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3. Incidence, associated disease burden and healthcare utilization due to Staphylococcus aureus prosthetic joint infection in European hospitals: the COMBACTE-NET ARTHR-IS multi-centre study

Author

Espíndola, R., Vella, V., Benito, N., Mur, I., Tedeschi, S., Zamparini, E., Hendriks, J.G.E., Sorlí, L., Murillo, O., Soldevila, L., Scarborough, M., Scarborough, C., Kluytmans, J., Ferrari, M.C., Pletz, M.W., McNamara, I., Escudero-Sanchez, R., Arvieux, C., Batailler, C., Dauchy, F.-A., Liu, W.-Y., Lora-Tamayo, J., Praena, J., Ustianowski, A., Cinconze, E., Pellegrini, M., Bagnoli, F., Rodríguez-Baño, J., and del-Toro-López, M.-D.

Published
2023
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5. Gram-negative bacteraemia; a multi-centre prospective evaluation of empiric antibiotic therapy and outcome in English acute hospitals

Author

Melzer, Mark, Pink, Frederick, Fitzpatrick, Jennifer, Jones, Gill, Llewelyn, Martin, Peters, Joanna, Biswas, Jason, Edgeworth, Jonathan, Guile, Lucy, Querol-Rubiera, Antonio, Hussain, Abid, Jenkins, Neil, Moran, Ed, Pillay, Devedas, Scarborough, Matthew, Rawlinson, Tom, Judge, Ryan, Tilley, Robert, Lavery, Anita, Morris-Jones, Stephen, Price, James, Nsutebu, Emmanuel, Fitzpatrick, J.M., Biswas, J.S., Edgeworth, J.D., Islam, J., Jenkins, N., Judge, R., Lavery, A.J., Melzer, M., Morris-Jones, S., Nsutebu, E.F., Peters, J., Pillay, D.G., Pink, F., Price, J.R., Scarborough, M., Thwaites, G.E., Tilley, R., Walker, A.S., and Llewelyn, M.J.

Published
2016
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6. Vancomycin MIC as a predictor of outcome in MRSA bacteraemia in the UK context

Author

Hope, R., Blackburn, R. M., Verlander, N. Q., Johnson, A. P., Kearns, A., Hill, R., Hopkins, S., Sheridan, E., Livermore, D. M., Scarborough, M., Majumdar, S., Cunniffe, J., Farrington, M., Gouliouris, T., Marodi, C., Godwin, P., Tuck, A., Warren, R., Coe, P., Hassan, I., Mannion, P., Loudon, K., Youngs, E., Johnson, A., Lee, M., Weston, V., Guleri, A., Howe, R., Matthew, D., Cotterill, S., Todd, N., Patel, B., Mlangeni, D., Stockley, J. M., Spencer, R., Gardner, J., Thwaites, G., Kirby, A., Hopkins, S., Crook, D., Llewellyn, M., Price, J., Scarborough, M., Morris Jones, S., and Tilley, R.

Published
2013
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7. A genomic catalog of Earth’s microbiomes

Author

Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., Wu, D., Paez-Espino, D., Chen, I., Huntemann, M., Palaniappan, K., Ladau, J., Mukherjee, S., Reddy, T., Nielsen, T., Kirton, E., Faria, J., Edirisinghe, J., Henry, C., Jungbluth, S., Chivian, D., Dehal, P., Wood-Charlson, E., Arkin, A., Tringe, S., Visel, A., Abreu, H., Acinas, S., Allen, E., Allen, M., Alteio, L., Andersen, G., Anesio, A., Attwood, G., Avila-Magaña, V., Badis, Y., Bailey, J., Baker, B., Baldrian, P., Barton, H., Beck, D., Becraft, E., Beller, H., Beman, J., Bernier-Latmani, R., Berry, T., Bertagnolli, A., Bertilsson, S., Bhatnagar, J., Bird, J., Blanchard, J., Blumer-Schuette, S., Bohannan, B., Borton, M., Brady, A., Brawley, S., Brodie, J., Brown, S., Brum, J., Brune, A., Bryant, D., Buchan, A., Buckley, D., Buongiorno, J., Cadillo-Quiroz, H., Caffrey, S., Campbell, A., Campbell, B., Carr, S., Carroll, J., Cary, S., Cates, A., Cattolico, R., Cavicchioli, R., Chistoserdova, L., Coleman, M., Constant, P., Conway, J., Mac Cormack, W., Crowe, S., Crump, B., Currie, C., Daly, R., DeAngelis, K., Denef, V., Denman, S., Desta, A., Dionisi, H., Dodsworth, J., Dombrowski, N., Donohue, T., Dopson, M., Driscoll, T., Dunfield, P., Dupont, C., Dynarski, K., Edgcomb, V., Edwards, E., Elshahed, M., Figueroa, I., Flood, B., Fortney, N., Fortunato, C., Francis, C., Gachon, C., Garcia, S., Gazitua, M., Gentry, T., Gerwick, L., Gharechahi, J., Girguis, P., Gladden, J., Gradoville, M., Grasby, S., Gravuer, K., Grettenberger, C., Gruninger, R., Guo, J., Habteselassie, M., Hallam, S., Hatzenpichler, R., Hausmann, B., Hazen, T., Hedlund, B., Henny, C., Herfort, L., Hernandez, M., Hershey, O., Hess, M., Hollister, E., Hug, L., Hunt, D., Jansson, J., Jarett, J., Kadnikov, V., Kelly, C., Kelly, R., Kelly, W., Kerfeld, C., Kimbrel, J., Klassen, J., Konstantinidis, K., Lee, L., Li, W., Loder, A., Loy, A., Lozada, M., MacGregor, B., Magnabosco, C., Maria da Silva, A., McKay, R., McMahon, K., McSweeney, C., Medina, M., Meredith, L., Mizzi, J., Mock, T., Momper, L., Moran, M., Morgan-Lang, C., Moser, D., Muyzer, G., Myrold, D., Nash, M., Nesbø, C., Neumann, A., Neumann, R., Noguera, D., Northen, T., Norton, J., Nowinski, B., Nüsslein, K., O’Malley, M., Oliveira, R., Maia de Oliveira, V., Onstott, T., Osvatic, J., Ouyang, Y., Pachiadaki, M., Parnell, J., Partida-Martinez, L., Peay, K., Pelletier, D., Peng, X., Pester, M., Pett-Ridge, J., Peura, S., Pjevac, P., Plominsky, A., Poehlein, A., Pope, P., Ravin, N., Redmond, M., Reiss, R., Rich, V., Rinke, C., Rodrigues, J., Rodriguez-Reillo, W., Rossmassler, K., Sackett, J., Salekdeh, G., Saleska, S., Scarborough, M., Schachtman, D., Schadt, C., Schrenk, M., Sczyrba, A., Sengupta, A., Setubal, J., Shade, A., Sharp, C., Sherman, D., Shubenkova, O., Sierra-Garcia, I., Simister, R., Simon, H., Sjöling, S., Slonczewski, J., Correa de Souza, R., Spear, J., Stegen, J., Stepanauskas, R., Stewart, F., Suen, G., Sullivan, M., Sumner, D., Swan, B., Swingley, W., Tarn, J., Taylor, G., Teeling, H., Tekere, M., Teske, A., Thomas, T., Thrash, C., Tiedje, J., Ting, C., Tully, B., Tyson, G., Ulloa, O., Valentine, D., Van Goethem, M., VanderGheynst, J., Verbeke, T., Vollmers, J., Vuillemin, A., Waldo, N., Walsh, D., Weimer, B., Whitman, T., van der Wielen, P., Wilkins, M., Williams, T., Woodcroft, B., Woolet, J., Wrighton, K., Ye, J., Young, E., Youssef, N., Yu, F., Zemskaya, T., Ziels, R., Woyke, T., Mouncey, N., Ivanova, N., Kyrpides, N., Eloe-Fadrosh, E., Consortium, I., and Agencia Estatal de Investigación (España)

Subjects
Resource, Life sciences, biology, Biomedical Engineering, FILOGENIA, Bioengineering, Genomics, Biology, Microbiology, Applied Microbiology and Biotechnology, Genome, purl.org/becyt/ford/1 [https], 03 medical and health sciences, ddc:570, EARTH MICROBIOME PROJECT, Microbiome, purl.org/becyt/ford/1.6 [https], 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Phylum, 15. Life on land, biology.organism_classification, Computational biology and bioinformatics, Phylogenetic diversity, Evolutionary biology, Earth Microbiome Project, Molecular Medicine, Evolutionary ecology, MAGS, GENOMICS, Biotechnology, Archaea, MICROBIAL DIVERSITY
Abstract

13 pages, 5 figures, supplementary information https://doi.org/10.1038/s41587-020-0718-6.-- Data availability: All available metagenomic data, bins and annotations are available through the IMG/M portal (https://img.jgi.doe.gov/). Bulk download for the 52,515 MAGs is available at https://genome.jgi.doe.gov/GEMs and https://portal.nersc.gov/GEM. Genome-scale metabolic models for the nonredundant, high-quality GEMs are summarized at https://doi.org/10.25982/53247.64/1670777 and available in KBase (https://narrative.kbase.us/#org/jgimags). IMG/M identifiers of all metagenomes binned, including detailed information for each metagenome, are available in Supplementary Table 1.-- The pipeline used to generate the metagenome bins is available at https://bitbucket.org/berkeleylab/metabat/src/master/, Publisher Correction: A genomic catalog of Earth’s microbiomes; Nature Biotechnology 39: 520 (2021); https://doi.org/10.1038/s41587-020-00769-4, The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes, This work was conducted by the US DOE Joint Genome Institute, a DOE Office of Science User Facility (contract no. DE-AC02–05CH11231), and used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the US DOE (contract no. DE-AC02–05CH11231). This work was also supported as part of the Genomic Sciences Program DOE Systems Biology KBase (award nos. DE-AC02-05CH11231, DE-AC02-06CH11357, DE-AC05-00OR22725, and DE-AC02-98CH10886).-- With the funding support of the ‘Severo Ochoa Centre of Excelle

Published
2020

9. Lower Success Rate of Debridement and Implant Retention in Late Acute versus Early Acute Periprosthetic Joint Infection Caused by Staphylococcus spp. Results from a Matched Cohort Study

Author

Wouthuyzen-Bakker M, Sebillotte M, Huotari K, Escudero Sánchez R, Benavent E, Parvizi J, Fernandez-Sampedro M, Barbero-Allende JM, Garcia-Cañete J, Trebse R, Del Toro M, Vicens Diaz de Brito Fernandez, Sanchez M, Scarborough M, Soriano A, and ESCMID Study Group for Implant-Associated Infections (ESGIAI)

Abstract

BACKGROUND: Surgical débridement, antibiotics and implant retention (DAIR) is currently recommended by international guidelines for both early acute (postsurgical) and late acute (hematogenous) periprosthetic joint infections (PJIs). However, due to a different pathogenesis of infection, a different treatment strategy may be needed. QUESTIONS/PURPOSES: (1) Compared with early acute PJIs, are late acute PJIs associated with a higher risk of DAIR failure? (2) When stratified by microorganism, is the higher risk of failure in late acute PJI associated with Staphylocococcus aureus infection? (3) When analyzing patients with S. aureus infection, what factors are independently associated with DAIR failure? METHODS: In this multicenter observational study, early acute and late acute PJIs treated with DAIR were retrospectively evaluated and matched according to treating center, year of diagnosis, and infection-causing microorganism. If multiple matches were available, the early acute PJI diagnosed closest to the late acute PJI was selected. A total of 132 pairs were included. Treatment success was defined as a retained implant during follow-up without the need for antibiotic suppressive therapy. RESULTS: Late acute PJIs had a lower treatment success (46% [60 of 132]) compared with early acute PJIs (76% [100 of 132]), OR 3.9 [95% CI 2.3 to 6.6]; p < 0.001), but the lower treatment success of late acute PJIs was only observed when caused by Staphylococcus spp (S. aureus: 34% versus 75%; p < 0.001; coagulase-negative staphylococci: 46% versus 88%; p = 0.013, respectively). On multivariable analysis, late acute PJI was the only independent factor associated with an unsuccessful DAIR when caused by S. aureus (OR 4.52 [95% CI 1.79 to 11.41]; p < 0.001). CONCLUSIONS: Although DAIR seems to be a successful therapeutic strategy in the management of early acute PJI, its use in late acute PJI should be reconsidered when caused by Staphylococcus spp. Our results advocate the importance of isolating the causative microorganism before surgery. LEVEL OF EVIDENCE: Level III, therapeutic study.

Published
2020

10. Reducing Implant Infection in Orthopaedics (RIIiO): Results of a pilot study comparing the influence of forced air and resistive fabric warming technologies on postoperative infections following orthopaedic implant surgery

Author

Kümin, M., primary, Deery, J., additional, Turney, S., additional, Price, C., additional, Vinayakam, P., additional, Smith, A., additional, Filippa, A., additional, Wilkinson-Guy, L., additional, Moore, F., additional, O'Sullivan, M., additional, Dunbar, M., additional, Gaylard, J., additional, Newman, J., additional, Harper, C.M., additional, Minney, D., additional, Parkin, C., additional, Mew, L., additional, Pearce, O., additional, Third, K., additional, Shirley, H., additional, Reed, M., additional, Jefferies, L., additional, Hewitt-Gray, J., additional, Scarborough, C., additional, Lambert, D., additional, Jones, C.I., additional, Bremner, S., additional, Fatz, D., additional, Perry, N., additional, Costa, M., additional, and Scarborough, M., additional

Published
2019
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11. Cross-sectional study of the prevalence, causes and management of hospital-onset diarrhoea

Author

Mawer, D., primary, Byrne, F., additional, Drake, S., additional, Brown, C., additional, Prescott, A., additional, Warne, B., additional, Bousfield, R., additional, Skittrall, J.P., additional, Ramsay, I., additional, Somasunderam, D., additional, Bevan, M., additional, Coslett, J., additional, Rao, J., additional, Stanley, P., additional, Kennedy, A., additional, Dobson, R., additional, Long, S., additional, Obisanya, T., additional, Esmailji, T., additional, Petridou, C., additional, Saeed, K., additional, Brechany, K., additional, Davis-Blue, K., additional, O'Horan, H., additional, Wake, B., additional, Martin, J., additional, Featherstone, J., additional, Hall, C., additional, Allen, J., additional, Johnson, G., additional, Hornigold, C., additional, Amir, N., additional, Henderson, K., additional, McClements, C., additional, Liew, I., additional, Deshpande, A., additional, Vink, E., additional, Trigg, D., additional, Guilfoyle, J., additional, Scarborough, M., additional, Scarborough, C., additional, Wong, T.H.N., additional, Walker, T., additional, Fawcett, N., additional, Morris, G., additional, Tomlin, K., additional, Grix, C., additional, O'Cofaigh, E., additional, McCaffrey, D., additional, Cooper, M., additional, Corbett, K., additional, French, K., additional, Harper, S., additional, Hayward, C., additional, Reid, M., additional, Whatley, V., additional, Winfield, J., additional, Hoque, S., additional, Kelly, L., additional, King, I., additional, Bradley, A., additional, McCullagh, B., additional, Hibberd, C., additional, Merron, M., additional, McCabe, C., additional, Horridge, S., additional, Taylor, J., additional, Koo, S., additional, Elsanousi, F., additional, Saunders, R., additional, Lim, F., additional, Bond, A., additional, Stone, S., additional, Milligan, I.D., additional, Mack, D.J.F., additional, Nagar, A., additional, West, R.M., additional, Wilcox, M.H., additional, Kirby, A., additional, and Sandoe, J.A.T., additional

Published
2019
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13. Resistant fabric warming is a viable alternative to forced-air warming to prevent inadvertent perioperative hypothermia during hemiarthroplasty in the elderly.

Author

Kümin, M., Jones, C.I., Woods, A., Bremner, S., Reed, M., Scarborough, M., and Harper, C.M.

Abstract

Background: Surgical site infection (SSI) is associated with inadvertent perioperative hypothermia (IPH). This can be prevented by active patient warming. However, results from comparisons of warming techniques are conflicting. They are based mostly on elective surgery, are from small numbers of patients, and are dominated by the market leader, forced-air warming (FAW). Furthermore, the definition of hypothermia is debatable and systematic reviews of warming systems conclude that a stricter control of temperature is required to study the benefits of warming.Aim: To analyse core temperatures in detail in a large subset of elderly patients who took part in a randomized trial of patient warming following hemiarthroplasty who had received constant zero-flux thermometry to record their temperature.Methods: Regression models with a fixed effect for warming group and covariates related to temperature were compared for 257 participants randomized to FAW or resistant fabric warming (RFW) from a prior clinical trial.Findings: Those in the RFW group were -0.08°C cooler and had a cumulative hypothermia score -1.87 lower than those in the FAW group. There was no difference in the proportion of hypothermic patients at either <36.5°C or <36.0°C.Conclusions: This is the first study to provide accurate temperature measurements in patients undergoing a procedure predominantly under regional rather than general anaesthetic. It shows that RFW is a viable alternative to FAW for preventing IPH during hemiarthroplasty. Further studies are needed to measure the benefits of patient warming in terms of clinically important outcomes. [ABSTRACT FROM AUTHOR]

Published
2021
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20. Fracture-related infection: A consensus on definition from an international expert group

Author

Metsemakers, W.J., Morgenstern, M., McNally, M.A., Moriarty, T.F., McFadyen, I., Scarborough, M., Athanasou, N.A., Ochsner, P.E., Kuehl, R., Raschke, M., Borens, O., Xie, Z., Velkes, S., Hungerer, S., Kates, S.L., Zalavras, C., Giannoudis, P.V., Richards, R.G., and Verhofstad, MHJ

Subjects
Checklist, Consensus, Fractures, Bone/complications, Humans, Orthopedics, Osteomyelitis/classification, Osteomyelitis/etiology, Surgical Wound Infection/classification, Terminology as Topic, Definition, Fracture, Fracture-related infection consensus definition, Infection
Abstract

Fracture-related infection (FRI) is a common and serious complication in trauma surgery. Accurately estimating the impact of this complication has been hampered by the lack of a clear definition. The absence of a working definition of FRI renders existing studies difficult to evaluate or compare. In order to address this issue, an expert group comprised of a number of scientific and medical organizations has been convened, with the support of the AO Foundation, in order to develop a consensus definition. The process that led to this proposed definition started with a systematic literature review, which revealed that the majority of randomized controlled trials in fracture care do not use a standardized definition of FRI. In response to this conclusion, an international survey on the need for and key components of a definition of FRI was distributed amongst all registered AOTrauma users. Approximately 90% of the more than 2000 surgeons who responded suggested that a definition of FRI is required. As a final step, a consensus meeting was held with an expert panel. The outcome of this process led to a consensus definition of FRI. Two levels of certainty around diagnostic features were defined. Criteria could be confirmatory (infection definitely present) or suggestive. Four confirmatory criteria were defined: Fistula, sinus or wound breakdown; Purulent drainage from the wound or presence of pus during surgery; Phenotypically indistinguishable pathogens identified by culture from at least two separate deep tissue/implant specimens; Presence of microorganisms in deep tissue taken during an operative intervention, as confirmed by histopathological examination. Furthermore, a list of suggestive criteria was defined. These require further investigations in order to look for confirmatory criteria. In the current paper, an overview is provided of the proposed definition and a rationale for each component and decision. The intention of establishing this definition of FRI was to offer clinicians the opportunity to standardize clinical reports and improve the quality of published literature. It is important to note that the proposed definition was not designed to guide treatment of FRI and should be validated by prospective data collection in the future.

Published
2018

21. Fracture-related infection

Author

Metsemakers, WJ., primary, Morgenstern, M., additional, McNally, M.A., additional, Moriarty, T.F., additional, McFadyen, I., additional, Scarborough, M., additional, Athanasou, N.A., additional, Ochsner, P.E., additional, Kuehl, R., additional, Raschke, M., additional, Borens, O., additional, Xie, Z., additional, Velkes, S., additional, Hungerer, S., additional, Kates, S.L., additional, Zalavras, C., additional, Giannoudis, P.V., additional, Richards, R.G., additional, and Verhofstad, M.H.J., additional

Published
2019
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23. Fracture-related infection: A consensus on definition from an international expert group

Author

Metsemakers, WJ., primary, Morgenstern, M., additional, McNally, M.A., additional, Moriarty, T.F., additional, McFadyen, I., additional, Scarborough, M., additional, Athanasou, N.A., additional, Ochsner, P.E., additional, Kuehl, R., additional, Raschke, M., additional, Borens, O., additional, Xie, Z., additional, Velkes, S., additional, Hungerer, S., additional, Kates, S.L., additional, Zalavras, C., additional, Giannoudis, P.V., additional, Richards, R.G., additional, and Verhofstad, M.H.J., additional

Published
2018
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25. Pencil Beam Scanning Proton Radiation Therapy Reduces Dose to the Planned Surgical Skin Flap and Uninvolved Bone in Preoperative Radiation Therapy for Soft Tissue Sarcomas of the Lower Extremity

Author

Nurkic, S.R.W., primary, Wilke, B., additional, Li, Z., additional, Shen, X., additional, Ho, M.W., additional, Indelicato, D.J., additional, Gibbs, C.P., additional, Spiguel, A., additional, Scarborough, M., additional, Zlotecki, R.A., additional, and Rutenberg, M.S., additional

Published
2017
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28. Gram-negative bacteraemia; a multi-centre prospective evaluation of empiric antibiotic therapy and outcome in English acute hospitals

Author

Fitzpatrick, J.M., primary, Biswas, J.S., additional, Edgeworth, J.D., additional, Islam, J., additional, Jenkins, N., additional, Judge, R., additional, Lavery, A.J., additional, Melzer, M., additional, Morris-Jones, S., additional, Nsutebu, E.F., additional, Peters, J., additional, Pillay, D.G., additional, Pink, F., additional, Price, J.R., additional, Scarborough, M., additional, Thwaites, G.E., additional, Tilley, R., additional, Walker, A.S., additional, Llewelyn, M.J., additional, Melzer, Mark, additional, Pink, Frederick, additional, Fitzpatrick, Jennifer, additional, Jones, Gill, additional, Llewelyn, Martin, additional, Peters, Joanna, additional, Biswas, Jason, additional, Edgeworth, Jonathan, additional, Guile, Lucy, additional, Querol-Rubiera, Antonio, additional, Hussain, Abid, additional, Jenkins, Neil, additional, Moran, Ed, additional, Pillay, Devedas, additional, Scarborough, Matthew, additional, Rawlinson, Tom, additional, Judge, Ryan, additional, Tilley, Robert, additional, Lavery, Anita, additional, Morris-Jones, Stephen, additional, Price, James, additional, and Nsutebu, Emmanuel, additional

Published
2016
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