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Kao YT, Calabrese S, Borst N, Lehnert M, Lai YK, Schlenker F, Juelg P, Zengerle R, Garstecki P, von Stetten F. Microfluidic One-Pot Digital Droplet FISH Using LNA/DNA Molecular Beacons for Bacteria Detection and Absolute Quantification. BIOSENSORS 2022; 12:bios12040237. [PMID: 35448297 PMCID: PMC9032532 DOI: 10.3390/bios12040237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 02/06/2023]
Abstract
We demonstrate detection and quantification of bacterial load with a novel microfluidic one-pot wash-free fluorescence in situ hybridization (FISH) assay in droplets. The method offers minimal manual workload by only requiring mixing of the sample with reagents and loading it into a microfluidic cartridge. By centrifugal microfluidic step emulsification, our method partitioned the sample into 210 pL (73 µm in diameter) droplets for bacterial encapsulation followed by in situ permeabilization, hybridization, and signal detection. Employing locked nucleic acid (LNA)/DNA molecular beacons (LNA/DNA MBs) and NaCl-urea based hybridization buffer, the assay was characterized with Escherichia coli, Klebsiella pneumonia, and Proteus mirabilis. The assay performed with single-cell sensitivity, a 4-log dynamic range from a lower limit of quantification (LLOQ) at ~3 × 103 bacteria/mL to an upper limit of quantification (ULOQ) at ~3 × 107 bacteria/mL, anda linearity R2 = 0.976. The total time-to-results for detection and quantification was around 1.5 hours.
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Affiliation(s)
- Yu-Ting Kao
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Silvia Calabrese
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Nadine Borst
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Michael Lehnert
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Yu-Kai Lai
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Franziska Schlenker
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Peter Juelg
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Roland Zengerle
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
| | - Piotr Garstecki
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland;
| | - Felix von Stetten
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (Y.-T.K.); (N.B.); (Y.-K.L.); (R.Z.)
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; (S.C.); (M.L.); (F.S.); (P.J.)
- Correspondence: ; Tel.: +49-761-203-73243
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Peng Y, Zhang Z, Tu H, Li X. Automatic Segmentation of Novel Coronavirus Pneumonia Lesions in CT Images Utilizing Deep-Supervised Ensemble Learning Network. Front Med (Lausanne) 2022; 8:755309. [PMID: 35047520 PMCID: PMC8761973 DOI: 10.3389/fmed.2021.755309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The novel coronavirus disease 2019 (COVID-19) has been spread widely in the world, causing a huge threat to the living environment of people. Objective: Under CT imaging, the structure features of COVID-19 lesions are complicated and varied greatly in different cases. To accurately locate COVID-19 lesions and assist doctors to make the best diagnosis and treatment plan, a deep-supervised ensemble learning network is presented for COVID-19 lesion segmentation in CT images. Methods: Since a large number of COVID-19 CT images and the corresponding lesion annotations are difficult to obtain, a transfer learning strategy is employed to make up for the shortcoming and alleviate the overfitting problem. Based on the reality that traditional single deep learning framework is difficult to extract complicated and varied COVID-19 lesion features effectively that may cause some lesions to be undetected. To overcome the problem, a deep-supervised ensemble learning network is presented to combine with local and global features for COVID-19 lesion segmentation. Results: The performance of the proposed method was validated in experiments with a publicly available dataset. Compared with manual annotations, the proposed method acquired a high intersection over union (IoU) of 0.7279 and a low Hausdorff distance (H) of 92.4604. Conclusion: A deep-supervised ensemble learning network was presented for coronavirus pneumonia lesion segmentation in CT images. The effectiveness of the proposed method was verified by visual inspection and quantitative evaluation. Experimental results indicated that the proposed method has a good performance in COVID-19 lesion segmentation.
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Affiliation(s)
- Yuanyuan Peng
- School of Electrical and Automation Engineering, East China Jiaotong University, Nanchang, China
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
| | - Zixu Zhang
- School of Electrical and Automation Engineering, East China Jiaotong University, Nanchang, China
| | - Hongbin Tu
- School of Electrical and Automation Engineering, East China Jiaotong University, Nanchang, China
- Technique Center, Hunan Great Wall Technology Information Co. Ltd., Changsha, China
| | - Xiong Li
- School of Software, East China Jiaotong University, Nanchang, China
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3
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Hartley MG, Norville IH, Richards MI, Barnes KB, Bewley KR, Vipond J, Rayner E, Vente A, Armstrong SJ, Harding SV. Finafloxacin, a Novel Fluoroquinolone, Reduces the Clinical Signs of Infection and Pathology in a Mouse Model of Q Fever. Front Microbiol 2021; 12:760698. [PMID: 34917048 PMCID: PMC8670379 DOI: 10.3389/fmicb.2021.760698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/26/2021] [Indexed: 11/21/2022] Open
Abstract
Finafloxacin is a novel fluoroquinolone with optimal antibacterial activity in low pH environments, therefore offering a therapeutic advantage over some traditional antibiotics, in treating bacterial infections associated with acidic foci. Coxiella burnetii, the causative agent of Q fever, is a bacterium which resides and replicates in acidic intracellular parasitic vacuoles. The efficacy of finafloxacin was evaluated in vivo using the A/J mouse model of inhalational Q fever and was compared to doxycycline, the standard treatment for this infection and ciprofloxacin, a comparator fluoroquinolone. Finafloxacin reduced the severity of the clinical signs of infection and weight loss associated with Q fever, but did not reduce the level of bacterial colonization in tissues compared to doxycycline or ciprofloxacin. However, histopathological analysis suggested that treatment with finafloxacin reduced tissue damage associated with C. burnetii infection. In addition, we report for the first time, the use of viable counts on axenic media to evaluate antibiotic efficacy in vivo.
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Affiliation(s)
- M Gill Hartley
- CBR Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, United Kingdom
| | - Isobel H Norville
- CBR Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mark I Richards
- CBR Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, United Kingdom
| | - Kay B Barnes
- CBR Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, United Kingdom
| | - Kevin R Bewley
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Julia Vipond
- Public Health England, Porton Down, Salisbury, United Kingdom
| | - Emma Rayner
- Public Health England, Porton Down, Salisbury, United Kingdom
| | | | - Stuart J Armstrong
- CBR Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, United Kingdom
| | - Sarah V Harding
- CBR Division, Defence Science and Technology Laboratory (Dstl), Porton Down, Salisbury, United Kingdom
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4
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Evaluation of the Efficacy of Doxycycline, Ciprofloxacin, Levofloxacin and Co-trimoxazole using in vitro and in vivo models of Q fever. Antimicrob Agents Chemother 2021; 65:e0067321. [PMID: 34370577 PMCID: PMC8522727 DOI: 10.1128/aac.00673-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Q fever, caused by the intracellular pathogen Coxiella burnetii, is traditionally treated using tetracycline antibiotics, such as doxycycline. Doxycycline is often poorly tolerated and antibiotic resistant strains have been isolated. In this study, we have evaluated a panel of antibiotics (doxycycline, ciprofloxacin, levofloxacin, and, co-trimoxazole) against C. burnetii using in vitro methods (determination of MIC using liquid and solid media; efficacy assessment in a THP cell infection model) and in vivo methods (wax moth larvae and mouse models of infection). In addition, the schedule for antibiotic treatment has been evaluated, with therapy initiated at 24 h pre or post challenge. Both doxycycline and levofloxacin limited overt clinical signs during treatment in the AJ mouse model of aerosol infection, but further studies are required to investigate the possibility of disease relapse or incomplete bacterial clearance after the antibiotics are stopped. Levofloxacin was well tolerated and therefore warrants further investigation as an alternative to the current recommended treatment with doxycycline.
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Abdelhamid MK, Rychlik I, Hess C, Hatfaludi T, Crhanova M, Karasova D, Lagler J, Liebhart D, Hess M, Paudel S. Typhlitis induced by Histomonas meleagridis affects relative but not the absolute Escherichia coli counts and invasion in the gut in turkeys. Vet Res 2021; 52:92. [PMID: 34158121 PMCID: PMC8220719 DOI: 10.1186/s13567-021-00962-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022] Open
Abstract
Unlike in chickens, dynamics of the gut microbiome in turkeys is limitedly understood and no data were yet published in context of pathological changes following experimental infection. Thus, the impact of Histomonas meleagridis-associated inflammatory changes in the caecal microbiome, especially the Escherichia coli population and their caecal wall invasion in turkeys was investigated. Birds experimentally inoculated with attenuated and/or virulent H. meleagridis and non-inoculated negative controls were divided based on the severity of macroscopic caecal lesions. The high throughput amplicon sequencing of 16SrRNA showed that the species richness and diversity of microbial community significantly decreased in severely affected caeca. The relative abundances of operational taxonomic units belonging to Anaerotignum lactatifermentans, E. coli, and Faecalibacterium prausnitzii were higher and paralleled with a decreased abundances of those belonging to Alistipes putredinis, Streptococcusalactolyticus, Lactobacillus salivarius and Lactobacillus reuteri in birds with the highest lesion scores. Although the relative abundance of E. coli was higher, the absolute count was not affected by the severity of pathological lesions. Immunohistochemistry showed that E. coli was only present in the luminal content of caecum and did not penetrate even severely inflamed and necrotized caecal wall. Overall, it was demonstrated that the fundamental shift in caecal microbiota of turkeys infected with H. meleagridis was attributed to the pathology induced by the parasite, which only led to relative but not absolute changes in E. coli population. Furthermore, E. coli cells did not show tendency to penetrate the caecal tissue even when the intestinal mucosal barriers were severely compromised.
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Affiliation(s)
- Mohamed Kamal Abdelhamid
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Ivan Rychlik
- Department of Immunology, Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Claudia Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Tamas Hatfaludi
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Christian Doppler Laboratory for Innovative Poultry Vaccines (IPOV), University of Veterinary Medicine, Vienna, Austria
| | - Magdalena Crhanova
- Department of Immunology, Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Daniela Karasova
- Department of Immunology, Veterinary Research Institute, 62100, Brno, Czech Republic
| | - Julia Lagler
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Section of Immunology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Dieter Liebhart
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Michael Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.,Christian Doppler Laboratory for Innovative Poultry Vaccines (IPOV), University of Veterinary Medicine, Vienna, Austria
| | - Surya Paudel
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.
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Nelson M, Salguero FJ, Hunter L, Atkins TP. A Novel Marmoset ( Callithrix jacchus) Model of Human Inhalational Q Fever. Front Cell Infect Microbiol 2021; 10:621635. [PMID: 33585288 PMCID: PMC7876459 DOI: 10.3389/fcimb.2020.621635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
Common marmosets (Callithrix jacchus) were shown to be susceptible to inhalational infection with Coxiella burnetii, in a dose-dependent manner, producing a disease similar to human Q fever, characterized by a resolving febrile response. Illness was also associated with weight loss, liver enzyme dysfunction, characteristic cellular activation, circulating INF-γ and bacteraemia. Viable C. burnetii was recovered from various tissues during disease and from 75% of the animal's lungs on 28 days post challenge, when there were no overt clinical features of disease but there was histological evidence of macrophage and lymphocyte infiltration into the lung resulting in granulomatous alveolitis. Taken together, these features of disease progression, physiology and bacterial spread appear to be consistent with human disease and therefore the common marmoset can be considered as a suitable model for studies on the pathogenesis or the development of medical counter measures of inhalational Q fever.
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Affiliation(s)
- Michelle Nelson
- CBR Division, Defence Science and Technology Laboratory (Dstl), Salisbury, United Kingdom
| | | | - Laura Hunter
- Public Health England, Salisbury, United Kingdom
| | - Timothy P Atkins
- CBR Division, Defence Science and Technology Laboratory (Dstl), Salisbury, United Kingdom
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