrees of similarity estimated from whole-cell polypeptide profiles and those obtained from REA for the dissimilar isolates. Therefore, inferences of genetic relatedness made on the basis of these data should be interpreted with caution. rRNA gene restriction patterns also confirmed the groupings suggested by the other two techniques. We conclude that the three methods were highly discriminatory and that whole-cell polypeptide patterns or REA with BamHI would be appropriate techniques for epidemiological studies of noncapsulate H. influenzae.
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Affiliation(s)
- K D Bruce
- Department of Medical Microbiology, University of Aberdeen Medical School, United Kingdom
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