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Hammond JA, Gordon EA, Socarras KM, Chang Mell J, Ehrlich GD. Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis. Biochem Soc Trans 2020; 48:2437-2455. [PMID: 33245329 PMCID: PMC7752077 DOI: 10.1042/bst20190713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023]
Abstract
The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host-bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.
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Affiliation(s)
- Jocelyn A. Hammond
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Emma A. Gordon
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Kayla M. Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Joshua Chang Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
- Department of Otolaryngology – Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, U.S.A
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Ide N, Frogner BK, LeRouge CM, Vigil P, Thompson M. What's on your keyboard? A systematic review of the contamination of peripheral computer devices in healthcare settings. BMJ Open 2019; 9:e026437. [PMID: 30852549 PMCID: PMC6429971 DOI: 10.1136/bmjopen-2018-026437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To determine the extent and type of microbial contamination of computer peripheral devices used in healthcare settings, evaluate the effectiveness of interventions to reduce contamination of these devices and establish the risk of patient and healthcare worker infection from contaminated devices. DESIGN Systematic review METHODS: We searched four online databases: MEDLINE, CINAHL, Embase and Scopus for articles reporting primary data collection on contamination of computer-related equipment (including keyboards, mice, laptops and tablets) and/or studies demonstrating the effectiveness of a disinfection technique. Pooling of contamination rates was conducted where possible, and narrative synthesis was used to describe the rates of device contamination, types of bacterial and viral contamination, effectiveness of interventions and any associations between device contamination and human infections. RESULTS Of the 4432 records identified, a total of 75 studies involving 2804 computer devices were included. Of these, 50 studies reported contamination of computer-related hardware, and 25 also measured the effects of a decontamination intervention. The overall proportion of contamination ranged from 24% to 100%. The most common microbial contaminants were skin commensals, but also included potential pathogens including methicillin-resistantStaphylococcus aureus, Clostridiumdifficile, vancomycin-resistantenterococci and Escherichia coli. Interventions demonstrating effective decontamination included wipes/pads using isopropyl alcohol, quaternary ammonium, chlorhexidine or dipotassium peroxodisulfate, ultraviolet light emitting devices, enhanced cleaning protocols and chlorine/bleach products. However, results were inconsistent, and there was insufficient data to demonstrate comparative effectiveness. We found little evidence on the link between device contamination and patient/healthcare worker colonisation or infection. CONCLUSIONS Computer keyboards and peripheral devices are frequently contaminated; however, our findings do not allow us to draw firm conclusions about their relative impact on the transmission of pathogens or nosocomial infection. Additional studies measuring the incidence of healthcare-acquired infections from computer hardware, the relative risk they pose to healthcare and evidence for effective and practical cleaning methods are needed.
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Affiliation(s)
- Nicole Ide
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Bianca K Frogner
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Cynthia M LeRouge
- Department of Information Systems & Business Analytics, Florida International University, Miami, Florida, USA
| | - Patrick Vigil
- Family Medicine, Pacific Northwest University, Yakima, Washington, USA
| | - Matthew Thompson
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
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3
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Raible KM, Sen B, Law N, Bias TE, Emery CL, Ehrlich GD, Joshi SG. Molecular characterization of β-lactamase genes in clinical isolates of carbapenem-resistant Acinetobacter baumannii. Ann Clin Microbiol Antimicrob 2017; 16:75. [PMID: 29145853 PMCID: PMC5691885 DOI: 10.1186/s12941-017-0248-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 11/08/2017] [Indexed: 01/26/2023] Open
Abstract
Background Acinetobacter baumannii is a nosocomial pathogen which is establishing as a major cause of morbidity and mortality within the healthcare community. The success of this pathogen is largely due to its ability to rapidly gain resistance to antimicrobial therapies and its capability to persist in an abiotic environment through the production of a biofilm. Our tertiary-care hospital has showed high incidence of carbapenem-resistant Acinetobacter baumannii (CRAB) isolates. Methods In this study we explore both genotypic and phenotypic properties of 26 CRAB isolates: 16 isolates were collected from January 2010 to March 2011, and 10 were collected between February and May 2015. Results We determined that all 26 CRAB isolates possessed multiple β-lactamase genes, including genes from Groups A, C, and D. Specifically, 42% of the isolates possesses the potentially plasmid-borne genes of OXA-23-like or OXA-40-like β-lactamase. The presence of mobile gene element integron cassettes and/or integrases in 88% of the isolates suggests a possible mechanism of dissemination of antibiotic resistance genes. Additionally, the location of insertion sequence (IS) ISAba1 in promotor region of of the OXA-51-like, ADC-7, and ampC genes was confirmed. Multilocus sequence typing (MLST) demonstrated that all 26 CRAB isolates were either sequence type (ST)-229 or ST-2. Interestingly, ST-2 went from being the minority CRAB strain in the 2010–2011 isolates to the predominant strain in the 2015 isolates (from 32 to 90%). We show that the ST-2 strains have an enhanced ability to produce biofilms in comparison to the ST-229 strains, and this fact has potentially led to more successful colonization of the clinical environment over time. Conclusions This study provides a longitudinal genetic and phenotypic survey of two CRAB sequence types, and suggests how their differing phenotypes may interact with the selective pressures of a hospital setting effecting strain dominance over a 5-year period. Electronic supplementary material The online version of this article (10.1186/s12941-017-0248-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kevin M Raible
- Center for Surgical Infections & Biofilms, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Bhaswati Sen
- Center for Surgical Infections & Biofilms, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Nancy Law
- Center for Surgical Infections & Biofilms, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Tiffany E Bias
- Center for Surgical Infections & Biofilms, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Christopher L Emery
- Center for Surgical Infections & Biofilms, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Department of Pathology and Lab Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Garth D Ehrlich
- Center for Surgical Infections & Biofilms, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA
| | - Suresh G Joshi
- Center for Surgical Infections & Biofilms, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA. .,Center for Genomic Sciences, Institute of Molecular Medicine and Infectious diseases, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA. .,Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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4
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Green C, Pamplin JC, Chafin KN, Murray CK, Yun HC. Pulsed-xenon ultraviolet light disinfection in a burn unit: Impact on environmental bioburden, multidrug-resistant organism acquisition and healthcare associated infections. Burns 2017; 43:388-396. [DOI: 10.1016/j.burns.2016.08.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/25/2016] [Indexed: 10/20/2022]
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Patel R, Alijanipour P, Parvizi J. Advancements in Diagnosing Periprosthetic Joint Infections after Total Hip and Knee Arthroplasty. Open Orthop J 2016; 10:654-661. [PMID: 28144375 PMCID: PMC5220175 DOI: 10.2174/1874325001610010654] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/16/2016] [Accepted: 07/15/2016] [Indexed: 02/08/2023] Open
Abstract
Periprosthetic joint infection (PJI) is a complication of total joint arthroplasty that is challenging to diagnose. Currently, there is no "gold standard" for definite diagnosis of PJI. A multi-criteria definition has been described for PJI based on microbiology cultures, serum markers, such as erythrocyte sedimentation rate and C-reactive protein (CRP), synovial fluid biomarkers, such as leukocyte esterase and histopathology assessment of the periprosthetic tissue. The conventional serum markers are generally nonspecific and can be elevated in inflammatory conditions. Therefore, they cannot be relied on for definite diagnosis of PJI. Hence, with the use of proteomics, synovial fluid biomarkers such as α-defensin, IL-6, and CRP have been proposed as more accurate biomarkers for PJI. Current methods to culture micro-organisms have several limitations, and can be false-negative and false-positive in a considerable number of cases. In an attempt to improve culture sensitivity, diagnostic methods to target biofilms have recently been studied. The understanding of the concept of biofilms has also allowed for the development of novel techniques for PJI diagnosis, such as visualizing biofilms with fluorescent in-situ hybridization and detection of bacteria via DNA microarray. Lastly, the use of amplification-based molecular techniques has provided methods to identify specific species of bacteria that cause culture-negative PJI. While diagnosing PJI is difficult, these advances could be valuable tools for clinicians.
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Affiliation(s)
- Ripal Patel
- Rothman Institute at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Pouya Alijanipour
- Rothman Institute at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Javad Parvizi
- Rothman Institute at Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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6
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Rudkjøbing VB, Thomsen TR, Xu Y, Melton-Kreft R, Ahmed A, Eickhardt S, Bjarnsholt T, Poulsen SS, Nielsen PH, Earl JP, Ehrlich GD, Moser C. Comparing culture and molecular methods for the identification of microorganisms involved in necrotizing soft tissue infections. BMC Infect Dis 2016; 16:652. [PMID: 27821087 PMCID: PMC5100109 DOI: 10.1186/s12879-016-1976-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/26/2016] [Indexed: 12/26/2022] Open
Abstract
Background Necrotizing soft tissue infections (NSTIs) are a group of infections affecting all soft tissues. NSTI involves necrosis of the afflicted tissue and is potentially life threatening due to major and rapid destruction of tissue, which often leads to septic shock and organ failure. The gold standard for identification of pathogens is culture; however molecular methods for identification of microorganisms may provide a more rapid result and may be able to identify additional microorganisms that are not detected by culture. Methods In this study, tissue samples (n = 20) obtained after debridement of 10 patients with NSTI were analyzed by standard culture, fluorescence in situ hybridization (FISH) and multiple molecular methods. The molecular methods included analysis of microbial diversity by 1) direct 16S and D2LSU rRNA gene Microseq 2) construction of near full-length 16S rRNA gene clone libraries with subsequent Sanger sequencing for most samples, 3) the Ibis T5000 biosensor and 4) 454-based pyrosequencing. Furthermore, quantitative PCR (qPCR) was used to verify and determine the relative abundance of Streptococcus pyogenes in samples. Results For 70 % of the surgical samples it was possible to identify microorganisms by culture. Some samples did not result in growth (presumably due to administration of antimicrobial therapy prior to sampling). The molecular methods identified microorganisms in 90 % of the samples, and frequently detected additional microorganisms when compared to culture. Although the molecular methods generally gave concordant results, our results indicate that Microseq may misidentify or overlook microorganisms that can be detected by other molecular methods. Half of the patients were found to be infected with S. pyogenes, but several atypical findings were also made including infection by a) Acinetobacter baumannii, b) Streptococcus pneumoniae, and c) fungi, mycoplasma and Fusobacterium necrophorum. Conclusion The study emphasizes that many pathogens can be involved in NSTIs, and that no specific “NSTI causing” combination of species exists. This means that clinicians should be prepared to diagnose and treat any combination of microbial pathogens. Some of the tested molecular methods offer a faster turnaround time combined with a high specificity, which makes supplemental use of such methods attractive for identification of microorganisms, especially for fulminant life-threatening infections such as NSTI.
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Affiliation(s)
- Vibeke Børsholt Rudkjøbing
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Trine Rolighed Thomsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Life Science Division, The Danish Technological Institute, Taastrup, Denmark
| | - Yijuan Xu
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Life Science Division, The Danish Technological Institute, Taastrup, Denmark
| | - Rachael Melton-Kreft
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Pittsburgh, USA
| | - Azad Ahmed
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Pittsburgh, USA
| | - Steffen Eickhardt
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Denmark
| | - Steen Seier Poulsen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Joshua P Earl
- Center for Genomic Sciences, Philadelphia, PA, USA.,Departments of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Philadelphia, PA, USA.,Departments of Microbiology and Immunology, Philadelphia, PA, USA
| | - Garth D Ehrlich
- Center for Genomic Sciences, Philadelphia, PA, USA.,Departments of Microbiology and Immunology, Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Philadelphia, PA, USA.,Departments of Microbiology and Immunology, Philadelphia, PA, USA.,Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Claus Moser
- Department of Clinical Microbiology, Copenhagen University Hospital, Rigshospitalet, Denmark.
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Palmer MP, Melton-Kreft R, Nistico L, Hiller NL, Kim LHJ, Altman GT, Altman DT, Sotereanos NG, Hu FZ, De Meo PJ, Ehrlich GD. Polymerase Chain Reaction-Electrospray-Time-of-Flight Mass Spectrometry Versus Culture for Bacterial Detection in Septic Arthritis and Osteoarthritis. Genet Test Mol Biomarkers 2016; 20:721-731. [PMID: 27749085 PMCID: PMC5180073 DOI: 10.1089/gtmb.2016.0080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background: Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. Aims: The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. Patients and Methods: Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction–electrospray ionization–time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content. Patients were grouped by diagnosis into one of two cohorts, those with clinical suspicion of septic arthritis (n = 44) and those undergoing primary arthroplasty of the knee for OA (n = 21). In all cases where discrepant culture and MDx results were obtained, we performed species-specific 16S rRNA fluorescence in situ hybridization (FISH) as a confirmatory test. Results: MDx testing identified bacteria in 50% of the suspected septic arthritis cases and 29% of the arthroplasty cases, whereas culture detected bacteria in only 16% of the former and 0% of the latter group. The overall difference in detection rates for culture and MDx was very highly significant, p-value = 2.384 × 10−7. All of the culture-positive cases were typed as Staphylococcus aureus. Two of the septic arthritis cases were polymicrobial as was one of the OA cases by MDx. FISH testing of the specimens with discordant results supported the MDx findings in 91% (19/21) of the cases, including one case where culture detected S. aureus and MDx detected Streptococcus agalactiae.Conclusions: MDx were more sensitive than culture, as confirmed by FISH. FISH only identifies bacteria that are embedded or infiltrated within the tissue and is thus not susceptible to contamination. Not all suspected cases of septic arthritis contain bacteria, but a significant percent of patients with OA, and no signs of infection, have FISH-confirmed bacterial biofilms present in the knee.
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Affiliation(s)
- Michael P Palmer
- 1 88th Surgical Operations Squadron, Orthopedic Surgery , Wright-Patterson Airforce Base, Dayton, Ohio
| | - Rachael Melton-Kreft
- 2 Center of Excellence in Biofilm Research , Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Laura Nistico
- 2 Center of Excellence in Biofilm Research , Allegheny Health Network, Pittsburgh, Pennsylvania
| | - N Louisa Hiller
- 3 Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania
| | - Leon H J Kim
- 3 Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania
| | - Gregory T Altman
- 4 Department of Orthopaedic Surgery, Allegheny General Hospital , Pittsburgh, Pennsylvania
| | - Daniel T Altman
- 4 Department of Orthopaedic Surgery, Allegheny General Hospital , Pittsburgh, Pennsylvania
| | - Nicholas G Sotereanos
- 4 Department of Orthopaedic Surgery, Allegheny General Hospital , Pittsburgh, Pennsylvania
| | - Fen Z Hu
- 5 Institute for Molecular Medicine and Infectious Disease, Center for Genomic Sciences, Drexel University College of Medicine , Philadelphia, Pennsylvania
| | - Patrick J De Meo
- 4 Department of Orthopaedic Surgery, Allegheny General Hospital , Pittsburgh, Pennsylvania
| | - Garth D Ehrlich
- 5 Institute for Molecular Medicine and Infectious Disease, Center for Genomic Sciences, Drexel University College of Medicine , Philadelphia, Pennsylvania.,6 Institute for Molecular Medicine and Infectious Disease, Center for Advanced Microbial Processing, Drexel University College of Medicine , Philadelphia, Pennsylvania.,7 Department of Microbiology and Immunology, Drexel University College of Medicine , Philadelphia, Pennsylvania.,8 Department of Otolaryngology-Head and Neck Surgery, Drexel University College of Medicine , Philadelphia, Pennsylvania
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8
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Vetor R, Murray CK, Mende K, Melton-Kreft R, Akers KS, Wenke J, Spirk T, Guymon C, Zera W, Beckius ML, Schnaubelt ER, Ehrlich G, Vento TJ. The use of PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) to detect bacterial and fungal colonization in healthy military service members. BMC Infect Dis 2016; 16:338. [PMID: 27448413 PMCID: PMC4957419 DOI: 10.1186/s12879-016-1651-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 06/07/2016] [Indexed: 11/13/2022] Open
Abstract
Background The role of microbial colonization in disease is complex. Novel molecular tools to detect colonization offer theoretical improvements over traditional methods. We evaluated PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) as a screening tool to study colonization of healthy military service members. Methods We assessed 101 healthy Soldiers using PCR/ESI-TOF-MS on nares, oropharynx, and groin specimens for the presence of gram-positive and gram-negative bacteria (GNB), fungi, and antibiotic resistance genes. A second set of swabs was processed by traditional culture, followed by identification using the BD Phoenix automated system; comparison between PCR/ESI-TOF-MS and culture was carried out only for GNB. Results Using PCR/ESI-TOF-MS, at least one colonizing organism was found on each individual: mean (SD) number of organisms per subject of 11.8(2.8). The mean number of organisms in the nares, groin and oropharynx was 3.8(1.3), 3.8(1.4) and 4.2(2), respectively. The most commonly detected organisms were aerobic gram-positive bacteria: primarily coagulase-negative Staphylococcus (101 subjects: 341 organisms), Streptococcus pneumoniae (54 subjects: 57 organisms), Staphylococcus aureus (58 subjects: 80 organisms) and Nocardia asteroides (45 subjects: 50 organisms). The mecA gene was found in 96 subjects. The most commonly found GNB was Haemophilus influenzae (20 subjects: 21 organisms) and the most common anaerobe was Propionibacterium acnes (59 subjects). Saccharomyces species (30 subjects) were the most common fungi detected. Only one GNB (nares E. coli) was identified in the same subject by both diagnostic systems. Conclusion PCR/ESI-TOF-MS detected common colonizing organisms and identified more typically-virulent bacteria in asymptomatic, healthy adults. PCR/ESI-TOF-MS appears to be a useful method for detecting bacterial and fungal organisms, but further clinical correlation and validation studies are needed.
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Affiliation(s)
- Ryan Vetor
- San Antonio Military Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Clinton K Murray
- San Antonio Military Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA.,Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Katrin Mende
- San Antonio Military Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA.,Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Rachel Melton-Kreft
- Center for Genomic Sciences, Allegheny Singer Research Institute, Pittsburgh, PA, USA
| | - Kevin S Akers
- Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA.,US Army Institute of Surgical Research, Fort Sam Houston, San Antonio, TX, USA
| | - Joseph Wenke
- US Army Institute of Surgical Research, Fort Sam Houston, San Antonio, TX, USA
| | - Tracy Spirk
- Center for Genomic Sciences, Allegheny Singer Research Institute, Pittsburgh, PA, USA
| | - Charles Guymon
- US Army Institute of Surgical Research, Fort Sam Houston, San Antonio, TX, USA
| | - Wendy Zera
- San Antonio Military Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA.,Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Miriam L Beckius
- San Antonio Military Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA
| | | | - Garth Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Pittsburgh, PA, USA
| | - Todd J Vento
- San Antonio Military Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA. .,Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA. .,Infectious Disease Service, (MCHE-MDI), Brooke Army Medical Center, 3551 Roger Brooke Drive, JBSA Fort Sam Houston, 78234, Texas, USA.
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9
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Zautner AE, Goldschmidt AM, Thürmer A, Schuldes J, Bader O, Lugert R, Groß U, Stingl K, Salinas G, Lingner T. SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs. BMC Genomics 2015; 16:1088. [PMID: 26689587 PMCID: PMC4687069 DOI: 10.1186/s12864-015-2317-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Campylobacter species are the most prevalent bacterial pathogen causing acute enteritis worldwide. In contrast to Campylobacter jejuni, about 5 % of Campylobacter coli strains exhibit susceptibility to restriction endonuclease digestion by DpnI cutting specifically 5'-G(m)ATC-3' motifs. This indicates significant differences in DNA methylation between both microbial species. The goal of the study was to analyze the methylome of a C. coli strain susceptible to DpnI digestion, to identify its methylation motifs and restriction modification systems (RM-systems), and compare them to related organisms like C. jejuni and Helicobacter pylori. RESULTS Using one SMRT cell and the PacBio RS sequencing technology followed by PacBio Modification and Motif Analysis the complete genome of the DpnI susceptible strain C. coli BfR-CA-9557 was sequenced to 500-fold coverage and assembled into a single contig of 1.7 Mbp. The genome contains a CJIE1-like element prophage and is phylogenetically closer to C. coli clade 1 isolates than clade 3. 45,881 6-methylated adenines (ca. 2.7 % of genome positions) that are predominantly arranged in eight different methylation motifs and 1,788 4-methylated cytosines (ca. 0.1 %) have been detected. Only two of these motifs correspond to known restriction modification motifs. Characteristic for this methylome was the very high fraction of methylation of motifs with mostly above 99 %. CONCLUSIONS Only five dominant methylation motifs have been identified in C. jejuni, which have been associated with known RM-systems. C. coli BFR-CA-9557 shares one (RAATTY) of these, but four ORFs could be assigned to putative Type I RM-systems, seven ORFs to Type II RM-systems and three ORFs to Type IV RM-systems. In accordance with DpnI prescreening RM-system IIP, methylation of GATC motifs was detected in C. coli BfR-CA-9557. A homologous IIP RM-system has been described for H. pylori. The remaining methylation motifs are specific for C. coli BfR-CA-9557 and have been neither detected in C. jejuni nor in H. pylori. The results of this study give us new insights into epigenetics of Campylobacteraceae and provide the groundwork to resolve the function of RM-systems in C. coli.
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Affiliation(s)
- Andreas E Zautner
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany.
| | - Anne-Marie Goldschmidt
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Andrea Thürmer
- Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Jörg Schuldes
- Institute for Microbiology and Genetics, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Oliver Bader
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Raimond Lugert
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Uwe Groß
- Institute for Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, D-37075, Göttingen, Germany
| | - Kerstin Stingl
- Federal Institute for Risk Assessment (BfR), Department of Biological Safety - National Reference Laboratory for Campylobacter, D-12277, Berlin, Germany
| | - Gabriela Salinas
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep-Sequencing Core Facility, University Medical Center Göttingen, Justus-von-Liebig-Weg 11, D-37077, Göttingen, Germany
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Zang T, Broszczak DA, Broadbent JA, Cuttle L, Lu H, Parker TJ. The biochemistry of blister fluid from pediatric burn injuries: proteomics and metabolomics aspects. Expert Rev Proteomics 2015; 13:35-53. [PMID: 26581649 DOI: 10.1586/14789450.2016.1122528] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Burn injury is a prevalent and traumatic event for pediatric patients. At present, the diagnosis of burn injury severity is subjective and lacks a clinically relevant quantitative measure. This is due in part to a lack of knowledge surrounding the biochemistry of burn injuries and that of blister fluid. A more complete understanding of the blister fluid biochemistry may open new avenues for diagnostic and prognostic development. Burn insult induces a highly complex network of signaling processes and numerous changes within various biochemical systems, which can ultimately be examined using proteome and metabolome measurements. This review reports on the current understanding of burn wound biochemistry and outlines a technical approach for 'omics' profiling of blister fluid from burn wounds of differing severity.
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Affiliation(s)
- Tuo Zang
- a Tissue Repair and Regeneration Program , Institute of Health and Biomedical Innovation , Kelvin Grove , Australia.,b School of Biomedical Sciences , Queensland University of Technology , Brisbane , Australia.,c Wound Management Innovation Co-operative Research Centre , West End , Australia
| | - Daniel A Broszczak
- a Tissue Repair and Regeneration Program , Institute of Health and Biomedical Innovation , Kelvin Grove , Australia.,b School of Biomedical Sciences , Queensland University of Technology , Brisbane , Australia.,c Wound Management Innovation Co-operative Research Centre , West End , Australia
| | - James A Broadbent
- a Tissue Repair and Regeneration Program , Institute of Health and Biomedical Innovation , Kelvin Grove , Australia.,b School of Biomedical Sciences , Queensland University of Technology , Brisbane , Australia.,c Wound Management Innovation Co-operative Research Centre , West End , Australia
| | - Leila Cuttle
- a Tissue Repair and Regeneration Program , Institute of Health and Biomedical Innovation , Kelvin Grove , Australia.,b School of Biomedical Sciences , Queensland University of Technology , Brisbane , Australia.,d Centre for Children's Burns and Trauma Research , Queensland University of Technology, Institute of Health and Biomedical Innovation at the Centre for Children's Health Research , South Brisbane , Australia
| | - Haitao Lu
- a Tissue Repair and Regeneration Program , Institute of Health and Biomedical Innovation , Kelvin Grove , Australia.,b School of Biomedical Sciences , Queensland University of Technology , Brisbane , Australia
| | - Tony J Parker
- a Tissue Repair and Regeneration Program , Institute of Health and Biomedical Innovation , Kelvin Grove , Australia.,b School of Biomedical Sciences , Queensland University of Technology , Brisbane , Australia
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Fleurbaaij F, van Leeuwen HC, Klychnikov OI, Kuijper EJ, Hensbergen PJ. Mass Spectrometry in Clinical Microbiology and Infectious Diseases. Chromatographia 2015. [DOI: 10.1007/s10337-014-2839-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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12
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Emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management. BIOMED RESEARCH INTERNATIONAL 2014; 2014:375681. [PMID: 25343142 PMCID: PMC4197867 DOI: 10.1155/2014/375681] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/22/2014] [Accepted: 08/28/2014] [Indexed: 12/25/2022]
Abstract
Atypical and multidrug resistance, especially ESBL and carbapenemase expressing Enterobacteriaceae, is globally spreading. Therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. Consequently, rapid antibiotic resistance testing is essential. Various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. PCR- and sequencing-based approaches are the most expensive but the most frequently applied modes of testing, suitable for the detection of resistance genes even from primary material. Next generation sequencing, based either on assessment of allelic single nucleotide polymorphisms or on the detection of nonubiquitous resistance mechanisms might allow for sequence-based bacterial resistance testing comparable to viral resistance testing on the long term. Fluorescence in situ hybridization (FISH), based on specific binding of fluorescence-labeled oligonucleotide probes, provides a less expensive molecular bridging technique. It is particularly useful for detection of resistance mechanisms based on mutations in ribosomal RNA. Approaches based on MALDI-TOF-MS, alone or in combination with molecular techniques, like PCR/electrospray ionization MS or minisequencing provide the fastest resistance results from pure colonies or even primary samples with a growing number of protocols. This review details the various approaches of rapid resistance testing, their pros and cons, and their potential use for the diagnostic laboratory.
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The interaction of bacteria with engineered nanostructured polymeric materials: a review. ScientificWorldJournal 2014; 2014:410423. [PMID: 25025086 PMCID: PMC4084677 DOI: 10.1155/2014/410423] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/08/2014] [Accepted: 05/10/2014] [Indexed: 12/17/2022] Open
Abstract
Bacterial infections are a leading cause of morbidity and mortality worldwide. In spite of great advances in biomaterials research and development, a significant proportion of medical devices undergo bacterial colonization and become the target of an implant-related infection. We present a review of the two major classes of antibacterial nanostructured materials: polymeric nanocomposites and surface-engineered materials. The paper describes antibacterial effects due to the induced material properties, along with the principles of bacterial adhesion and the biofilm formation process. Methods for antimicrobial modifications of polymers using a nanocomposite approach as well as surface modification procedures are surveyed and discussed, followed by a concise examination of techniques used in estimating bacteria/material interactions. Finally, we present an outline of future sceneries and perspectives on antibacterial applications of nanostructured materials to resist or counteract implant infections.
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