1
|
Sasiene ZJ, LeBrun ES, Velappan N, Anderson AR, Patterson NH, Dufresne M, Farrow MA, Norris JL, Caprioli RM, Mach PM, McBride EM, Glaros TG. Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers. Analyst 2024; 149:3564-3574. [PMID: 38717518 DOI: 10.1039/d4an00325j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.
Collapse
Affiliation(s)
- Zachary J Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Erick S LeBrun
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nileena Velappan
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Austin R Anderson
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nathan H Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Melissa A Farrow
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Phillip M Mach
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Ethan M McBride
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Trevor G Glaros
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| |
Collapse
|
2
|
Shen H, Xie J, Gao W, Wang L, Chen L, Qian H, Yu S, Feng B, Yang F. Detection limit of FT-IR-based bacterial typing based on optimized sample preparation and typing model. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123633. [PMID: 37952427 DOI: 10.1016/j.saa.2023.123633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Accurate and efficient bacterial typing methods are crucial to microbiology. Fourier transform infrared (FT-IR) spectroscopy enables highly distinguishable fingerprint identification of closely related bacterial strains by producing highly specific fingerprints of bacteria, which is increasingly being considered as an alternative to genotypic methods, such as pulsed field gel electrophoresis (PFGE) and whole genome sequencing (WGS), for bacterial typing. Compared with genotypic methods, FT-IR has significant advantages of convenient operation, fast speed, and low cost. Fundamental research into the detection limit based on optimized analytical conditions for FT-IR bacterial typing, which can avoid excessive bacterial culture time or sampling volume, is particularly important, especially in clinical practice. However, the corresponding parameters have not been fully investigated. In this study, we developed a simplified and reliable procedure for sample preparation, optimized the data analysis procedure, and evaluated the FT-IR detection limit based on the above conditions. In particular, we combined the film mold and calcium fluoride plate for sample preparation. We evaluated the detection limit (about 108 CFU/mL) after parameter optimization using hierarchical cluster analysis (HCA) and artificial neural network (ANN). The optimization and evaluation of these key fundamentals will better promote future application of FT-IR-based bacterial typing.
Collapse
Affiliation(s)
- Hao Shen
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jinghang Xie
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wenjing Gao
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | | | - Heng Qian
- Shanghai University of Finance and Economics, Shanghai 200433, China
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Bin Feng
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| |
Collapse
|
3
|
Muselius B, Roux-Dalvai F, Droit A, Geddes-McAlister J. Resolving the Temporal Splenic Proteome during Fungal Infection for Discovery of Putative Dual Perspective Biomarker Signatures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1928-1940. [PMID: 37222660 PMCID: PMC10487597 DOI: 10.1021/jasms.3c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/06/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
Fungal pathogens are emerging threats to global health with the rise of incidence associated with climate change and increased geographical distribution; factors also influencing host susceptibility to infection. Accurate detection and diagnosis of fungal infections is paramount to offer rapid and effective therapeutic options. For improved diagnostics, the discovery and development of protein biomarkers presents a promising avenue; however, this approach requires a priori knowledge of infection hallmarks. To uncover putative novel biomarkers of disease, profiling of the host immune response and pathogen virulence factor production is indispensable. In this study, we use mass-spectrometry-based proteomics to resolve the temporal proteome of Cryptococcus neoformans infection of the spleen following a murine model of infection. Dual perspective proteome profiling defines global remodeling of the host over a time course of infection, confirming activation of immune associated proteins in response to fungal invasion. Conversely, pathogen proteomes detect well-characterized C. neoformans virulence determinants, along with novel mapped patterns of pathogenesis during the progression of disease. Together, our innovative systematic approach confirms immune protection against fungal pathogens and explores the discovery of putative biomarker signatures from complementary biological systems to monitor the presence and progression of cryptococcal disease.
Collapse
Affiliation(s)
- Benjamin Muselius
- Department
of Molecular and Cellular Biology, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Florence Roux-Dalvai
- Proteomics
platform, CHU de Québec - Université
Laval Research Center, Québec
City, Québec G1
V 4G2, Canada
- Computational
Biology Laboratory, CHU de Québec
- Université Laval Research Center, Québec City, Québec G1 V 4G2, Canada
- Canadian
Proteomics and Artificial Intelligence Consortium, Guelph, Ontario N1G 2W1, Canada
| | - Arnaud Droit
- Proteomics
platform, CHU de Québec - Université
Laval Research Center, Québec
City, Québec G1
V 4G2, Canada
- Computational
Biology Laboratory, CHU de Québec
- Université Laval Research Center, Québec City, Québec G1 V 4G2, Canada
- Canadian
Proteomics and Artificial Intelligence Consortium, Guelph, Ontario N1G 2W1, Canada
| | - Jennifer Geddes-McAlister
- Department
of Molecular and Cellular Biology, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
- Canadian
Proteomics and Artificial Intelligence Consortium, Guelph, Ontario N1G 2W1, Canada
| |
Collapse
|
4
|
Nyblom M, Johnning A, Frykholm K, Wrande M, Müller V, Goyal G, Robertsson M, Dvirnas A, Sewunet T, KK S, Ambjörnsson T, Giske CG, Sandegren L, Kristiansson E, Westerlund F. Strain-level bacterial typing directly from patient samples using optical DNA mapping. COMMUNICATIONS MEDICINE 2023; 3:31. [PMID: 36823379 PMCID: PMC9950433 DOI: 10.1038/s43856-023-00259-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Identification of pathogens is crucial to efficiently treat and prevent bacterial infections. However, existing diagnostic techniques are slow or have a too low resolution for well-informed clinical decisions. METHODS In this study, we have developed an optical DNA mapping-based method for strain-level bacterial typing and simultaneous plasmid characterisation. For the typing, different taxonomical resolutions were examined and cultivated pure Escherichia coli and Klebsiella pneumoniae samples were used for parameter optimization. Finally, the method was applied to mixed bacterial samples and uncultured urine samples from patients with urinary tract infections. RESULTS We demonstrate that optical DNA mapping of single DNA molecules can identify Escherichia coli and Klebsiella pneumoniae at the strain level directly from patient samples. At a taxonomic resolution corresponding to E. coli sequence type 131 and K. pneumoniae clonal complex 258 forming distinct groups, the average true positive prediction rates are 94% and 89%, respectively. The single-molecule aspect of the method enables us to identify multiple E. coli strains in polymicrobial samples. Furthermore, by targeting plasmid-borne antibiotic resistance genes with Cas9 restriction, we simultaneously identify the strain or subtype and characterize the corresponding plasmids. CONCLUSION The optical DNA mapping method is accurate and directly applicable to polymicrobial and clinical samples without cultivation. Hence, it has the potential to rapidly provide comprehensive diagnostics information, thereby optimizing early antibiotic treatment and opening up for future precision medicine management.
Collapse
Affiliation(s)
- My Nyblom
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Anna Johnning
- grid.5371.00000 0001 0775 6028Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96 Sweden ,grid.452079.dDepartment of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, 412 88 Sweden ,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30 Sweden
| | - Karolin Frykholm
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Marie Wrande
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Vilhelm Müller
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Gaurav Goyal
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Miriam Robertsson
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Albertas Dvirnas
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Tsegaye Sewunet
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden
| | - Sriram KK
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Tobias Ambjörnsson
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Christian G. Giske
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden ,grid.24381.3c0000 0000 9241 5705Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, 171 76 Sweden
| | - Linus Sandegren
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
| |
Collapse
|
5
|
Lopez P, Bridel S, Saulnier D, David R, Magariños B, Torres BS, Bernardet JF, Duchaud E. Genomic characterization of Tenacibaculum maritimum O-antigen gene cluster and development of a multiplex PCR-based serotyping scheme. Transbound Emerg Dis 2022; 69:e2876-e2888. [PMID: 35731505 PMCID: PMC9796276 DOI: 10.1111/tbed.14637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/06/2022] [Accepted: 06/17/2022] [Indexed: 01/01/2023]
Abstract
Tenacibaculum maritimum is a devastating bacterial pathogen affecting a large variety of marine fish species. It is responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyse bacterial diversity and population structure. Serological heterogeneity has been observed and up to four different serotypes have been described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping and genome-wide association study, we identified the genomic loci likely involved in the O-antigen biosynthesis. This finding allowed the development of a robust multiplex PCR-based serotyping scheme able to detect subgroups within each serotype and therefore performs better than conventional serotyping. This scheme was successfully applied to a large number of isolates from worldwide origin and retrieved from a large variety of fish species. No obvious correlations were observed between the mPCR-based serotype and the host species or the geographic origin of the isolates. Strikingly, the distribution of mPCR-based serotypes does not follow the core genome phylogeny. Nevertheless, this simple and cost-effective mPCR-based serotyping method could be useful for different applications such as population structure analysis, disease surveillance, vaccine formulation and efficacy follow-up.
Collapse
Affiliation(s)
- Pierre Lopez
- IfremerIRDInstitut Louis MalardéUniv Polynésie FrançaiseEIOLabex CorailTaravaoFrench Polynesia,Université Paris‐SaclayINRAEUVSQVIMJouy‐en‐JosasFrance
| | - Sébastien Bridel
- Université Paris‐SaclayINRAEUVSQVIMJouy‐en‐JosasFrance,Biodiversity and Epidemiology of Bacterial PathogensInstitut Pasteur, Université de ParisParis75015France
| | - Denis Saulnier
- IfremerIRDInstitut Louis MalardéUniv Polynésie FrançaiseEIOLabex CorailTaravaoFrench Polynesia
| | - Rarahu David
- DRM, Direction des Ressources MarinesFare Ute Immeuble Le caillPapeeteFrench Polynesia
| | - Beatriz Magariños
- Departamento de Microbiología, Facultad de Biología/CIBUSUniversidad de Santiago de CompostelaSantiago de CompostelaSpain
| | - Beatriz S. Torres
- Departamento de Microbiología, Facultad de Biología/CIBUSUniversidad de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Eric Duchaud
- Université Paris‐SaclayINRAEUVSQVIMJouy‐en‐JosasFrance
| |
Collapse
|
6
|
Feng Y, Cheng Z, Wei X, Chen M, Zhang J, Zhang Y, Xue L, Chen M, Li F, Shang Y, Liang T, Ding Y, Wu Q. Novel method for rapid identification of Listeria monocytogenes based on metabolomics and deep learning. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
7
|
Mann C, Downard KM. Analysis of bacterial biotyping datasets with a mass-based phylonumerics approach. Anal Bioanal Chem 2022; 414:3411-3417. [DOI: 10.1007/s00216-022-03961-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/04/2022] [Accepted: 02/04/2022] [Indexed: 11/01/2022]
|
8
|
Development of an artificial zinc finger - Luciferase fusion protein for the rapid detection of Salmonella typhimurium. Biochem Biophys Res Commun 2021; 579:35-39. [PMID: 34583193 DOI: 10.1016/j.bbrc.2021.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/16/2021] [Indexed: 11/20/2022]
Abstract
A novel artificial Zinc finger - luciferase fusion protein was successfully developed for rapid detection of Salmonella typhimurium, a worldwide-distributed foodborne pathogen. The designed Zinc finger (ZF) protein bound specifically to a 12 bp region of the Salmonella spp invasion gene invA. While the luciferase from Gaussia princeps called Gaussia luciferase (Gluc) was for the first time fused with the artificial ZF domain to improve the detection sensitivity. The fusion protein successfully recognized and bound to the synthesized invA dsDNA with high specificity and sensitivity. The detection limit was as low as 10 fmol of dsNDA. Then, the bacteria PCR products were subsequently used to assess the zinc finger - luciferase fusion protein. The final results indicated that the ZF-Gluc fusion protein system could detect S. typhimurium as low as 1 CFU/mL in 2 h after the PCR. Therefore, this study provided us with a novel artificial zinc finger fusion protein and an efficient method to accomplish the rapid detection of the major foodborne pathogen S. typhimurium. In addition, the specific artificial ZF proteins that bund to particular dsDNA sequences could be easily designed, the ZF-Gluc might has broad application prospects in the field of rapid pathogenic bacteria detection.
Collapse
|
9
|
Moussa M, Cauvin E, Le Piouffle A, Lucas O, Bidault A, Paillard C, Benoit F, Thuillier B, Treilles M, Travers MA, Garcia C. A MALDI-TOF MS database for fast identification of Vibrio spp. potentially pathogenic to marine mollusks. Appl Microbiol Biotechnol 2021; 105:2527-2539. [PMID: 33590268 PMCID: PMC7954726 DOI: 10.1007/s00253-021-11141-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 02/05/2023]
Abstract
In mollusk aquaculture, a large number of Vibrio species are considered major pathogens. Conventional methods based on DNA amplification and sequencing used to accurately identify Vibrio species are unsuitable for monitoring programs because they are time-consuming and expensive. The aim of this study was, therefore, to develop the MALDI-TOF MS method in order to establish a rapid identification technique for a large panel of Vibrio species. We created the EnviBase containing 120 main spectra projections (MSP) of the Vibrio species that are potentially responsible for mollusk diseases, comprising 25 species: V. aestuarianus, V. cortegadensis, V. tapetis and species belonging to the Coralliilyticus, Harveyi, Mediterranei, and Orientalis clades. Each MSP was constructed by the merger of raw spectra obtained from three different media and generated by three collaborating laboratories to increase the diversity of the conditions and thus obtain a good technique robustness. Perfect discrimination was obtained with all of the MSP created for the Vibrio species and even for very closely related species as V. europaeus and V. bivalvicida. The new EnviBase library was validated through a blind test on 100 Vibrio strains performed by our three collaborators who used the direct transfer and protein extraction methods. The majority of the Vibrio strains were successfully identified with the newly created EnviBase by the three laboratories for both protocol methods. This study documents the first development of a freely accessible database exclusively devoted to Vibrio found in marine environments, taking into account the high diversity of this genus. KEY POINTS: • Development of a MALDI-TOF MS database to quickly affiliate Vibrio species. • Increase of the reactivity when faced with Vibrio associated with mollusk diseases. • Validation of MALDI-TOF MS as routine diagnostic tool.
Collapse
Affiliation(s)
- M Moussa
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, F-17390, La Tremblade, France
| | - E Cauvin
- Labeo-Manche, 1352 avenue de Paris, 50000, Saint-Lô, France
| | - A Le Piouffle
- Labocea, Avenue de la Plage des Gueux, 29330, Quimper, France
| | - O Lucas
- Qualyse, ZI Montplaisir, 79220, Champdeniers Saint-Denis, France
| | - A Bidault
- Univ Brest, CNRS, IRD, Ifremer, UMR6539 LEMAR, F-29280, Plouzané, France
| | - C Paillard
- Univ Brest, CNRS, IRD, Ifremer, UMR6539 LEMAR, F-29280, Plouzané, France
| | - F Benoit
- Labeo-Manche, 1352 avenue de Paris, 50000, Saint-Lô, France
| | - B Thuillier
- Labocea, Avenue de la Plage des Gueux, 29330, Quimper, France
| | - M Treilles
- Qualyse, ZI Montplaisir, 79220, Champdeniers Saint-Denis, France
| | - M A Travers
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, F-17390, La Tremblade, France
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, F-34090, Montpellier, France
| | - Céline Garcia
- Ifremer, SG2M-LGPMM, Laboratoire de Génétique et Pathologie des Mollusques Marins, F-17390, La Tremblade, France.
| |
Collapse
|
10
|
Wu N, Zhu T. Potential of Therapeutic Bacteriophages in Nosocomial Infection Management. Front Microbiol 2021; 12:638094. [PMID: 33633717 PMCID: PMC7901949 DOI: 10.3389/fmicb.2021.638094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
Nosocomial infections (NIs) are hospital-acquired infections which pose a high healthcare burden worldwide. The impact of NIs is further aggravated by the global spread of antimicrobial resistance (AMR). Conventional treatment and disinfection agents are often insufficient to catch up with the increasing AMR and tolerance of the pathogenic bacteria. This has resulted in a need for alternative approaches and raised new interest in therapeutic bacteriophages (phages). In contrast to the limited clinical options available against AMR bacteria, the extreme abundance and biodiversity of phages in nature provides an opportunity to establish an ever-expanding phage library that collectively provides sustained broad-spectrum and poly microbial coverage. Given the specificity of phage-host interactions, phage susceptibility testing can serve as a rapid and cost-effective method for bacterial subtyping. The library can also provide a database for routine monitoring of nosocomial infections as a prelude to preparing ready-to-use phages for patient treatment and environmental sterilization. Despite the remaining obstacles for clinical application of phages, the establishment of phage libraries, pre-stocked phage vials prepared to good manufacturing practice (GMP) standards, and pre-optimized phage screening technology will facilitate efforts to make phages available as modern medicine. This may provide the breakthrough needed to demonstrate the great potential in nosocomial infection management.
Collapse
Affiliation(s)
- Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Tongyu Zhu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Organ Transplantation, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
11
|
|
12
|
Confield LR, Black GP, Wilson BC, Lowe DJ, Theakstone AG, Baker MJ. Vibrational spectroscopic analysis of blood for diagnosis of infections and sepsis: a review of requirements for a rapid diagnostic test. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:157-168. [PMID: 33284291 DOI: 10.1039/d0ay01991g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Infections and sepsis represent a growing global burden. There is a widespread clinical need for a rapid, high-throughput and sensitive technique for the diagnosis of infections and detection of invading pathogens and the presence of sepsis. Current diagnostic methods primarily consist of laboratory-based haematology, biochemistry and microbiology that are time consuming, labour- and resource-intensive, and prone to both false positive and false negative results. Current methods are insufficient for the increasing demands on healthcare systems, causing delays in diagnosis and initiation of treatment, due to the intrinsic time delay in sample preparation, measurement, and analysis. Vibrational spectroscopic techniques can overcome these limitations by providing a rapid, label-free and low-cost method for blood analysis, with limited sample preparation required, potentially revolutionising clinical diagnostics by producing actionable results that enable early diagnosis, leading to improved patient outcomes. This review will discuss the challenges associated with the diagnosis of infections and sepsis, primarily within the UK healthcare system. We will consider the clinical potential of spectroscopic point-of-care technologies to enable blood analysis in the primary-care setting.
Collapse
Affiliation(s)
- L R Confield
- CDT Medical Devices, Department of Biomedical Engineering, Wolfson Centre, 106 Rottenrow, G4 0NW, UK
| | | | | | | | | | | |
Collapse
|
13
|
Cui JJ, Wang LY, Tan ZR, Zhou HH, Zhan X, Yin JY. MASS SPECTROMETRY-BASED PERSONALIZED DRUG THERAPY. MASS SPECTROMETRY REVIEWS 2020; 39:523-552. [PMID: 31904155 DOI: 10.1002/mas.21620] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/09/2019] [Indexed: 06/10/2023]
Abstract
Personalized drug therapy aims to provide tailored treatment for individual patient. Mass spectrometry (MS) is revolutionarily involved in this area because MS is a rapid, customizable, cost-effective, and easy to be used high-throughput method with high sensitivity, specificity, and accuracy. It is driving the formation of a new field, MS-based personalized drug therapy, which currently mainly includes five subfields: therapeutic drug monitoring (TDM), pharmacogenomics (PGx), pharmacomicrobiomics, pharmacoepigenomics, and immunopeptidomics. Gas chromatography-MS (GC-MS) and liquid chromatography-MS (LC-MS) are considered as the gold standard for TDM, which can be used to optimize drug dosage. Matrix-assisted laser desorption ionization-time of flight-MS (MALDI-TOF-MS) significantly improves the capability of detecting biomacromolecule, and largely promotes the application of MS in PGx. It is becoming an indispensable tool for genotyping, which is used to discover and validate genetic biomarkers. In addition, MALDI-TOF-MS also plays important roles in identity of human microbiome whose diversity can explain interindividual differences of drug response. Pharmacoepigenetics is to study the role of epigenetic factors in individualized drug treatment. MS can be used to discover and validate pharmacoepigenetic markers (DNA methylation, histone modification, and noncoding RNA). For the emerging cancer immunotherapy, personalized cancer vaccine has effective immunotherapeutic activity in the clinic. MS-based immunopeptidomics can effectively discover and screen neoantigens. This article systematically reviewed MS-based personalized drug therapy in the above mentioned five subfields. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
Collapse
Affiliation(s)
- Jia-Jia Cui
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P. R. China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P. R. China
| | - Zhi-Rong Tan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P. R. China
| | - Hong-Hao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P. R. China
| | - Xianquan Zhan
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P. R. China
- Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, P. R. China
- Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, 110 Xiangya Road, Changsha, 410078, P. R. China
- Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China
- National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P. R. China
- Hunan Provincial Gynecological Cancer Diagnosis and Treatment Engineering Research Center, Changsha, Hunan, 410078, P. R. China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha, Hunan, 410078, P. R. China
| |
Collapse
|
14
|
An immuno-MALDI mass spectrometry assay for the oral cancer biomarker, matrix metalloproteinase-1, in dried saliva spot samples. Anal Chim Acta 2020; 1100:118-130. [DOI: 10.1016/j.aca.2019.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/19/2019] [Accepted: 12/01/2019] [Indexed: 01/17/2023]
|
15
|
Tracking of Intentionally Inoculated Lactic Acid Bacteria Strains in Yogurt and Probiotic Powder. Microorganisms 2019; 8:microorganisms8010005. [PMID: 31861385 PMCID: PMC7022703 DOI: 10.3390/microorganisms8010005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 12/20/2022] Open
Abstract
The present work aimed at tracking intentionally inoculated lactic acid bacteria (LAB) strains in yogurt and probiotic powder. Leuconostoc (Leu.) mesenteroides (11251), Lactobacillus (L.) brevis (B151), and Lactobacillus plantarum (LB41K) strains were tracked in yogurt, and L. plantarum (LB41P) was tracked in a commercial probiotic powder. The yogurt was intentionally inoculated with the selected bacterial strains. Two types of yogurt with known and unknown bacterial pools were utilized. The standard 16S rRNA gene sequencing was used to evaluate the initial screening. The molecular typing tools, random amplified polymorphic DNA (RAPD), repetitive element palindromic PCR (rep-PCR), and comparative gene sequence analysis of selected housekeeping loci were used to track the inoculated dubious strains. Out of 30 random selections for each inoculation, the developed method identified seven (11251), nine (B151), and five (LB41K) colonies in the yogurt. The validation was performed by identifying 7 colonies (LB41P) out of 30 in the probiotic powder. The DNA banding profiles and the gene sequence alignments led to the identification of the correct inoculated strains. Overall, the study summarizes the use of molecular tools to identify the deliberately inoculated LAB strains. In conclusion, the proposed polyphasic approach effectively tracked the intentionally inoculated strains: Leu. mesenteroides, L. brevis, and L. plantarum (LB41K) in yogurt and L. plantarum (LB41P) in probiotic powder. The study demonstrates how to track industrially relevant misused LAB strains in marketable food products.
Collapse
|
16
|
Roux-Dalvai F, Gotti C, Leclercq M, Hélie MC, Boissinot M, Arrey TN, Dauly C, Fournier F, Kelly I, Marcoux J, Bestman-Smith J, Bergeron MG, Droit A. Fast and Accurate Bacterial Species Identification in Urine Specimens Using LC-MS/MS Mass Spectrometry and Machine Learning. Mol Cell Proteomics 2019; 18:2492-2505. [PMID: 31585987 PMCID: PMC6885708 DOI: 10.1074/mcp.tir119.001559] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
Fast identification of microbial species in clinical samples is essential to provide an appropriate antibiotherapy to the patient and reduce the prescription of broad-spectrum antimicrobials leading to antibioresistances. MALDI-TOF-MS technology has become a tool of choice for microbial identification but has several drawbacks: it requires a long step of bacterial culture before analysis (≥24 h), has a low specificity and is not quantitative. We developed a new strategy for identifying bacterial species in urine using specific LC-MS/MS peptidic signatures. In the first training step, libraries of peptides are obtained on pure bacterial colonies in DDA mode, their detection in urine is then verified in DIA mode, followed by the use of machine learning classifiers (NaiveBayes, BayesNet and Hoeffding tree) to define a peptidic signature to distinguish each bacterial species from the others. Then, in the second step, this signature is monitored in unknown urine samples using targeted proteomics. This method, allowing bacterial identification in less than 4 h, has been applied to fifteen species representing 84% of all Urinary Tract Infections. More than 31,000 peptides in 190 samples were quantified by DIA and classified by machine learning to determine an 82 peptides signature and build a prediction model. This signature was validated for its use in routine using Parallel Reaction Monitoring on two different instruments. Linearity and reproducibility of the method were demonstrated as well as its accuracy on donor specimens. Within 4h and without bacterial culture, our method was able to predict the predominant bacteria infecting a sample in 97% of cases and 100% above the standard threshold. This work demonstrates the efficiency of our method for the rapid and specific identification of the bacterial species causing UTI and could be extended in the future to other biological specimens and to bacteria having specific virulence or resistance factors.
Collapse
Affiliation(s)
- Florence Roux-Dalvai
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Clarisse Gotti
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Mickaël Leclercq
- Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Marie-Claude Hélie
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada
| | | | | | - Frédéric Fournier
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Isabelle Kelly
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Judith Marcoux
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada
| | - Julie Bestman-Smith
- Laboratoire de microbiologie-infectiologie, CHU de Québec-Université Laval, pavillon Hôpital de l'Enfant-Jésus, Québec City, Québec, Canada
| | - Michel G Bergeron
- Centre de Recherche en Infectiologie de l'Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, Canada; Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Québec City, Québec, Canada
| | - Arnaud Droit
- Proteomics platform, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada; Computational Biology Laboratory, CHU de Québec - Université Laval Research Center, Québec City, Québec, Canada; Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC, Canada.
| |
Collapse
|
17
|
Zhong Q, Cheng F, Liang J, Wang X, Chen Y, Fang X, Hu L, Hang Y. Profiles of volatile indole emitted by Escherichia coli based on CDI-MS. Sci Rep 2019; 9:13139. [PMID: 31511564 PMCID: PMC6739388 DOI: 10.1038/s41598-019-49436-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/24/2019] [Indexed: 12/25/2022] Open
Abstract
Escherichia coli is an important pathogen of nosocomial infection in clinical research, Thus, exploring new methods for the rapid detection of this pathogen is urgent. We reported the early release of molecular volatile indole vapour of E. coli cultures and blood cultures analyzed by direct atmospheric corona discharge ionization mass spectrometry (CDI-MS). The concentration of indole in E. coli cultures remarkably increases during the early log and lag phases of bacterial growth, thereby enabling early detection. Technical replicates were cultivated for 3 days for reference diagnosis using current conventional bacteraemia detection. A reference MS screen of common microbes from other genera confirmed that the peaks at m/z 116 signal corresponded to indole were specifically present in E. coli. Our results indicated that volatile indole based on CDI-MS without the need for any sample pretreatment is highly suitable for the reliable and cost-efficient differentiation of E. coli, especially for bacteraemia in humans.
Collapse
Affiliation(s)
- Qiaoshi Zhong
- Department of clinical laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, P.R. China
| | - Feng Cheng
- Department of clinical laboratory, Jiangxi Chest (third people) Hospital, Nanchang, 330006, P.R. China
| | - Juchao Liang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, 330013, P.R. China
| | - Xiaozhong Wang
- Department of clinical laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, P.R. China
| | - Yanhui Chen
- Department of clinical laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, P.R. China
| | - Xueyao Fang
- Department of clinical laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, P.R. China
| | - Longhua Hu
- Department of clinical laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, P.R. China.
| | - Yaping Hang
- Department of clinical laboratory, Jiangxi Province Key Laboratory of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, P.R. China.
| |
Collapse
|
18
|
Grenga L, Pible O, Armengaud J. Pathogen proteotyping: A rapidly developing application of mass spectrometry to address clinical concerns. CLINICAL MASS SPECTROMETRY 2019; 14 Pt A:9-17. [DOI: 10.1016/j.clinms.2019.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/25/2019] [Accepted: 04/27/2019] [Indexed: 12/13/2022]
|
19
|
Identification of Pathogenic Bacteria from Public Libraries via Proteomics Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16060912. [PMID: 30875719 PMCID: PMC6466425 DOI: 10.3390/ijerph16060912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/25/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022]
Abstract
Hazardous organisms may thrive on surfaces that are often exposed to human contact, including children’s library books. In this study, swab samples were taken from 42 children’s books collected from four public libraries in Texas and California. Samples were then cultivated in brain–heart infusion (BHI) medium and then in Luria broth (LB) medium containing either ampicillin or kanamycin. All 42 samples (100%) were positive for bacterial growth in normal BHI medium. Furthermore, 35 samples (83.3%) and 20 samples (47.6%) in total were positive in LB medium containing ampicillin or kanamycin, respectively. Bacterial populations were then identified in samples using an Orbitrap Fusion™ Tribrid ™ mass spectrometer, a state-of-the-art proteomic analysis tool. Identified bacterial species grown in ampicillin included Bacillus, Acinetobacter, Pseudomonas, Staphylococcus, Enterobacter, Klebsiella, Serratia, Streptococcus, Escherichia, Salmonella, and Enterococcus. In contrast, identified bacteria grown in kanamycin included Staphylococcus, Streptococcus, Enterococcus, and Bacillus. The presences of pathogenic bacteria species were also confirmed. The results of this study warrant follow up studies to assess the potential health risks of identified pathogens. This study demonstrates the utility of proteomics in identifying environmental pathogenic bacteria for specific public health risk evaluations.
Collapse
|
20
|
Gal-Mor O. Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae. Clin Microbiol Rev 2019; 32:e00088-18. [PMID: 30487167 PMCID: PMC6302356 DOI: 10.1128/cmr.00088-18] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.
Collapse
Affiliation(s)
- Ohad Gal-Mor
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
21
|
Yang K, Kruse RL, Lin WV, Musher DM. Corynebacteria as a cause of pulmonary infection: a case series and literature review. Pneumonia (Nathan) 2018; 10:10. [PMID: 30324081 PMCID: PMC6173903 DOI: 10.1186/s41479-018-0054-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/18/2018] [Indexed: 11/23/2022] Open
Abstract
Background In most cases of community-acquired pneumonia (CAP), an etiologic agent is not determined; the most common report from the microbiological evaluation of sputum cites “normal respiratory flora.” Non-diphtheria Corynebacterium spp., a component of this flora, is commonly viewed as a contaminant, but it may be the cause of pneumonia and the frequency with which it causes CAP may be underestimated. Case presentations This report present 3 cases of CAP in which Corynebacterium spp. was clearly the predominant isolate; identification was confirmed by matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry. Two cases were caused by C. propinquum and one by C. striatum. Two patients had a tracheostomy and one was on hemodialysis. Patients who received an appropriate antibiotic responded well. Conclusion When identified as the predominant isolate in sputum from a patient with CAP, Corynebacterium spp. should be considered as a potential cause of the infection. In cases with patients who have compromised airway clearance or who are immunocompromised, microaspiration may be responsible. While some Corynebacterium spp. are suspectible to antibiotics usually prescribed for CAP, others are susceptible only to vancomycin or aminoglycosides. Vancomycin is thus the appropriate empiric antibiotic, pending speciation and susceptibility test results. The number of reported cases with result of antibiotic susceptibility testing, however, remains limited, and further investigation is needed. Non-diphtheria Corynebacterium spp. represent a noteworthy clinical cause of pneumonia. Identification by Gram stain and as a predominant organism on culture demands careful consideration for management.
Collapse
Affiliation(s)
| | | | - Weijie V Lin
- 1Baylor College of Medicine, Houston, TX 77030 USA
| | - Daniel M Musher
- 1Baylor College of Medicine, Houston, TX 77030 USA.,2Infectious Disease Section, Michael E. DeBakey Veterans Affairs Medical Center, 2002 Holcombe Boulevard, Houston, TX 77030 USA
| |
Collapse
|
22
|
13-Docosenamide release by bacteria in response to glucose during growth-fluorescein quenching and clinical application. Appl Microbiol Biotechnol 2018; 102:6673-6685. [PMID: 29860593 DOI: 10.1007/s00253-018-9127-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/10/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022]
Abstract
Our investigations on extracellular biochemical events to find readily and sensitively detectable/measurable molecular targets for developing easier, simpler, and quicker diagnostic methods and tools for bacterial pathogens led to the observation that bacteria grown in the presence of glucose produced a compound capable of quenching fluorescein. Under the experimental conditions, among various sugars, glucose was found to induce maximum amount of the quencher when Escherichia coli was grown in presence of 50 mM glucose in rarified LB. The release of quencher closely following bacterial growth significantly from fourth hour after moderate inoculation. This fluorescein-quencher was purified using TLC and HPLC and identified using GC-MS as 13-docosenamide or erucamide, originally known as plant lipid, is a neuroactive compound in human and animals. Fluorescence and UV-absorption spectral analysis showed that the compound formed stable adduct with fluorescein in the ground state. Commercial 13-docosonamide enabled quantitation of the compound produced in micromolar quantities during glucose utilization from the medium. Twenty-seven different commonly encountered bacteria, pathogens or otherwise, could produce the quencher. A simple microplate-based growth monitoring method was developed exploiting quenching as an easily and readily measurable signal, either using a reader or an imager. While 13-docosenamide release by bacteria may be relevant in host-bacteria interactions, especially when growing under conditions that provide glucose, the new approach with inexpensive reagents can provide a new antibiogram technique.
Collapse
|