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Bohm K, Taylor W, Gyawali P, Pattis I, Gutiérrez Ginés MJ. Black soldier fly-based bioconversion of biosolids: Microbial community dynamics and fate of antibiotic resistance genes. Sci Total Environ 2024; 930:172823. [PMID: 38679091 DOI: 10.1016/j.scitotenv.2024.172823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/07/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Biosolids as by-products of wastewater treatment can contain a large spectrum of pathogens and antibiotic resistance genes (ARGs). Insect-based bioconversion using black soldier fly larvae (BSFL) is an emerging technology that has shown to reduce significant amounts of biosolids quickly and produce larvae biomass containing low heavy metal concentrations. However, to the best of our knowledge, this is the first study investigating the transfer of pathogens and ARGs from biosolids into the process' end-products, BSFL and frass. We hypothesized that BSF-based bioconversion can decrease the abundance of pathogenic bacteria and ARGs in biosolids. In this study, we performed BSFL feeding trials with biosolids blended or not blended with wheat bran, and wheat bran alone as a low bioburden diet (control). We conducted 16S rRNA amplicon sequencing to monitor changes of the BSFL-associated microbial community and the fate of biosolids-associated pathogens. A diverse set of ARGs (ermB, intl1, sul1, tetA, tetQ, tetW, and blaCTX-M-32) were quantified by qPCR and were linked to changes in substrate- and BSFL-associated microbiomes. BSF-based bioconversion of biosolids-containing substrates led to a significant reduction of the microbial diversity, the abundance of several pathogenic bacteria and the investigated ARGs (< 99 %). Feeding with a high bioburden biosolid diet resulted in a higher microbial diversity, and the accumulation of pathogenic bacteria and ARGs in the BSFL. Results of this study demonstrated that BSF-based bioconversion can be a suitable waste management technology to (1) reduce significant amounts of biosolids and (2) reduce the presence of pathogens and ARGs. However, the resulting larvae biomass would need to undergo further post-treatment to reduce the pathogenic load to allow them as animal feed.
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Affiliation(s)
- Kristin Bohm
- Institute of Environmental Science and Research Ltd., Porirua 5022, New Zealand
| | - Will Taylor
- Institute of Environmental Science and Research Ltd., Christchurch 8041, New Zealand
| | - Pradip Gyawali
- Food Standards Australia New Zealand, Wellington 6011, New Zealand
| | - Isabelle Pattis
- Institute of Environmental Science and Research Ltd., Christchurch 8041, New Zealand
| | - María J Gutiérrez Ginés
- Institute of Environmental Science and Research Ltd., Christchurch 8041, New Zealand; School of Earth and Environment, University of Canterbury, Christchurch 8041, New Zealand.
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Hill J, Messina J, Jeremic A, Zderic V. Analyzing Gene Expression After Administration of Low-Intensity Therapeutic Ultrasound in Human Islet Cells. J Ultrasound Med 2024; 43:1131-1141. [PMID: 38414281 DOI: 10.1002/jum.16441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/01/2024] [Accepted: 02/17/2024] [Indexed: 02/29/2024]
Abstract
OBJECTIVES Diabetes mellitus is a complex heterogenous metabolic disease that significantly affects the world population. Although many treatments exist, including medications such as metformin, sulfonylureas, and glucagon-like peptide-1 (GLP) receptor agonist, there is growing interest in finding alternative methods to noninvasively treat this disease. It has been previously shown that low-intensity ultrasound stimulation of pancreatic β-cells in mice can elicit insulin secretion as a potential treatment for this disease. This is desirable as therapeutic ultrasound has the ability to induce bioeffects while selectively focusing deep within tissues, allowing for modulation of hormone secretion in the pancreas to mitigate insufficient levels of insulin. METHODS Exactly 800 kHz ultrasound with intensity 0.5 W/cm2 was administered 5 minutes continuously, that is, 100% duty cycle, to donor pancreatic human islets, followed by 1 hour incubation and RT-qPCR to assess the effect of ultrasound stimulation on gene expression. The genes were insulin (INS), glucagon (Glu), amylin (Amy), and binding immunoglobulin protein (BiP). Nine donor pancreatic human islets were used to assess insulin and glucagon secretion, while eight samples were used for amylin and BiP. Fold change (FC) was calculated to analyze the effect of ultrasound stimulation on the gene expression of the donor islet cells. High-glucose and thapsigargin-treated islets were utilized as positive controls. Cell viability testing was done using a Trypan Blue Exclusion Test. RESULTS Ultrasound stimulation did not cause a statistically significant upregulation in any of the tested genes (INS FC = 1.15, P-value = .5692; Glu FC = 1.60, P-value = .2231; Amy FC, P-value = .2863; BiP FC = 2.68, P-value = .3907). CONCLUSIONS The results of this study show that the proposed ultrasound treatment parameters do not appear to significantly affect gene expression of any gene tested.
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Affiliation(s)
- John Hill
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | - James Messina
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
| | - Aleksandar Jeremic
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Vesna Zderic
- Department of Biomedical Engineering, The George Washington University, Washington, DC, USA
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Saleem F, Li E, Tran KL, Rudra B, Edge TA, Schellhorn HE, Gupta RS. Utilizing novel Escherichia coli-specific conserved signature proteins for enhanced monitoring of recreational water quality. Microbiologyopen 2024; 13:e1410. [PMID: 38682792 PMCID: PMC11057252 DOI: 10.1002/mbo3.1410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/19/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Escherichia coli serves as a proxy indicator of fecal contamination in aquatic ecosystems. However, its identification using traditional culturing methods can take up to 24 h. The application of DNA markers, such as conserved signature proteins (CSPs) genes (unique to all species/strains of a specific taxon), can form the foundation for novel polymerase chain reaction (PCR) tests that unambiguously identify and detect targeted bacterial taxa of interest. This paper reports the identification of three new highly-conserved CSPs (genes), namely YahL, YdjO, and YjfZ, which are exclusive to E. coli/Shigella. Using PCR primers based on highly conserved regions within these CSPs, we have developed quantitative PCR (qPCR) assays for the evaluation of E. coli/Shigella species in water ecosystems. Both in-silico and experimental PCR testing confirmed the absence of sequence match when tested against other bacteria, thereby confirming 100% specificity of the tested CSPs for E. coli/Shigella. The qPCR assays for each of the three CSPs provided reliable quantification for all tested enterohaemorrhagic and environmental E. coli strains, a requirement for water testing. For recreational water samples, CSP-based quantification showed a high correlation (r > 7, p < 0.01) with conventional viable E. coli enumeration. This indicates that novel CSP-based qPCR assays for E. coli can serve as robust tools for monitoring water ecosystems and other critical areas, including food monitoring.
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Affiliation(s)
- Faizan Saleem
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Enze Li
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Kevin L. Tran
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Bashudev Rudra
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonOntarioCanada
| | - Thomas A. Edge
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | | | - Radhey S. Gupta
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonOntarioCanada
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Modlin IM, Kidd M, Drozdov IA, Boegemann M, Bodei L, Kunikowska J, Malczewska A, Bernemann C, Koduru SV, Rahbar K. Development of a multigenomic liquid biopsy (PROSTest) for prostate cancer in whole blood. Prostate 2024; 84:850-865. [PMID: 38571290 DOI: 10.1002/pros.24704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/04/2024] [Accepted: 03/25/2024] [Indexed: 04/05/2024]
Abstract
INTRODUCTION We describe the development of a molecular assay from publicly available tumor tissue mRNA databases using machine learning and present preliminary evidence of functionality as a diagnostic and monitoring tool for prostate cancer (PCa) in whole blood. MATERIALS AND METHODS We assessed 1055 PCas (public microarray data sets) to identify putative mRNA biomarkers. Specificity was confirmed against 32 different solid and hematological cancers from The Cancer Genome Atlas (n = 10,990). This defined a 27-gene panel which was validated by qPCR in 50 histologically confirmed PCa surgical specimens and matched blood. An ensemble classifier (Random Forest, Support Vector Machines, XGBoost) was trained in age-matched PCas (n = 294), and in 72 controls and 64 BPH. Classifier performance was validated in two independent sets (n = 263 PCas; n = 99 controls). We assessed the panel as a postoperative disease monitor in a radical prostatectomy cohort (RPC: n = 47). RESULTS A PCa-specific 27-gene panel was identified. Matched blood and tumor gene expression levels were concordant (r = 0.72, p < 0.0001). The ensemble classifier ("PROSTest") was scaled 0%-100% and the industry-standard operating point of ≥50% used to define a PCa. Using this, the PROSTest exhibited an 85% sensitivity and 95% specificity for PCa versus controls. In two independent sets, the metrics were 92%-95% sensitivity and 100% specificity. In the RPCs (n = 47), PROSTest scores decreased from 72% ± 7% to 33% ± 16% (p < 0.0001, Mann-Whitney test). PROSTest was 26% ± 8% in 37 with normal postoperative PSA levels (<0.1 ng/mL). In 10 with elevated postoperative PSA, PROSTest was 60% ± 4%. CONCLUSION A 27-gene whole blood signature for PCa is concordant with tissue mRNA levels. Measuring blood expression provides a minimally invasive genomic tool that may facilitate prostate cancer management.
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Affiliation(s)
- Irvin M Modlin
- Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mark Kidd
- Wren Laboratories LLC, Branford, Connecticut, USA
| | | | - Martin Boegemann
- Department of Urology, Münster University Hospital, Münster, Germany
| | - Lisa Bodei
- Department of Radiology, Molecular Imaging and Therapy Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jolanta Kunikowska
- Department of Nuclear Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Malczewska
- Department of Endocrinology, Medical University of Silesia, Katowice, Poland
| | | | | | - Kambiz Rahbar
- Department of Nuclear Medicine, Münster University Hospital, Münster, Germany
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Edouard S, Boschi C, Colson P, Million M, Fournier PE, La Scola B, Fenollar F. Incidental diagnosis of mpox virus infection in patients undergoing sexually transmitted infection screening-findings from a study in France. Int J Infect Dis 2024; 143:107009. [PMID: 38521449 DOI: 10.1016/j.ijid.2024.107009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/06/2024] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
OBJECTIVES This study aimed to investigate the prevalence of mpox virus (MPXV) infections in the general population consulting for routine sexually transmitted infections (STIs) in our Marseille public hospital. In fact, the recent worldwide MPXV outbreak mainly impacted men who have sex with men and the prevalence of MPXV infections in the general population remains poorly defined. METHODS All samples addressed routinely to our microbiological laboratory for STIs between July 1 and October 15, 2022 were screened with MPXV-specific quantitative polymerase chain reaction. RESULTS A total of 2688 samples from 1896 patients suspected of having STIs were tested and eight (0.4%) patients were incidentally diagnosed with MPXV infection, including six men and two women. MPXV was detected in rectal swabs (n = 2), urine (n = 2), vaginal swabs (n = 2), a urethral swab (n = 1), and a skin swab (n = 1). CONCLUSIONS This study suggests that some MPXV infections are likely to be underdiagnosed because of their non-specific clinical presentation and/or insufficient clinical knowledge of the disease. Our data showed that systematic screening was particularly useful for detecting MPXV in patients without classic lesions or cases of asymptomatic carriage in patients reporting recent high-risk exposure and in patients presenting no obvious risk factor.
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Affiliation(s)
- Sophie Edouard
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, AP-HM, SSA, RITMES, Marseille, France
| | - Céline Boschi
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, AP-HM, MEPHI, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, AP-HM, MEPHI, Marseille, France
| | - Matthieu Million
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, AP-HM, MEPHI, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, AP-HM, SSA, RITMES, Marseille, France
| | - Bernard La Scola
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille University, AP-HM, SSA, RITMES, Marseille, France.
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Nambiar A, Pan C, Rana V, Cheraghchi M, Ribeiro J, Maslov S, Milenkovic O. Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads. BMC Bioinformatics 2024; 25:195. [PMID: 38760692 DOI: 10.1186/s12859-024-05798-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 04/26/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Pathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial challenges to healthcare systems worldwide. Efficient and timely testing plays a critical role in disease control and transmission prevention. Group testing is a well-established method for reducing the number of tests needed to screen large populations when the disease prevalence is low. However, it does not fully utilize the quantitative information provided by qPCR methods, nor is it able to accommodate a wide range of pathogen loads. RESULTS To address these issues, we introduce a novel adaptive semi-quantitative group testing (SQGT) scheme to efficiently screen populations via two-stage qPCR testing. The SQGT method quantizes cycle threshold (Ct) values into multiple bins, leveraging the information from the first stage of screening to improve the detection sensitivity. Dynamic Ct threshold adjustments mitigate dilution effects and enhance test accuracy. Comparisons with traditional binary outcome GT methods show that SQGT reduces the number of tests by 24% on the only complete real-world qPCR group testing dataset from Israel, while maintaining a negligible false negative rate. CONCLUSION In conclusion, our adaptive SQGT approach, utilizing qPCR data and dynamic threshold adjustments, offers a promising solution for efficient population screening. With a reduction in the number of tests and minimal false negatives, SQGT holds potential to enhance disease control and testing strategies on a global scale.
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Affiliation(s)
- Ananthan Nambiar
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Chao Pan
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Vishal Rana
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Mahdi Cheraghchi
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - João Ribeiro
- NOVA LINCS and NOVA School of Science and Technology, Caparica, Portugal
| | - Sergei Maslov
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Center for Artificial Intelligence and Modeling, Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Sivaganesan M, Willis JR, Diedrich A, Shanks OC. A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements. Water Res 2024; 255:121482. [PMID: 38598887 DOI: 10.1016/j.watres.2024.121482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Adam Diedrich
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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Perez-Bou L, Gonzalez-Martinez A, Cabrera JJ, Juarez-Jimenez B, Rodelas B, Gonzalez-Lopez J, Correa-Galeote D. Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR. Microb Ecol 2024; 87:71. [PMID: 38748252 PMCID: PMC11096201 DOI: 10.1007/s00248-024-02385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R2 > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.
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Affiliation(s)
- Lizandra Perez-Bou
- Environmental Microbiology Group, Department of Microbiology and Virology, Faculty of Biology, University of Havana, Havana, Cuba
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
| | - Alejandro Gonzalez-Martinez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Juan J Cabrera
- Nitrogen Metabolism Group, Zaidín Experimental Station, Spanish National Research Council, EEZ-CSIC, Granada, Spain
| | - Belen Juarez-Jimenez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Belen Rodelas
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David Correa-Galeote
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain.
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.
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Mejia EM, Hizon NA, Dueck CE, Lidder R, Daigle J, Wonitowy Q, Medina NG, Mohammed UP, Cox GW, Safronetz D, Hagan M, Strong J, Nichani A, Mulvey MR, Mangat CS. Detection of mpox virus in wastewater provides forewarning of clinical cases in Canadian cities. Sci Total Environ 2024; 933:173108. [PMID: 38729376 DOI: 10.1016/j.scitotenv.2024.173108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Wastewater-based surveillance (WBS) has shown to be an effective tool in monitoring the spread of SARS-CoV-2 and has helped guide public health actions. Consequently, WBS has expanded to now include the monitoring of mpox virus (MPXV) to contribute to its mitigation efforts. In this study, we demonstrate a unique sample processing and a molecular diagnostic strategy for MPXV detection that can inform on the epidemiological situation of mpox outbreaks through WBS. We conducted WBS for MPXV in 22 Canadian wastewater treatment plants (WWTPs) for 14 weeks. Three MPXV qPCR assays were assessed in this study for the detection of MPXV which include the G2R assays (G2R_WA and G2R_G) developed by the Centers for Disease Control and Prevention (CDC) in 2010, and an in-house-developed assay that we have termed G2R_NML. The G2R_NML assay was designed using reference genomes from the 2022 MPXV outbreak and provides a larger qPCR amplicon size to facilitate Sanger sequencing. Results show that all three assays have similar limits of detection and are able to detect the presence of MPXV in wastewater. The G2R_NML assay produced a significantly greater number of Sanger sequence-confirmed MPXV results compared to the CDC G2R assays. Detection of MPXV was possible where provincial surveillance indicated overall low caseloads, and in some sites forewarning of up to several weeks was observed. Overall, this study proposes that WBS of MPXV provides additional information to help fill knowledge gaps in clinical case-surveillance and is potentially an essential component to the management of mpox.
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Affiliation(s)
- Edgard M Mejia
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - Nikho A Hizon
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Codey E Dueck
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ravinder Lidder
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jade Daigle
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Quinn Wonitowy
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Nestor G Medina
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Umar P Mohammed
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Graham W Cox
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - David Safronetz
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mable Hagan
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Jim Strong
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anil Nichani
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michael R Mulvey
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Antimicrobial Resistance Nosocomial Infections, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chand S Mangat
- Wastewater Surveillance Unit, Bacterial Pathogens, AMR, and Wastewater, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Antimicrobial Resistance Nosocomial Infections, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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Dias AP, Orsel K, De Buck J. Quantifying and mapping digital dermatitis-associated bacteria in lesion and nonlesion body sites and dairy farm environment. J Dairy Sci 2024; 107:3252-3268. [PMID: 38135044 DOI: 10.3168/jds.2023-24160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023]
Abstract
The source of infection of digital dermatitis (DD), an infectious lameness condition, is still uncertain. In this cross-sectional study, we aimed to identify potential reservoirs of DD bacteria in dairy cattle body sites with different stages of the disease and farm environments. We collected skin swabs from 85 dairy cows from 5 herds, 3 with and 2 without DD, from foot, hock, and udder cleft skin (with lesions or not), saliva, urine, and feces. We also obtained environmental samples. Real-time quantitative PCR targeted Treponema phagedenis, Treponema medium, Treponema pedis, Porphyromonas levii, Bacteroides pyogenes, Fusobacterium necrophorum, and Fusobacterium mortiferum. Digital dermatitis-associated Treponema spp. were exclusively detected in DD-affected herds in DD-foot and other skin lesions, healthy skin, saliva, and environmental samples. In contrast, the non-Treponema spp. were found in samples from both DD-negative and affected herds. As expected, DD lesions had higher bacterial loads than healthy skin. Interestingly, similar counts were observed in udder cleft lesions, indicating a potential opportunistic behavior on compromised skin. None of the targeted species were detected in fecal samples, but P. levii, B. pyogenes, and F. necrophorum were detected in urine. All 7 species were detected in saliva, although in low quantities. No associations were observed between the presence of each bacterial species in DD lesions and urine; however, there was an association between the presence of DD-Treponema spp. in lesions and saliva, hock, and udder skin. Feces and urine do not seem to be a DD bacteria primary source, but saliva and other skin lesions may play a role. Longitudinal studies would improve our understanding of DD-associated bacteria's transient or persistent presence in these sites. Investigating the sources of DD-associated bacteria will guide future interventions to minimize bacterial shedding and transmission, ultimately more effectively reducing bacterial load, transmission, and sources of infection in dairy herds.
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Affiliation(s)
- A P Dias
- Faculty of Veterinary Medicine, University of Calgary, AB, T2N 4N1, Canada
| | - K Orsel
- Faculty of Veterinary Medicine, University of Calgary, AB, T2N 4N1, Canada
| | - J De Buck
- Faculty of Veterinary Medicine, University of Calgary, AB, T2N 4N1, Canada.
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11
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Hodgeman R, Liu Y, Rochfort S, Rodoni B. Development and evaluation of genomics informed real-time PCR assays for the detection and strain typing of Mycobacterium avium subsp. paratuberculosis. J Appl Microbiol 2024; 135:lxae107. [PMID: 38684472 DOI: 10.1093/jambio/lxae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
AIMS This study aimed to identify specific genomic targets for the detection and strain typing of Map and analyse their sensitivity and specificity, and detect Map directly from faeces. METHODS AND RESULTS A comparative genomics approach was used to identify specific genomic targets for the detection and strain typing of Map. A Map specific qPCR using the primer pair 7132 that targets a DNA segregation ATPase protein was able to detect all strains of Map and is more sensitive than the current Johne's disease PCR assays with a sensitivity of 0.0002 fg µl-1. A strain specific qPCR using the Atsa primer pair that targets the arylsulfase gene was able to differentiate between Type S and Type C strains of Map and was more sensitive than the IS1311 PCR and REA with a sensitivity of 40 fg µl-1 and was specific for Type S Map. Both assays successfully detected Map directly from faeces. CONCLUSION This study developed and validated two genomics informed qPCR assays, 7132B Map and Atsa Type S and found both assays to be highly specific and sensitive for the detection of Map from culture and directly from faeces. This is the first time that a probe-based qPCR has been designed and developed for Map strain typing, which will greatly improve the response time during outbreak investigations.
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Affiliation(s)
- Rachel Hodgeman
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Yuhong Liu
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
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12
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Wilcox TM, Kronenberger JA, Young MK, Mason DH, Franklin TW, Schwartz MK. The unknown unknown: A framework for assessing environmental DNA assay specificity against unsampled taxa. Mol Ecol Resour 2024; 24:e13932. [PMID: 38263813 DOI: 10.1111/1755-0998.13932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
Taxon-specific quantitative PCR (qPCR) assays are commonly used for environmental DNA sampling-based inference of animal presence. These assays require thorough validation to ensure that amplification truly indicates detection of the target taxon, but a thorough validation is difficult when there are potentially many non-target taxa, some of which may have incomplete taxonomies. Here, we use a previously published, quantitative model of cross-amplification risk to describe a framework for assessing qPCR assay specificity when there is missing information and it is not possible to assess assay specificity for each individual non-target confamilial. In this framework, we predict assay specificity against unsampled taxa (non-target taxa without sequence data available) using the sequence information that is available for other confamilials. We demonstrate this framework using four case study assays for: (1) An endemic, freshwater arthropod (meltwater stonefly; Lednia tumana), (2) a globally distributed, marine ascidian (Didemnum perlucidum), (3) a continentally distributed freshwater crustacean (virile crayfish; Faxonius virilis, deanae and nais species complex) and (4) a globally distributed freshwater teleost (common carp; Cyprinus carpio and its close relative C. rubrofuscus). We tested the robustness of our approach to missing information by simulating application of our framework for all possible subsamples of 20-all non-target taxa. Our results suggest that the modelling framework results in estimates which are largely concordant with observed levels of cross-amplification risk using all available sequence data, even when there are high levels of data missingness. We explore potential limitations and extensions of this approach for assessing assay specificity and provide users with an R Markdown template for generating reproducible reports to support their own assay validation efforts.
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Affiliation(s)
- Taylor M Wilcox
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - John A Kronenberger
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Young
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Daniel H Mason
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Thomas W Franklin
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
| | - Michael K Schwartz
- USDA Forest Service, Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Forestry Sciences Laboratory, Missoula, Montana, USA
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13
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Dias AP, Aguilar XF, De Buck J, Kutz S, Arrazuria R. Digital dermatitis-associated Treponema species detection and quantification in migratory tundra caribou (Rangifer tarandus). Res Vet Sci 2024; 171:105210. [PMID: 38460203 DOI: 10.1016/j.rvsc.2024.105210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/27/2024] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
Treponema spp. are associated with infectious lameness in livestock and wild ruminants. While extensive research has been conducted on cattle, investigations in wild ruminants are scarce. Hoof disease is common in caribou populations (Rangifer tarandus), but investigations are limited due to the remoteness of the Arctic. Our study aimed to assess the presence of Treponema spp. associated with bovine digital dermatitis in caribou. DNA was extracted from coronary band tissues from forty-eight caribou without visible hoof lesions and analyzed using two PCR methods (qPCR and nPCR). Treponema spp. were detected in low copy numbers/mg of tissue (3.6 to 6.6 × 101). T. phagedenis was the most prevalent and abundant species in 58% of samples by qPCR, followed by T. medium (44%), and T. pedis (10%). The qPCR and nPCR agreement ranged between 65% and 75% (Cohen's kappa 0.22-0.51). Sanger sequencing of thirteen nPCR products confirmed that treponemes in caribou are remarkably similar to those found in domestic ruminants and wild elk. Our study highlights the colonization of treponemes in healthy hooves of a wild ruminant in the Arctic, where there is no presence of livestock, and expands knowledge on the host range and distribution of treponemes. These findings also emphasize the need for further research into the multifactorial nature of treponema-associated hoof diseases and the putative role of treponemes in infectious lameness affecting caribou.
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Affiliation(s)
- Angelica P Dias
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Xavier F Aguilar
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada; Wildlife Conservation Medicine Research Group (WildCoM), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona, Bellaterra, Spain.
| | - Jeroen De Buck
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Susan Kutz
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Rakel Arrazuria
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4Z6, Canada.
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14
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van der Pouw Kraan D, Graham CT, Kavanagh F, Mirimin L. Development and validation of a DNA-based multi-species biomonitoring toolkit using a high-throughput qPCR platform: A case study of Irish shellfish species. Mol Ecol Resour 2024; 24:e13945. [PMID: 38429942 DOI: 10.1111/1755-0998.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Biomonitoring of marine life has been enhanced in recent years by the integration of innovative DNA-based approaches, which offer advantages over more laborious techniques (e.g. microscopy). However, trade-offs between throughput, sensitivity and quantitative measurements must be made when choosing between the prevailing molecular methodologies (i.e. metabarcoding or qPCR/dPCR). Thus, the aim of the present study was to demonstrate the utility of a microfluidic-enabled high-throughput quantitative PCR platform (HTqPCR) for the rapid and cost-effective development and validation of a DNA-based multi-species biomonitoring toolkit, using larvae of 23 commercially targeted bivalve and crustacean species as a case study. The workflow was divided into three main phases: definition of (off-) target taxa and establishment of reference databases (PHASE 1); selection/development and assessment of molecular assays (PHASE 2); and protocol optimization and field validation (PHASE 3). 42 assays were eventually chosen and validated. Genetic signal not only showed good correlation with direct visual counts by microscopy but also showed the ability to provide quantitative data at the highest taxonomic resolution (species level) in a time- and cost-effective fashion. This study developed a biomonitoring toolkit, demonstrating the considerable advantages of this state-of-the-art technology in boosting the developmental testing and application of panels of molecular assays for the monitoring and management of natural resources. Once developed, this approach provides a cost and time-effective alternative compared to other multi-species approaches (e.g. metabarcoding). In addition, it is transferable to a wide range of species and will aid future monitoring programmes.
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Affiliation(s)
- Dennis van der Pouw Kraan
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Conor T Graham
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Fiona Kavanagh
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
| | - Luca Mirimin
- Marine and Freshwater Research Centre, Department of Natural Resources and the Environment, Atlantic Technological University (ATU), Galway, Ireland
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15
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Guo S, Wan Q, Xu M, Chen M, Chen Z. Transcriptome analysis of host anti-Aeromonas hydrophila infection revealed the pathogenicity of A. hydrophila to American eels (Anguilla rostrata). Fish & Shellfish Immunology 2024; 148:109504. [PMID: 38508539 DOI: 10.1016/j.fsi.2024.109504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Aeromonas hydrophila is a commonly pathogenic bacterium in cultivated eels, but its pathogenicity to American eel (Anguilla rostrata) and the molecular mechanism of host anti-A. hydrophila infection remains uncertain. In this study, LD50 of A. hydrophila to American eels was determined and bacterial load in the liver and kidney of eels was assessed post 2.56 doses of LD50 of A. hydrophila infection. The results showed that the LD50 of A. hydrophila to American eels was determined to be 3.9 × 105 cfu/g body weight (7.8 × 106 cfu/fish), and the bacterial load peaked at 36 h post the infection (hpi) in the liver. Then, the histopathology was highlighted by congestion in splenic blood vessels, atrophied glomeruli, and necrotic hepatocytes. Additionally, the results of qRT-PCR revealed that 18 host immune-related genes showed significantly up or downregulated post-infection compare to that of pre-infection. Finally, results of the RNA-seq revealed 10 hub DEGs and 7 encoded proteins play essential role to the anti-A. hydrophila infection in American eels. Pathogenicity of A. hydrophila to American eels and RNA-seq of host anti-A. hydrophila infection were firstly reported in this study, shedding new light on our understanding of the A. hydrophila pathogenesis and the host immune response to the A. hydrophila infection strategies in gene transcript.
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Affiliation(s)
- Songlin Guo
- Fisheries College, Jimei University, China; Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PR China, Xiamen, 361021, China; State Key Laboratory of Mariculture Breeding, Fisheries College of Jimei University, China.
| | - Qijuan Wan
- Fisheries College, Jimei University, China; Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PR China, Xiamen, 361021, China
| | - Ming Xu
- Fisheries College, Jimei University, China
| | - Minxia Chen
- Fisheries College, Jimei University, China; Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PR China, Xiamen, 361021, China
| | - Zihao Chen
- Fisheries College, Jimei University, China; Engineering Research Center of the Modern Industry Technology for Eel. Ministry of Education of PR China, Xiamen, 361021, China
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16
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Li S, Jian Y, Zhang K, Li X, Wang R, Zhang L, Jian F. Host specific Eimeria genus diagnosis and qPCR development in Ovis aries and Capra hircus. J Microbiol Methods 2024; 220:106910. [PMID: 38452905 DOI: 10.1016/j.mimet.2024.106910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 02/26/2024] [Accepted: 03/01/2024] [Indexed: 03/09/2024]
Abstract
The objective of the present study was to develop a real-time PCR (qPCR) technique for the diagnosis of Eimeria spp. in Ovis aries and Capra hircus. The qPCR technique was developed using SYBR Green, resulting in a PCR with high sensitivity, specificity, and reproducibility.
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Affiliation(s)
- Shijie Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yichen Jian
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Kaihui Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Xiaoying Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Rongjun Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Fuchun Jian
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China.
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17
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Maniego J, Pesko B, Habershon-Butcher J, Hincks P, Taylor P, Stewart G, Proudman C, Ryder E. Detection of adeno-associated viral DNA in equine post-administration frozen blood and plasma samples after long-term storage. Drug Test Anal 2024; 16:498-503. [PMID: 37671588 DOI: 10.1002/dta.3569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 09/07/2023]
Abstract
Gene doping in horses is a threat to the fairness in sport and has serious implications for animal welfare. To investigate the effect of long-term storage on the detection of AAV in plasma and whole blood, samples from an administration study using an adeno-associated virus serotype 6 expressing green fluorescence protein (AAV6-GFP) were stored at -20°C for 8 months before analysis. The AAV vector was detected in stored plasma samples, following the same detection profile as the fresh plasma samples. The stored blood showed lower overall DNA detection but followed the same detection profile as the plasma samples. This study provides confidence that re-analysing plasma samples and/or analysing a frozen 'B' sample with different matrix such as whole blood after prolonged storage will still result in the detection of gene doping material.
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Affiliation(s)
| | - Bogumila Pesko
- Sport and Specialised Analytical Services, LGC, Fordham, UK
| | | | - Pamela Hincks
- Sport and Specialised Analytical Services, LGC, Fordham, UK
| | - Polly Taylor
- Sport and Specialised Analytical Services, LGC, Fordham, UK
| | - Graham Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | | | - Edward Ryder
- Sport and Specialised Analytical Services, LGC, Fordham, UK
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18
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Ouaddane I, Goumballa N, Tran XD, Diouf C, Diene SM, Rolain JM, Sokhna C, Gautret P. Epidemiology of bacterial resistance at the Grand Magal of Touba in Senegal. Travel Med Infect Dis 2024; 59:102709. [PMID: 38479605 DOI: 10.1016/j.tmaid.2024.102709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 03/05/2024] [Indexed: 03/17/2024]
Abstract
BACKGROUND The Grand Magal of Touba (GMT) associates with risks of infection, but no study on the circulation of resistant bacteria has yet been conducted. MATERIALS AND METHODS qPCR was performed on rectal samples from GMT pilgrims between 2018 and 2021, before and after their participation in the gathering. Rectal samples from between 2018 and 2020 were also cultured on specific media, and antibiotic susceptibility testing was performed. RESULTS Forty-one of the 296 (13.8%) pilgrims had at least one gastrointestinal symptom and 91/290 (31.4%) acquired pathogenic bacteria, mostly Escherichia coli. A total of 54.7% of pilgrims reported washing their hands more frequently than usual and 89.2% used soap. One hundred and five (36.2%) acquired at least one resistance gene, notably CTX-M A (21.0%), SHV (16.5%) and TEM (8.2%). The strains isolated by culture were mostly E. coli. These bacteria were found to be sensitive to carbapenems and resistant to amoxicillin and amoxicillin-clavulanic acid. The acquisition of enteroaggregative E. coli was independently associated with CTX-M A and TEM acquisition. CONCLUSION Pilgrims presented a risk for acquisition of CTX-M A after the GMT. Surveillance of the prevalence of resistant bacteria and the occurrence of associated clinical infections among pilgrims are necessary in the future.
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Affiliation(s)
- Ihssane Ouaddane
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Ndiaw Goumballa
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; VITROME, Campus International IRD-UCAD de L'IRD, Dakar, Senegal
| | - Xuan Duong Tran
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Coumba Diouf
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; VITROME, Campus International IRD-UCAD de L'IRD, Dakar, Senegal
| | - Seydina M Diene
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; VITROME, Campus International IRD-UCAD de L'IRD, Dakar, Senegal
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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19
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Peachey MH, Kubow KE, Blyer KB, Halterman JA. Use of saliva-based qPCR diagnostics for the accurate, rapid, and inexpensive detection of strep throat. Diagnosis (Berl) 2024; 11:178-185. [PMID: 38178595 DOI: 10.1515/dx-2023-0134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
OBJECTIVES Outpatient health care facilities are essential for quickly diagnosing common infectious diseases such as bacterial and viral pharyngitis. The only form of pharyngitis requiring antibiotics is strep throat (ST); however, antibiotic prescription rates are much higher than ST prevalence, suggesting antibiotics are being inappropriately prescribed. Current rapid ST diagnostics may be contributing to this problem due to the low sensitivity and variable specificity of these tests. It is best practice to verify a negative ST diagnosis with a group A Streptococcus (GAS) culture, but many clinics do not perform this test due to the additional cost and 24-72 h required to obtain results. This indicates there is great need for more accurate rapid diagnostic tools in outpatient facilities. We hypothesized that next generation qPCR technology could be adapted to detect GAS DNA from saliva samples (instead of the traditional throat swab) by creating a simple, fast, and inexpensive protocol. METHODS Saliva specimens collected from patients at James Madison University Health Center were used to test the effectiveness of our Chelex 100-based rapid DNA extraction method, followed by a fast protocol developed for the Open qPCR machine to accurately detect ST. RESULTS Our final saliva processing and qPCR protocol required no specialized training to perform and was able to detect ST with 100 % sensitivity and 100 % specificity (n=102) in 22-26 min, costing only $1.12 per sample. CONCLUSIONS Saliva can be rapidly analyzed via qPCR for the accurate and inexpensive detection of ST.
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Affiliation(s)
- Madeline H Peachey
- Department of Biology, Eastern Mennonite University, Harrisonburg, VA, USA
| | | | - Kristina B Blyer
- University Health Center, James Madison University, Harrisonburg, VA, USA
| | - Julia A Halterman
- Department of Biology, Eastern Mennonite University, Harrisonburg, VA, USA
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20
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Valdivieso-Shephard JL, Matas-Pérez E, García-Bujalance S, Mirones-Aguilar I, González-Martínez B, Pérez-Martínez A, López-Granados E, Martínez-Feito A, Sánchez-Zapardiel E. The challenge of standardizing CAR-T cell monitoring: A comparison of two flow-cytometry methods and correlation with qPCR technique. Cytometry A 2024; 105:368-375. [PMID: 38327134 DOI: 10.1002/cyto.a.24825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 01/10/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
Chimeric antigen receptor (CAR) T-cell therapy is a breakthrough in hematologic malignancies, such as acute B lymphoblastic leukemia (B-ALL). Monitoring this treatment is recommended, although standardized protocols have not been developed yet. This work compares two flow cytometry monitoring strategies and correlates this technique with qPCR method. CAR-T cells were detected by two different flow-cytometry protocols (A and B) in nine blood samples from one healthy donor and five B-ALL patients treated with Tisagenlecleucel (Kymriah®, USA). HIV-1 viral load allowed CAR detection by qPCR, using samples from seven healthy donors and nine B-ALL patients. CAR detection by protocol A and B did not yield statistically significant differences (1.9% vs. 11.8% CD3 + CAR+, p = 0.07). However, protocol B showed a better discrimination of the CD3 + CAR+ population. A strong correlation was observed between protocol B and qPCR (r = 0.7, p < 0.0001). CD3 + CAR+ cells were detected by flow cytometry only when HIV-1 viral load was above 104 copies/mL. In conclusion, protocol B was the most specific flow-cytometry procedure for the identification of CAR-T cells and showed a high correlation with qPCR. Further efforts are needed to achieve a standardized monitoring approach.
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Affiliation(s)
| | | | | | - Isabel Mirones-Aguilar
- Advanced Therapy Medicinal Products Production Unit, Haemato-Oncology Service, La Paz University Hospital, Madrid, Spain
| | - Berta González-Martínez
- Translational Research Unit in Paediatric Haemato-Oncology, Hematopoietic Stem Cell Transplantation and Cell Therapy, La Paz University Hospital, Madrid, Spain
- Paediatric Haemato-Oncology Department, La Paz University Hospital, Madrid, Spain
| | - Antonio Pérez-Martínez
- Translational Research Unit in Paediatric Haemato-Oncology, Hematopoietic Stem Cell Transplantation and Cell Therapy, La Paz University Hospital, Madrid, Spain
- Paediatric Haemato-Oncology Department, La Paz University Hospital, Madrid, Spain
| | - Eduardo López-Granados
- Immunology Department, La Paz University Hospital, Madrid, Spain
- CIBERER U767, Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research (IdiPAZ), Madrid, Spain
| | - Ana Martínez-Feito
- Immunology Department, La Paz University Hospital, Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research (IdiPAZ), Madrid, Spain
| | - Elena Sánchez-Zapardiel
- Immunology Department, La Paz University Hospital, Madrid, Spain
- Lymphocyte Pathophysiology in Immunodeficiencies Group, La Paz Institute of Biomedical Research (IdiPAZ), Madrid, Spain
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21
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Castañeda S, Acosta CP, Vasquez-A LR, Patiño LH, Mejía R, Ramírez JD. Molecular detection of intestinal parasites in a rural community of Colombia: A one health approach to explore potential environmental-zoonotic transmission. Zoonoses Public Health 2024. [PMID: 38688683 DOI: 10.1111/zph.13138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
AIMS Protozoan and helminth parasitic infections pose significant public health challenges, especially in developing countries with rural populations marked by suboptimal hygiene practices and socio-economic constraints. The parasites are the etiological agents of these infections and have a notably elevated global prevalence. Therefore, this study focuses on estimating the frequency and transmission dynamics of several parasitic species, including Blastocystis, Giardia, Cryptosporidium spp., Entamoeba histolytica, Ascaris lumbricoides, Trichuris trichiura, Taenia spp. and hookworms, within a rural community in southwest Colombia with a particular emphasis on the One Health framework, considering environmental and zoonotic transmission potentials. METHODS AND RESULTS This study involved the analysis of 125 samples, encompassing human participants (n = 99), their domestic pets (dogs) (n = 24) and water sources (n = 2). Parasite detection was carried out utilizing a combination of microscopy and molecular techniques. Furthermore, the characterization of Blastocystis subtypes (STs) was achieved through Oxford Nanopore sequencing of the rRNA-18S gene. The investigation also entailed the examination of potential associations between intestinal parasitism and various sociodemographic factors. Results revealed a high frequency of parasitic infections when employing molecular methods, with Blastocystis (n = 109/87%), Giardia (n = 20/16%), Ancylostoma duodenale (n = 28/22%), Ancylostoma ceylanicum (n = 7/5.6%), E. histolytica (n = 6/4.8%), Cryptosporidium spp. (n = 12/9.6%) and even Taenia (n = 1/0.8%) detected. Cryptosporidium spp. was also identified in water samples. Coinfections were prevalent, with 57% (n = 70) of samples exhibiting single-parasite infections and 43% (n = 53) showing various degrees of polyparasitism, emphasizing the complexity of transmission dynamics. Blastocystis subtyping, conducted via Oxford Nanopore sequencing, revealed a diversity of subtypes and coexistence patterns, with ST2 being the most prevalent. CONCLUSIONS This research underscores the importance of using molecular techniques for frequency estimation, particularly emphasizing the relevance of zoonotic transmission in parasitic infections. It highlights the significance of the One Health approach in comprehending the circulation of parasites among animals, humans and environmental sources, thereby directly impacting public health and epidemiological surveillance.
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Affiliation(s)
- Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Claudia Patricia Acosta
- Grupo de investigación en Genética Humana, Departamento de Ciencias Fisiológicas, Facultad de Ciencias de la Salud, Universidad del Cauca, Popayán, Colombia
| | - Luis Reinel Vasquez-A
- Centro de Estudios en Microbiología y Parasitología, Facultad de Ciencias de la Salud, Universidad del Cauca, Popayán, Colombia
| | - Luz H Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Rojelio Mejía
- Department of Pediatrics, Division of Tropical Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York city, New York, USA
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22
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Caballero Méndez A, Reynoso de la Rosa RA, Abreu Bencosme ME, Sosa Ortiz MN, Pichardo Beltré E, de la Cruz García DM, Piñero Santana NJ, Bacalhau de León JC. Development and performance evaluation of a qPCR-based assay for the fully automated detection of group B Streptococcus (GBS) on the Panther Fusion Open Access system. Microbiol Spectr 2024:e0005724. [PMID: 38682931 DOI: 10.1128/spectrum.00057-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
Streptococcus agalactiae [group B Streptococcus (GBS)] poses a major threat as the primary cause of early-onset neonatal invasive disease, particularly when mothers are colonized rectovaginally. Although culture remains the gold standard for antepartum GBS screening, quantitative polymerase chain reaction (qPCR) offers advantages in terms of sensitivity and turnaround time. The aim of this study was to validate the clinical utility of an automated qPCR laboratory-developed test (LDT) for antepartum GBS screening using the Panther Fusion Open Access system (Hologic, California, USA). The LDT targeted a conserved region of the GBS surface immunogenic protein gene, demonstrating no cross-reactivity and high coverage (99.82%-99.99%). The limit of detection (LoD) was 118 CFU/mL. Comparison with commercial qPCR assays (Panther Fusion GBS and VIASURE Streptococcus B Real-Time) revealed an overall agreement of 99.7%, with a robust Cohen's kappa coefficient of 0.992. Testing of 285 rectovaginal swabs from pregnant women and 15 external quality assessment samples demonstrated exceptional diagnostic performance of the LDT, achieving a diagnostic sensitivity and specificity of 100%, underscoring its accuracy. Prevalence and predictive values were also determined to reinforce test reliability. Our research highlights the limitations of culture-based screening and supports the suitability of our qPCR-based LDT for GBS detection in a clinical setting.IMPORTANCERectovaginal colonization by GBS is a major risk factor for early-onset invasive neonatal disease. The most effective approach to reducing the incidence of early-onset disease (EOD) has been described as universal screening, involving assessment of GBS colonization status in late pregnancy and intrapartum antibiotic prophylaxis. Despite its turnaround time and sensitivity limitations, culture remains the gold standard method for GBS screening. However, nucleic acid amplification-based tests, such as qPCR, have been utilized due to their speed and high sensitivity and specificity. This study validated the clinical usefulness of an automated qPCR-LDT for antepartum GBS screening through the Panther Fusion Open Access system (Hologic). Our study addresses the critical need for more robust, sensitive, and rapid strategies for GBS screening in pregnant women that could favorably impact the incidence of EOD.
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Affiliation(s)
- Andy Caballero Méndez
- Molecular Biology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
| | - Roberto A Reynoso de la Rosa
- Molecular Biology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
| | - Miguel E Abreu Bencosme
- Molecular Biology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
| | - Mayeline N Sosa Ortiz
- Molecular Biology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
| | - Eliezel Pichardo Beltré
- Molecular Biology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
| | - Darah M de la Cruz García
- Molecular Biology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
| | - Nelson J Piñero Santana
- Molecular Biology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
| | - Joana C Bacalhau de León
- Microbiology Department, Referencia Laboratorio Clínico, Santo Domingo Oeste, Santo Domingo, Dominican Republic
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23
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Limardi PC, Panigoro SS, Siregar NC, Sutandyo N, Witjaksono F, Priliani L, Oktavianthi S, Malik SG. Higher peripheral blood mitochondrial DNA copy number and relative telomere length in under 48 years Indonesian breast cancer patients. BMC Res Notes 2024; 17:120. [PMID: 38679744 PMCID: PMC11057172 DOI: 10.1186/s13104-024-06783-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
OBJECTIVE Breast cancer is the leading cause of cancer incidence and mortality among Indonesian women. A comprehensive investigation is required to enhance the early detection of this disease. Mitochondrial DNA copy number (mtDNA-CN) and relative telomere length (RTL) have been proposed as potential biomarkers for several cancer risks, as they are linked through oxidative stress mechanisms. We conducted a case-control study to examine peripheral blood mtDNA-CN and RTL patterns in Indonesian breast cancer patients (n = 175) and healthy individuals (n = 181). The relative ratios of mtDNA-CN and RTL were determined using quantitative real-time PCR (qPCR). RESULTS Median values of mtDNA-CN and RTL were 1.62 and 0.70 in healthy subjects and 1.79 and 0.73 in breast cancer patients, respectively. We found a positive association between peripheral blood mtDNA-CN and RTL (p < 0.001). In under 48 years old breast cancer patients, higher peripheral blood mtDNA-CN (mtDNA-CN ≥ 1.73 (median), p = 0.009) and RTL (continuous variable, p = 0.010) were observed, compared to the corresponding healthy subjects. We also found a significantly higher 'High-High' pattern of mtDNA-CN and RTL in breast cancer patients under 48 years old (p = 0.011). Our findings suggest that peripheral blood mtDNA-CN and RTL could serve as additional minimally invasive biomarkers for breast cancer risk evaluation.
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Affiliation(s)
- Prisca C Limardi
- Master's Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Genome Diversity and Diseases Division, Mochtar Riady Institute for Nanotechnology, Jl. Boulevard Jenderal Sudirman 1688, Lippo Karawaci, Tangerang, Banten, 15811, Indonesia
| | - Sonar Soni Panigoro
- Department of Surgical Oncology, Dr. Cipto Mangunkusumo Hospital-Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Nurjati Chairani Siregar
- Department of Anatomical Pathology, Dr. Cipto Mangunkusumo Hospital-Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Noorwati Sutandyo
- Department of Hematology and Medical Oncology, Dharmais Hospital National Cancer Center, Jakarta, Indonesia
| | - Fiastuti Witjaksono
- Department of Nutrition, Dr. Cipto Mangunkusumo Hospital-Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Lidwina Priliani
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Genome Diversity and Diseases Division, Mochtar Riady Institute for Nanotechnology, Jl. Boulevard Jenderal Sudirman 1688, Lippo Karawaci, Tangerang, Banten, 15811, Indonesia
| | - Sukma Oktavianthi
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Genome Diversity and Diseases Division, Mochtar Riady Institute for Nanotechnology, Jl. Boulevard Jenderal Sudirman 1688, Lippo Karawaci, Tangerang, Banten, 15811, Indonesia
| | - Safarina G Malik
- Master's Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.
- Genome Diversity and Diseases Division, Mochtar Riady Institute for Nanotechnology, Jl. Boulevard Jenderal Sudirman 1688, Lippo Karawaci, Tangerang, Banten, 15811, Indonesia.
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Zhang G, Wang J, Li Y, Zhang Z, Wang X, Chen F, Shi Q, Huang Y, Wang E, Lyu S. POLB Regulates Proliferation and Apoptosis of Bovine Primary Myocytes. Animals (Basel) 2024; 14:1323. [PMID: 38731327 PMCID: PMC11083859 DOI: 10.3390/ani14091323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/30/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
DNA polymerase β (DNA polymerase beta (POLB)) belongs to a member of the DNA polymerase X family, mainly involved in various biological metabolic processes, such as eukaryotic DNA replication, DNA damage repair, gene recombination, and cell cycle regulation. In this study, the muscle development-related gene POLB was screened by selection signature and RNA-seq analysis and then validated for the proliferation and apoptosis of bovine primary myocytes. It was also found that overexpression of the POLB gene had a pro-apoptosis effect, but interfering with the expression of the gene had no significant effect on cells. Then, the analysis of related apoptotic genes revealed that POLB overexpression affected CASP9 gene expression.
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Affiliation(s)
- Geyang Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Jiamei Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (J.W.); (Y.H.)
| | - Yulong Li
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Xiangnan Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Fuying Chen
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (J.W.); (Y.H.)
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (G.Z.); (Y.L.); (Z.Z.); (X.W.); (F.C.); (Q.S.)
- The Shennong Laboratory, Zhengzhou 450002, China
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25
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Nabeshima K, Kuriyama T, Takagi S, Sugimoto T, Yokoyama M, Goka K, Onuma M. Novel approach for detecting classical swine fever virus from swabs of wild boar cut tails using nested real-time PCR. J Vet Med Sci 2024:24-0062. [PMID: 38658334 DOI: 10.1292/jvms.24-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
We devised a method to detect the classical swine fever virus (CSFV) in tail-wiped swabs from wild boars. The CSFV gene in swabs was detected with high sensitivity using nested real-time polymerase chain reaction (PCR), which is a combination of reverse transcription-PCR (RT-PCR) and real-time PCR. We compared CSFV gene detection from boar tissue using the conventional and our tail-wiped swab method. The tail-wiped swab method showed sensitivity and specificity of 100% (26/26) and 98.8% (172/174), respectively compared to the conventional method. Thus, the swab-based CSFV detection method was considered to have detection sensitivity comparable to that of conventional methods. Additionally, we conducted surveillance for CSFV in wild boars on Awaji Island. CSFV was detected in 10.7% (45/420) of samples.
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Affiliation(s)
- Kei Nabeshima
- Ecological Risk Assessment and Control Section Center for Environmental Biology and Ecosystem, National Institute for Environmental Studies
| | - Takeo Kuriyama
- Institute of Natural and Environmental Sciences, University of Hyogo
- Wildlife Management Research Center, Hyogo
| | - Shun Takagi
- Institute of Natural and Environmental Sciences, University of Hyogo
- Wildlife Management Research Center, Hyogo
| | - Taro Sugimoto
- Institute of Natural and Environmental Sciences, University of Hyogo
| | - Mayumi Yokoyama
- Institute of Natural and Environmental Sciences, University of Hyogo
- Wildlife Management Research Center, Hyogo
| | - Koichi Goka
- Ecological Risk Assessment and Control Section Center for Environmental Biology and Ecosystem, National Institute for Environmental Studies
| | - Manabu Onuma
- Ecological Risk Assessment and Control Section Center for Environmental Biology and Ecosystem, National Institute for Environmental Studies
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26
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Favacho JDFR, Leite KK, Jacomasso T, Farias AB, Franco Filho LC, Gomes STM, dos Reis HS, Mota GD, Schluga PHDC, Tassi WS, Rampazzo RDCP, West SK, Gaydos CA, da Cunha AJLA, Costa ADT. Validation of a New Duplex Real-Time Polymerase Chain Reaction for Chlamydia trachomatis DNA Detection in Ocular Swab Samples. Diagnostics (Basel) 2024; 14:892. [PMID: 38732307 PMCID: PMC11083659 DOI: 10.3390/diagnostics14090892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 05/13/2024] Open
Abstract
Trachoma is the world-leading infectious cause of preventable blindness and is caused by the bacteria Chlamydia trachomatis. In developing countries, diagnosis is usually based on clinical evaluation. Serological-based tests are cheaper than molecular-based ones, but the latter are more sensitive and specific. The present study developed a new duplex qPCR which concomitantly detects the C. trachomatis cryptic plasmid and the human 18S rRNA gene, with an LOD95% for C. trachomatis DNA of 13.04 genome equivalents per reaction. The new qPCR was tested using 50 samples from an endemic area and 12 from a non-endemic area that were previously characterized using direct immunofluorescence assay (DFA) and clinical evaluation. Among the 50 endemic samples, 3 were found to be positive by clinical evaluation (6%), 18 were found to be positive by DFA (36%), and 48 were found to be positive by qPCR (96%). Next, the new duplex qPCR was validated using 50 samples previously characterized by qPCR. Validation was carried out on a benchtop instrument (ABI7500) or on a portable point-of-care instrument (Q3-Plus), showing 95% specificity and 100% sensitivity. The ubiquitous presence of C. trachomatis DNA in samples from the endemic region confirms that constant monitoring is of paramount importance for the effective measurement of the elimination of trachoma. The newly developed duplex qPCR presented in this study, along with its validation in a portable qPCR system, constitutes important tools toward achieving this goal.
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Affiliation(s)
- Joana da Felicidade Ribeiro Favacho
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Keren Kariene Leite
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Thiago Jacomasso
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Aline Burda Farias
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | - Luciano Chaves Franco Filho
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Samara Tatielle Monteiro Gomes
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Herald Souza dos Reis
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | - Gardene Dourado Mota
- Evandro Chagas Institute, Secretariat of Health and Environment Surveillance, Ministry of Health (IEC/SVSA/MS), Ananindeua 67030-000, PA, Brazil; (L.C.F.F.); (H.S.d.R.)
| | | | - Walleyd Sami Tassi
- Institute of Molecular Biology of Paraná (IBMP), Curitiba 81350-010, PR, Brazil (T.J.)
| | | | - Sheila Kay West
- Dana Center for Preventative Ophthalmology, Johns Hopkins University, Baltimore, MD 21287, USA;
| | - Charlotte Ann Gaydos
- International Sexually Transmitted Disease Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, MD 21218, USA
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27
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Li Z, Tu M, Qin F, Shui G, Xu D, Zang X. Identification of Indicator Genes for Agar Accumulation in Gracilariopsis lemaneiformis (Rhodophyta). Int J Mol Sci 2024; 25:4606. [PMID: 38731824 PMCID: PMC11083068 DOI: 10.3390/ijms25094606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024] Open
Abstract
Agar, as a seaweed polysaccharide mainly extracted from Gracilariopsis lemaneiformis, has been commercially applied in multiple fields. To investigate factors indicating the agar accumulation in G. lemaneiformis, the agar content, soluble polysaccharides content, and expression level of 11 genes involved in the agar biosynthesis were analysed under 4 treatments, namely salinity, temperature, and nitrogen and phosphorus concentrations. The salinity exerted the greatest impact on the agar content. Both high (40‱) and low (10‱, 20‱) salinity promoted agar accumulation in G. lemaneiformis by 4.06%, 2.59%, and 3.00%, respectively. The content of agar as a colloidal polysaccharide was more stable than the soluble polysaccharide content under the treatments. No significant correlation was noted between the two polysaccharides, and between the change in the agar content and the relative growth rate of the algae. The expression of all 11 genes was affected by the 4 treatments. Furthermore, in the cultivar 981 with high agar content (21.30 ± 0.95%) compared to that (16.23 ± 1.59%) of the wild diploid, the transcriptional level of 9 genes related to agar biosynthesis was upregulated. Comprehensive analysis of the correlation between agar accumulation and transcriptional level of genes related to agar biosynthesis in different cultivation conditions and different species of G. lemaneiformis, the change in the relative expression level of glucose-6-phosphate isomerase II (gpiII), mannose-6-phosphate isomerase (mpi), mannose-1-phosphate guanylyltransferase (mpg), and galactosyltransferase II (gatII) genes was highly correlated with the relative agar accumulation. This study lays a basis for selecting high-yield agar strains, as well as for targeted breeding, by using gene editing tools in the future.
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Affiliation(s)
| | | | | | | | - Di Xu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Z.L.); (M.T.); (F.Q.); (G.S.)
| | - Xiaonan Zang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, Ocean University of China, Qingdao 266003, China; (Z.L.); (M.T.); (F.Q.); (G.S.)
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28
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Kampmann ML, Tfelt-Hansen J, Børsting C. Cleaning protocols in forensic genetic laboratories. Int J Legal Med 2024:10.1007/s00414-024-03232-0. [PMID: 38649547 DOI: 10.1007/s00414-024-03232-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024]
Abstract
It is pivotal to avoid cross-sample contamination in forensic genetic laboratories and optimal cleaning protocols for the removal of DNA are essential. A survey was performed, and ten forensic genetic laboratories shared their cleaning protocols in pre-PCR and post-PCR laboratories. The cleaning frequencies on different surface areas were somewhat similar, whereas none of the laboratories used the same cleaning reagents. Therefore, the efficiencies of the cleaning protocol utilised were tested and compared. The results showed that freshly made household bleach and Virkon® removed all amplifiable DNA from the surfaces, whereas DNA AWAY™ and the disinfection reagents ethanol, isopropanol, and ChemGene HLD4L did not.
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Affiliation(s)
- Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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29
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Silva RG, Kiupel M, Langohr IM, Wise A, Pereira SA, Gonçalves NP, da Conceição GMS, Ferreira LC, de Campos MP, Miranda LDFC, Figueiredo FB, de Oliveira RDVC, Keidel L, Menezes RC. Comparative Study of Colorimetric In Situ Hybridization and Quantitative Real-Time Polymerase Chain Reaction for Diagnosis of Infection by Leishmania infantum in Dogs in Formalin-Fixed and Paraffin-Embedded Skin. Trop Med Infect Dis 2024; 9:91. [PMID: 38668552 PMCID: PMC11054412 DOI: 10.3390/tropicalmed9040091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
The zoonotic visceral leishmaniasis is caused by the protozoan Leishmania infantum and dogs are reservoirs for this parasite. For the diagnosis of Leishmania at the species level in dogs in formalin-fixed, paraffin-embedded skin (FFPES) samples, colorimetric in situ hybridization (CISH) and quantitative real-time polymerase chain reaction (qPCR) are options, but their sensitivities are not well established. Therefore, the aim of this study was to determine the sensitivity of these two techniques in FFPES for the diagnosis of the L. infantum infection in dogs using culture as the reference standard. The FFPES of 48 dogs with cutaneous infection by L. infantum confirmed by culture and by multilocus enzyme electrophoresis were examined by CISH and qPCR using specific probes for L. infantum. The sensitivities of qPCR, CISH and their combination were, respectively, 77.0%, 58.0% and 83.3%. The sensitivities of qPCR in dogs with and without clinical signs were, respectively, 74.2% and 82.4%. The sensitivities of CISH in dogs with and without clinical signs were, respectively, 61.3% and 52.9%. The CISH and qPCR showed satisfactory sensitivities for the diagnosis of L. infantum in the FFPES of dogs, even in dogs without clinical signs, and their combination increases the sensitivity for this diagnosis.
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Affiliation(s)
- Ricardo Gonçalves Silva
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Matti Kiupel
- Veterinary Diagnostic Laboratory, Michigan State University, 4125 Beaumont Road, Lansing, MI 48910, USA; (M.K.); (A.W.)
| | - Ingeborg Maria Langohr
- Sanofi, Global Discovery Pathology, Translational Models Research Platform, 350 Water Street, Cambridge, MA 02141, USA;
| | - Annabel Wise
- Veterinary Diagnostic Laboratory, Michigan State University, 4125 Beaumont Road, Lansing, MI 48910, USA; (M.K.); (A.W.)
| | - Sandro Antonio Pereira
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Natália Pedra Gonçalves
- Bio-Manguinhos, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (N.P.G.); (G.M.S.d.C.)
| | | | - Luiz Cláudio Ferreira
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Monique Paiva de Campos
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba 81350-010, Brazil; (M.P.d.C.); (F.B.F.)
| | - Luciana de Freitas Campos Miranda
- Laboratory of Clinical Research and Surveillance of Leishmaniasis, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil;
| | - Fabiano Borges Figueiredo
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba 81350-010, Brazil; (M.P.d.C.); (F.B.F.)
| | | | - Lucas Keidel
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Rodrigo Caldas Menezes
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
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Karagülle G, Telli M. Effects of green light supplementation with red and blue combinations of LED light spectrums on the growth and transcriptional response of Haematococcus pluvialis. Biotechnol Prog 2024:e3462. [PMID: 38641974 DOI: 10.1002/btpr.3462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/11/2023] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Light management strategy is crucial for improving microalgal production in terms of higher biomass and economically valuable bioactive molecules. However, green light has received less attention in developing light managements for algae and higher plant due to its low absorption rate by chlorophyll. In this study, the effects of green light supplementation, in the combination with red and blue light were investigated in Haematococcus pluvialis. 10% and 20% of green light supplementations were applied in 3:2 ratios of red and blue LED light combinations as an expense of red-light. Growth rates, chlorophyll concentration, and dry weight were measured to assess the growth kinetics of H. pluvialis along with the relative transcript accumulations of four mRNAs: Rubisco, PTOX2, PsaB, and PsbS. Growth rates, chlorophyll concentrations and dry weight were found significantly higher in presence of 10% green light supplementation compared to red and blue light combinations. The relative transcript accumulations of Rubisco and PsbS genes showed significant upregulation at the end of the experiments (with the fold change of 42.91 ± 12.08 and 98.57 ± 27.38, respectively, relative to the beginning of the experiments) compared to combinations of red and blue light (fold change of 19.09 ± 3.0 and 47.77 ± 14.21, respectively, relative to beginning of the experiments). PsaB and PTOX2 transcripts did not show significant accumulation differences between treatments. It seems that green light has a dose dependent additive effect on the growth rate of H. pluvialis. The upregulation of Rubisco and PsbS may indicate green light dependent carbon assimilation and light-harvesting response in H. pluvialis.
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Affiliation(s)
- G Karagülle
- Department of Biology, Faculty of Arts and Sciences, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - M Telli
- Department of Biology, Faculty of Arts and Sciences, Bolu Abant İzzet Baysal University, Bolu, Turkey
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31
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Williams A, Porter J, Kingsley K, Howard KM. Higher Prevalence of the Periodontal Pathogen Selenomonas noxia among Pediatric and Adult Patients May Be Associated with Overweight and Obesity. Pathogens 2024; 13:338. [PMID: 38668293 PMCID: PMC11053746 DOI: 10.3390/pathogens13040338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024] Open
Abstract
New evidence has suggested that oral and gut microflora may have significant impacts on the predisposition, development, and stability of obesity in adults over time-although less is known about this phenomenon in children. Compared with healthy-weight controls, overweight and obese adult patients are now known to harbor specific pathogens, such as Selenomonas noxia (S. noxia), that are capable of digesting normally non-digestible cellulose and fibers that significantly increase caloric extraction from normal dietary intake. To evaluate this phenomenon, clinical saliva samples (N = 122) from subjects with a normal BMI (18-25) and a BMI over 25 (overweight, obese) from an existing biorepository were screened using qPCR. The prevalence of S. noxia in samples from normal-BMI participants were lower (21.4%) than in overweight-BMI (25-29; 46.1%) and obese-BMI (30 and above; 36.8%) samples-a strong, positive correlation that was not significantly affected by age or race and ethnicity. These data strongly suggest that S. noxia may be intricately associated with overweight and obesity among patients, and more research will be needed to determine the positive and negative feedback mechanisms that may be responsible for these observations as well as the interventions needed to remove or reduce the potential effects of this oral pathogen.
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Affiliation(s)
- Austin Williams
- Department of Advanced Education in Pediatric Dentistry, School of Dental Medicine, University of Nevada, Las Vegas, 1700 West Charleston Blvd, Las Vegas, NV 89106, USA
| | - Jace Porter
- Department of Clinical Sciences, School of Dental Medicine, University of Nevada, Las Vegas, 1700 West Charleston Blvd, Las Vegas, NV 89106, USA
| | - Karl Kingsley
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada, Las Vegas, 1001 Shadow Lane, Las Vegas, NV 89106, USA;
| | - Katherine M. Howard
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada, Las Vegas, 1001 Shadow Lane, Las Vegas, NV 89106, USA;
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Chowdhury G, Ghosh D, Zhou Y, Deb AK, Mukhopadhyay AK, Dutta S, Chakraborty S. Field evaluation of a simple and rapid diagnostic test, RLDT to detect Shigella and enterotoxigenic E. coli in Indian children. Sci Rep 2024; 14:8816. [PMID: 38627472 PMCID: PMC11021469 DOI: 10.1038/s41598-024-59181-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected additional 12% Shigella and 13% ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.
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Affiliation(s)
- Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Debjani Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Yiyi Zhou
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alok K Deb
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India.
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Moreno Y, Moreno-Mesonero L, Soler P, Zornoza A, Soriano A. Influence of drinking water biofilm microbiome on water quality: Insights from a real-scale distribution system. Sci Total Environ 2024; 921:171086. [PMID: 38382601 DOI: 10.1016/j.scitotenv.2024.171086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/07/2024] [Accepted: 02/17/2024] [Indexed: 02/23/2024]
Abstract
Biofilms, constituting over 95 % of the biomass in drinking water distribution systems, form an ecosystem impacting both the aesthetic and microbiological quality of water. This study investigates the microbiome of biofilms within a real-scale drinking water distribution system in eastern Spain, utilizing amplicon-based metagenomics. Forty-one biofilm samples underwent processing and sequencing to analyze both bacterial and eukaryotic microbiomes, with an assessment of active biomass. Genus-level analysis revealed considerable heterogeneity, with Desulfovibrio, Ralstonia, Bradyrhizobium, Methylocystis, and Bacillus identified as predominant genera. Notably, bacteria associated with corrosion processes, including Desulfovibrio, Sulfuricella, Hyphomicrobium, and Methylobacterium, were prevalent. Potentially pathogenic bacteria such as Helicobacter, Pseudomonas, and Legionella were also detected. Among protozoa, Opisthokonta and Archaeplastida were the most abundant groups in biofilm samples, with potential pathogenic eukaryotes (Acanthamoeba, Naegleria, Blastocystis) identified. Interestingly, no direct correlation between microbiota composition and pipe materials was observed. The study suggests that the usual concentration of free chlorine in bulk water proved insufficient to prevent the presence of undesirable bacteria and protozoa in biofilms, which exhibited a high concentration of active biomass.
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Affiliation(s)
- Yolanda Moreno
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - Laura Moreno-Mesonero
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Patricia Soler
- Empresa Mixta Valenciana de Aguas, S.A. (EMIVASA), Av. del Regne de València, 28, 46005, Valencia, Spain
| | - Andrés Zornoza
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; H2OCITIES, SL, Arte Mayor de la Seda, 15, 46950 Xirivella, Valencia, Spain
| | - Adela Soriano
- Empresa Mixta Valenciana de Aguas, S.A. (EMIVASA), Av. del Regne de València, 28, 46005, Valencia, Spain
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Ramirez-Calderon G, Saleh A, Hidalgo Castillo TC, Druet V, Almarhoon B, Almulla L, Adamo A, Inal S. Enhancing the Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes with an n-Type Organic Semiconductor Coating. ACS Appl Mater Interfaces 2024. [PMID: 38620064 DOI: 10.1021/acsami.3c18919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) are a promising cell source for cardiac regenerative medicine and in vitro modeling. However, hPSC-CMs exhibit immature structural and functional properties compared with adult cardiomyocytes. Various electrical, mechanical, and biochemical cues have been applied to enhance hPSC-CM maturation but with limited success. In this work, we investigated the potential application of the semiconducting polymer poly{[N,N'-bis(2-octyldodecyl)-naphthalene-1,4,5,8-bis(dicarboximide)-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)} (P(NDI2OD-T2)) as a light-sensitive material to stimulate hPSC-CMs optically. Our results indicated that P(NDI2OD-T2)-mediated photostimulation caused cell damage at irradiances applied long-term above 36 μW/mm2 and did not regulate cardiac monolayer beating (after maturation) at higher intensities applied in a transient fashion. However, we discovered that the cells grown on P(NDI2OD-T2)-coated substrates showed significantly enhanced expression of cardiomyocyte maturation markers in the absence of a light exposure stimulus. A combination of techniques, such as atomic force microscopy, scanning electron microscopy, and quartz crystal microbalance with dissipation monitoring, which we applied to investigate the interface of the cell with the n-type coating, revealed that P(NDI2OD-T2) impacted the nanostructure, adsorption, and viscoelasticity of the Matrigel coating used as a cell adhesion promoter matrix. This modified cellular microenvironment promoted the expression of cardiomyocyte maturation markers related to contraction, calcium handling, metabolism, and conduction. Overall, our findings demonstrate that conjugated polymers such as P(NDI2OD-T2) can be used as passive coatings to direct stem cell fate through interfacial engineering of cell growth substrates.
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Affiliation(s)
- Gustavo Ramirez-Calderon
- Laboratory of Stem Cells and Diseases, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Abdulelah Saleh
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Tania Cecilia Hidalgo Castillo
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Victor Druet
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Bayan Almarhoon
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Latifah Almulla
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Antonio Adamo
- Laboratory of Stem Cells and Diseases, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sahika Inal
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, KAUST, Thuwal 23955-6900, Saudi Arabia
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Ravindran S, Underwood SL, Dorrens J, Seeker LA, Watt K, Wilbourn RV, Sparks AM, Sinclair R, Chen Z, Pilkington JG, McNeilly TN, Harrington L, Pemberton JM, Nussey DH, Froy H. No correlative evidence of costs of infection or immunity on leucocyte telomere length in a wild population of Soay sheep. Proc Biol Sci 2024; 291:20232946. [PMID: 38565156 PMCID: PMC10987235 DOI: 10.1098/rspb.2023.2946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Telomere length (TL) is a biomarker hypothesized to capture evolutionarily and ecologically important physiological costs of reproduction, infection and immunity. Few studies have estimated the relationships among infection status, immunity, TL and fitness in natural systems. The hypothesis that short telomeres predict reduced survival because they reflect costly consequences of infection and immune investment remains largely untested. Using longitudinal data from a free-living Soay sheep population, we tested whether leucocyte TL was predicted by infection with nematode parasites and antibody levels against those parasites. Helminth parasite burdens were positively associated with leucocyte TL in both lambs and adults, which is not consistent with TL reflecting infection costs. We found no association between TL and helminth-specific IgG levels in either young or old individuals which suggests TL does not reflect costs of an activated immune response or immunosenescence. Furthermore, we found no support for TL acting as a mediator of trade-offs between infection, immunity and subsequent survival in the wild. Our results suggest that while variation in TL could reflect short-term variation in resource investment or environmental conditions, it does not capture costs of infection and immunity, nor does it behave like a marker of an individual's helminth-specific antibody immune response.
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Affiliation(s)
- Sanjana Ravindran
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sarah L. Underwood
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jennifer Dorrens
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Luise A. Seeker
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Kathryn Watt
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Rachael V. Wilbourn
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Alexandra M. Sparks
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Rona Sinclair
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Zhulin Chen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Jill G. Pilkington
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Tom N. McNeilly
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lea Harrington
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada H3C 3J7
| | - Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Daniel H. Nussey
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Hannah Froy
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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Tessin J, Jung A, Silberborth A, Rohn K, Schulz J, Visscher C, Kemper N. Detection of Enterococcus cecorum to identify persistently contaminated locations using faecal and environmental samples in broiler houses of clinically healthy flocks. Avian Pathol 2024:1-9. [PMID: 38525653 DOI: 10.1080/03079457.2024.2334682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024]
Abstract
RESEARCH HIGHLIGHTS Methodology is suitable to detect EC during production and after C&D.Locations were detected that may serve as a reservoir for EC.Cycles with fewer positive samples were observed.Cleaning and disinfection had a major impact on the detection of EC.
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Affiliation(s)
- Jesper Tessin
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Arne Jung
- Clinic for Poultry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Amanda Silberborth
- Clinic for Poultry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Karl Rohn
- Institute for Biometry, Epidemiology and Information Processing, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jochen Schulz
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Christian Visscher
- Institute for Animal Nutrition, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Nicole Kemper
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviour, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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37
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Paskey AC, Schully KL, Voegtly LJ, Arnold CE, Cer RZ, Frey KG, Blair PW, Clark DV, Ge H, Richards AL, Farris CM, Bishop-Lilly KA. A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens. Front Microbiol 2024; 15:1387208. [PMID: 38659991 PMCID: PMC11039911 DOI: 10.3389/fmicb.2024.1387208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
Infection with either Rickettsia prowazekii or Orientia tsutsugamushi is common, yet diagnostic capabilities are limited due to the short window for positive identification. Until now, although targeted enrichment had been applied to increase sensitivity of sequencing-based detection for various microorganisms, it had not been applied to sequencing of R. prowazekii in clinical samples. Additionally, hybridization-based targeted enrichment strategies had only scarcely been applied to qPCR of any pathogens in clinical samples. Therefore, we tested a targeted enrichment technique as a proof of concept and found that it dramatically reduced the limits of detection of these organisms by both qPCR and high throughput sequencing. The enrichment methodology was first tested in contrived clinical samples with known spiked-in concentrations of R. prowazekii and O. tsutsugamushi DNA. This method was also evaluated using clinical samples, resulting in the simultaneous identification and characterization of O. tsutsugamushi directly from clinical specimens taken from sepsis patients. We demonstrated that the targeted enrichment technique is helpful by lowering the limit of detection, not only when applied to sequencing, but also when applied to qPCR, suggesting the technique could be applied more broadly to include other assays and/or microbes for which there are limited diagnostic or detection modalities.
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Affiliation(s)
- Adrian C. Paskey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Kevin L. Schully
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Logan J. Voegtly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Leidos, Reston, VA, United States
| | - Catherine E. Arnold
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- Defense Threat Reduction Agency, Fort Belvoir, VA, United States
| | - Regina Z. Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Kenneth G. Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
| | - Paul W. Blair
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Danielle V. Clark
- Austere Environments Consortium for Enhanced Sepsis Outcomes (ACESO), Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Hong Ge
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Allen L. Richards
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Christina M. Farris
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Command, Silver Spring, MD, United States
| | - Kimberly A. Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Command, Frederick, MD, United States
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Varghese T, Mills JAP, Revathi R, Antoni S, Soeters HM, Emmanuel Njambe TO, Houpt ER, Tate JE, Parashar UD, Kang G. Etiology of diarrheal hospitalizations following rotavirus vaccine implementation and association of enteric pathogens with malnutrition among under-five children in India. Gut Pathog 2024; 16:22. [PMID: 38600552 PMCID: PMC11005126 DOI: 10.1186/s13099-024-00599-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/09/2024] [Indexed: 04/12/2024] Open
Abstract
Malnourished children are at higher risk of mortality and morbidity following diarrheal illness and certain enteropathogens have been associated with malnutrition in children. Very few studies have comprehensively looked at the etiology of diarrhea in malnourished children and most have used conventional diagnostic methods with suboptimal sensitivity. We used a highly sensitive molecular approach against a broad range of pathogens causing diarrhea and examined their association with malnutrition. In addition, we looked at the pathogen diversity of pediatric diarrhea, three years after the nationwide rotavirus vaccine introduction to understand the evolving landscape of pathogens, which is crucial for planning strategies to further reduce the diarrhea burden. Clinical details and diarrheal stool samples were collected from hospitalized children aged < 5 years from three sentinel sites in India for a period of one year. The samples were tested by qPCR for 16 established causes of diarrhea using TaqMan Array Cards. A total of 772 children were enrolled, from whom 482 (62.4%) stool specimens were tested. No specific pathogen was associated with diarrhea among children with acute or chronic malnutrition compared to those with better nutritional status. Overall, adenovirus was the leading pathogen (attributable fraction (AF) 16.9%; 95% CI 14.1 to 19.2) followed by rotavirus (AF 12.6%; 95% CI 11.8 to 13.1) and Shigella (AF 10.9%; 95% CI 8.4 to 16.4). The majority of diarrhea requiring hospitalization in children aged < 2 years could be attributed to viruses, while Shigella was the most common pathogen among children aged > 2 years. These data on the prevalence and epidemiology of enteropathogens identified potential pathogens for public health interventions.
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Affiliation(s)
- Tintu Varghese
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
| | - James A Platts Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - R Revathi
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | | | | | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jacqueline E Tate
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Umesh D Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
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Raele DA, Severini F, Toma L, Menegon M, Boccolini D, Tortorella G, Di Luca M, Cafiero MA. Anopheles sacharovi in Italy: first record of the historical malaria vector after over 50 years. Parasit Vectors 2024; 17:182. [PMID: 38600589 PMCID: PMC11005165 DOI: 10.1186/s13071-024-06252-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Anopheles sacharovi, a member of the Anopheles maculipennis complex, was a historical malaria vector in Italy, no longer found since the last report at the end of 1960s. In September 2022, within the Surveillance Project for the residual anophelism, a single specimen of An. maculipennis sensu lato collected in Lecce municipality (Apulia region) was molecularly identified as An. sacharovi. This record led to implement a targeted entomological survey in September 2023. METHODS Investigation was conducted in the areas around the first discovery, focusing on animal farms, riding stables and potential breeding sites. Adult and immature mosquitoes were collected, using active search or traps, in several natural and rural sites. Mosquitoes belonging to An. maculipennis complex were identified morphologically and molecularly by a home-made routine quantitative polymerase chain reaction (qPCR) assay, developed specifically for the rapid identification of An. labranchiae, and, when necessary, by amplification and sequencing of the ITS-2 molecular marker. RESULTS Out of the 11 sites investigated, 6 were positive for Anopheles presence. All 20 An. maculipennis s.l. (7 adults, 10 larvae and 3 pupae) collected in the areas were identified as An. sacharovi by ITS-2 sequencing. CONCLUSIONS The discovery of An. sacharovi, considered to have disappeared from Italy for over 50 years, has a strong health relevance and impact, highlighting an increase in the receptivity of the southern areas. As imported malaria cases in European countries are reported every year, the risk of Plasmodium introduction by gametocyte carriers among travellers from endemic countries should be taken into greater consideration. Our findings allow rethinking and building new models for the prediction and expansion of introduced malaria. Furthermore, to prevent the risk of reintroduction of the disease, the need to strengthen the surveillance of residual anophelism throughout the South should be considered.
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Affiliation(s)
- Donato Antonio Raele
- Istituto Zooprofilattico Sperimentale della Puglia e Della Basilicata, Via Manfredonia, 20, 71121, Foggia, Italia.
| | - Francesco Severini
- Dipartimento di Malattie Infettive, Reparto di Malattie Trasmesse da Vettori, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italia
| | - Luciano Toma
- Dipartimento di Malattie Infettive, Reparto di Malattie Trasmesse da Vettori, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italia
| | - Michela Menegon
- Dipartimento di Malattie Infettive, Reparto di Malattie Trasmesse da Vettori, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italia
| | - Daniela Boccolini
- Dipartimento di Malattie Infettive, Reparto di Malattie Trasmesse da Vettori, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italia
| | - Giovanni Tortorella
- Azienda Sanitaria Nazionale (ASL), Servizio Veterinario Sanità Animale, Viale Don Minzoni N. 8, 73100, Lecce, Italia
| | - Marco Di Luca
- Dipartimento di Malattie Infettive, Reparto di Malattie Trasmesse da Vettori, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161, Rome, Italia
| | - Maria Assunta Cafiero
- Istituto Zooprofilattico Sperimentale della Puglia e Della Basilicata, Via Manfredonia, 20, 71121, Foggia, Italia
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Sharma D, Wilson C, Kumar S, Ghose S, Sahoo R, Sharawat SK. Does presence of complex translocations involving BCR::ABL1 in chronic myeloid leukemia affect the response rate to tyrosine kinase inhibitors? A systematic review of the literature. Ann Diagn Pathol 2024; 71:152303. [PMID: 38636337 DOI: 10.1016/j.anndiagpath.2024.152303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 04/20/2024]
Abstract
Philadelphia (Ph) chromosome (9;22)(q34;q11) comprises 90-95 % of chronic myeloid leukemia (CML), while 5-10 % of CML have translocations involving three or more chromosomes. The outcome of treating patients harbouring complex Ph-positive cytogenetics with tyrosine kinase inhibitors (TKI) is unclear. In the present systematic review, we aim to summarise the response of patients with complex Ph-positive cytogenetics to treatment with TKI therapy. We collated all available literature from databases such as PubMed, Google Scholar, Web of Science database, Cochrane library, Scopus and Embase (up until January 31st, 2024), which describe cases of patients with CML, harbouring complex Ph-positive variations (three and four-way translocations), and summarised their response to TKI therapy. The studies were screened for the following criteria: documented TKI intervention and outcome (whether CR was achieved). Studies that did not report the same, were excluded. Additionally, we report a case from our center of a 55-year-old patient with CML, positive for the Ph-chromosome, harbouring a three-way translocation involving chromosome 15 i.e. 46XX, t(9;15;22) (q34;p11;q11). Identification of BCR::ABL and involvement of chromosome 15 was carried out using conventional cytogenetics, fluorescence in situ hybridization (FISH), and quantitative PCR (qPCR). Based on the inclusion criteria, a total of 15 studies were included from which a total of 87 cases were covered. Overall, we identified 38 unique complex three- and four-way translocations across 87 Ph-positive cases and found that 85 patients with complex Ph-positive cytogenetics achieved complete remission upon treatment and did not appear to have a lesser response to TKI therapy.
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Affiliation(s)
- Diwakar Sharma
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Christine Wilson
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Kumar
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Sampa Ghose
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Ranjit Sahoo
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India
| | - Surender K Sharawat
- Department of Medical Oncology, Dr.B.R.A. I.R.C.H., All India Institute of Medical Sciences, New Delhi, India.
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Moorhead KA, Adamovicz LA, Allender MC. Development and analytical validation of a novel quantitative PCR assay for the detection of Trachemys herpesvirus 1. J Virol Methods 2024; 327:114941. [PMID: 38599248 DOI: 10.1016/j.jviromet.2024.114941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Emerging infectious diseases are a threat that contributes to the decline of global chelonian species. Herpesviruses are among the most impactful pathogens described in chelonians and are frequently associated with a range of presentations across hosts with the potential for severe morbidity and mortality. Trachemys herpesvirus 1 (TrHV1) has been reported in red-eared and yellow-bellied sliders (Trachemys scripta elegans and Trachemys scripta scripta, respectively) but is largely understudied. Invasive red-eared sliders may serve as a reservoir for transmission to sympatric native species. This study aimed to develop a sensitive and specific quantitative real-time PCR (qPCR) assay for the detection of TrHV1 DNA to aid in the characterization of the epidemiology of this virus in aquatic turtles. Two TaqMan-MGB FAM-dye labeled primer-probe sets were designed and evaluated using plasmid dilutions. The higher performing assay was specific for TrHV1 DNA and had a linear dynamic range of 1.0 × 107 to 1.0 × 101 copies per reaction with an R2 of 0.999, slope of -3.386, and efficiency of 97.39%. The limit of detection was 101 copies per reaction, and there was no loss of reaction efficiency in the presence of TrHV1-negative chelonian oral-cloacal DNA. Overall, the Trachemys herpesvirus 1 assay meets established criteria for acceptable qPCR assays and will be a valuable tool in characterizing the epidemiology of Trachemys herpesvirus 1 in chelonians.
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Affiliation(s)
- Kaitlin A Moorhead
- Wildlife Epidemiology Lab, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA.
| | - Laura A Adamovicz
- Wildlife Epidemiology Lab, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA; Veterinary Diagnostic Lab, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
| | - Matthew C Allender
- Wildlife Epidemiology Lab, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA; Veterinary Diagnostic Lab, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA; Brookfield Zoo, Chicago Zoological Society, Brookfield, IL 60513, USA
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Sun H, Zheng J, Zhang Q, Ying F, Fu Y, Guan Y, Wu J, Zhou Y, Dong J, Xu M, Yang F, An N, Shi N, Zhang L, Zhu S, Liu J, Li M. Screening of Spinal Muscular Atrophy Carriers and Prenatal Diagnosis in Pregnant Women in Yancheng, China. Biochem Genet 2024:10.1007/s10528-024-10775-9. [PMID: 38581475 DOI: 10.1007/s10528-024-10775-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/06/2024] [Indexed: 04/08/2024]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder with an autosomal recessive inheritance pattern. Patients with severe symptoms may suffer respiratory failure, leading to death. The homozygous deletion of exon 7 in the SMN1 gene accounts for nearly 95% of all cases. Population carrier screening for SMA and prenatal diagnosis by amniocentesis for high-risk couples can assist in identifying the risk of fetal disease. We provided the SMA carrier screening process to 55,447 pregnant women in Yancheng from October 2020 to December 2022. Among them, 8185 participated in this process, with a participation rate of around 14.76% (95% CI 14.47-15.06%). Quantitative real-time polymerase chain reaction (qPCR) was used to detect deletions of SMN1 exons 7 and 8 (E7, E8) in screened pregnant women. 127 were identified as carriers (111 cases of E7 and E8 heterozygous deletions, 15 cases of E7 heterozygous deletions, and 1 case of E7 heterozygous deletions and E8 homozygous deletions), resulting in a carrying rate of around 1.55% (95% CI 1.30-1.84%). After genetic counseling, 114 spouses of pregnant women who tested positive underwent SMA carrier screening; three of them were screened as SMA carriers. Multiplexed ligation-dependent probe amplification (MLPA) was used for the prenatal diagnosis of the fetuses of high-risk couples. Two of them exhibited two copies of SMN1 exon 7 (normal), and the pregnancy was continued; one exhibited no copies of SMN1 exon 7 and exon 8 (SMA patient), and the pregnancy was terminated. Analyzing SMN1 mutations in Yancheng and provide clinical evidence for SMA genetic counseling and birth defect prevention. Interventional prenatal diagnosis for high-risk families can promote informed reproductive selection and prepare for the fetus's early treatment.
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Affiliation(s)
- Huilin Sun
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jianli Zheng
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Qing'e Zhang
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Feifei Ying
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Yadong Fu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Yongjuan Guan
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jing Wu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Yueyun Zhou
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jingjing Dong
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Mengjun Xu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Fangfang Yang
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Ning An
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Ning Shi
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Lu Zhang
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Shu Zhu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China
| | - Jianbing Liu
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China.
| | - Min Li
- The Affiliated Yancheng Maternity&Child Health Hospital of Yangzhou University Medical School, Yancheng, 224001, China.
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Teng F, Sun X, Ran Y, Liu C, Shi H, Tian Y. Role of Radiation-related Lung Function Genes in Prognosis and Immune Infiltration of Lung Adenocarcinoma. Comb Chem High Throughput Screen 2024; 27:CCHTS-EPUB-139562. [PMID: 38584564 DOI: 10.2174/0113862073275640231228124547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 04/09/2024]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a common malignant tumor with no obvious clinical symptoms in its early stages. Patients can be divided into radiotherapysensitive groups (RS) and radiotherapy-resistant groups (RR) due to their varying conditions. The therapeutic effect of radiotherapy is quite different between the two groups. Therefore, this paper explores the role of radiation-related lung function genes in LUAD and its immune landscape. METHODS Firstly, we divided LUAD samples from the TCGA cohort into RS and RR groups and analyzed differential expression to obtain differentially expressed genes (DEGs). Then, DEGs and patients' grouping information were input into the weighted co-expression network, and the genes in the radiotherapy-related modules were identified. Furthermore, after the intersection of DEGs and lung function-related genes, the prognosis-related genes were obtained through univariate Cox and Lasso-Cox analyses, respectively, and the risk model was constructed. Finally, the differences in prognosis and immunity of the samples in the risk model were explored. Additionally, we also performed a qPCR experiment on lung function-related genes. RESULTS In this paper, radiation-related genes of LUAD were identified through a series of bioinformatics analyses. By conducting enrichment analysis on these genes, several pathways related to LUAD radiation were identified, and DEGs associated with significant prognosis were determined. Furthermore, a radiation-related risk model of LUAD was developed. All samples were divided into high-risk and low-risk groups based on the risk score, and the differences in immune cell infiltration abundance and immune function between these groups were evaluated. The qPCR experimental results demonstrated a significant difference in the expression of genes related to lung function. CONCLUSION The prognosis-related genes identified in this paper and the risk model created can serve as a reference for diagnosing and treating LUAD.
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Affiliation(s)
- Fei Teng
- Department of Radiotherapy, Affiliated Hospital of Hebei University, Baoding, China
| | - Xiaojing Sun
- Department of Radiotherapy, Affiliated Hospital of Hebei University, Baoding, China
| | - Yuge Ran
- Department of Radiotherapy, Affiliated Hospital of Hebei University, Baoding, China
| | - Chan Liu
- Department of Radiotherapy, Affiliated Hospital of Hebei University, Baoding, China
| | - Hongyun Shi
- Department of Radiotherapy, Affiliated Hospital of Hebei University, Baoding, China
| | - Yuan Tian
- Department of Radiotherapy, Affiliated Hospital of Hebei University, Baoding, China
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Kissmann AK, Bolotnikov G, Li R, Müller F, Xing H, Krämer M, Gottschalk KE, Andersson J, Weil T, Rosenau F. IMPATIENT- qPCR: monitoring SELEX success during in vitro aptamer evolution. Appl Microbiol Biotechnol 2024; 108:284. [PMID: 38573322 PMCID: PMC10995058 DOI: 10.1007/s00253-024-13085-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 04/05/2024]
Abstract
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high-affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC content and Tm alone with a round-wise increase of aptamer affinity to the respective target. Based on nine successful and published previous SELEX processes, in which the evolution/selection of aptamer affinity/specificity was demonstrated, we here show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general. IMPATIENT-qPCR SELEX success monitoring. Selection and evolution of high-affinity aptamers using SELEX technology with direct aptamer evolution monitoring using melting curve shifting analyses to higher Tm by quantitative PCR with fluorescence dye SYBR Green I. KEY POINTS: • Fast and easy analysis. • Universal applicability shown for a series of real successful projects.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Grigory Bolotnikov
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Runliu Li
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Franziska Müller
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Kay-E Gottschalk
- Institute of Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Jakob Andersson
- AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210, Vienna, Austria
| | - Tanja Weil
- Max Planck Institute for Polymer Research Mainz, Ackermannweg 10, 55128, Mainz, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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Sangha JS, Barrett P, Curtis TP, Métris A, Jakubovics NS, Ofiteru ID. Effects of glucose and lactate on Streptococcus mutans abundance in a novel multispecies oral biofilm model. Microbiol Spectr 2024; 12:e0371323. [PMID: 38376204 PMCID: PMC10986578 DOI: 10.1128/spectrum.03713-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
The oral microbiome plays an important role in protecting oral health. Here, we established a controlled mixed-species in vitro biofilm model and used it to assess the impact of glucose and lactate on the ability of Streptococcus mutans, an acidogenic and aciduric species, to compete with commensal oral bacteria. A chemically defined medium was developed that supported the growth of S. mutans and four common early colonizers of dental plaque: Streptococcus gordonii, Actinomyces oris, Neisseria subflava, and Veillonella parvula. Biofilms containing the early colonizers were developed in a continuous flow bioreactor, exposed to S. mutans, and incubated for up to 7 days. The abundance of bacteria was estimated by quantitative polymerase chain reaction (qPCR). At high glucose and high lactate, the pH in bulk fluid rapidly decreased to approximately 5.2, and S. mutans outgrew other species in biofilms. In low glucose and high lactate, the pH remained above 5.5, and V. parvula was the most abundant species in biofilms. By contrast, in low glucose and low lactate, the pH remained above 6.0 throughout the experiment, and the microbial community in biofilms was relatively balanced. Fluorescence in situ hybridization confirmed that all species were present in the biofilm and the majority of cells were viable using live/dead staining. These data demonstrate that carbon source concentration is critical for microbial homeostasis in model oral biofilms. Furthermore, we established an experimental system that can support the development of computational models to predict transitions to microbial dysbiosis based on metabolic interactions.IMPORTANCEWe developed a controlled (by removing host factor) dynamic system metabolically representative of early colonization of Streptococcus mutans not measurable in vivo. Hypotheses on factors influencing S. mutans colonization, such as community composition and inoculation sequence and the effect of metabolite concentrations, can be tested and used to predict the effect of interventions such as dietary modifications or the use of toothpaste or mouthwash on S. mutans colonization. The defined in vitro model (species and medium) can be simulated in an in silico model to explore more of the parameter space.
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Affiliation(s)
- Jay S. Sangha
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Paul Barrett
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, United Kingdom
| | - Thomas P. Curtis
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Aline Métris
- Safety and Environmental Assurance Centre, Unilever, Colworth Science Park, Sharnbrook, United Kingdom
| | - Nicholas S. Jakubovics
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Irina D. Ofiteru
- School of Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
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Acheamfour CL, Parveen S, Gutierrez A, Handy ET, Behal S, Kim D, Kim S, East C, Xiong R, Haymaker JR, Micallef SA, Rosenberg Goldstein RE, Kniel KE, Sapkota AR, Hashem F, Sharma M. Detection of Salmonella enterica and Listeria monocytogenes in alternative irrigation water by culture and qPCR-based methods in the Mid-Atlantic U.S. Microbiol Spectr 2024; 12:e0353623. [PMID: 38376152 PMCID: PMC10986563 DOI: 10.1128/spectrum.03536-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
Alternative irrigation waters (rivers, ponds, and reclaimed water) can harbor bacterial foodborne pathogens like Salmonella enterica and Listeria monocytogenes, potentially contaminating fruit and vegetable commodities. Detecting foodborne pathogens using qPCR-based methods may accelerate testing methods and procedures compared to culture-based methods. This study compared detection of S. enterica and L. monocytogenes by qPCR (real-time PCR) and culture methods in irrigation waters to determine the influence of water type (river, pond, and reclaimed water), season (winter, spring, summer, and fall), or volume (0.1, 1, and 10 L) on sensitivity, accuracy, specificity, and positive (PPV), and negative (NPV) predictive values of these methods. Water samples were collected by filtration through modified Moore swabs (MMS) over a 2-year period at 11 sites in the Mid-Atlantic U.S. on a bi-weekly or monthly schedule. For qPCR, bacterial DNA from culture-enriched samples (n = 1,990) was analyzed by multiplex qPCR specific for S. enterica and L. monocytogenes. For culture detection, enriched samples were selectively enriched, isolated, and PCR confirmed. PPVs for qPCR detection of S. enterica and L. monocytogenes were 68% and 67%, respectively. The NPV were 87% (S. enterica) and 85% (L. monocytogenes). Higher levels of qPCR/culture agreement were observed in spring and summer compared to fall and winter for S. enterica; for L. monocytogenes, lower levels of agreement were observed in winter compared to spring, summer, and fall. Reclaimed and pond water supported higher levels of qPCR/culture agreement compared to river water for both S. enterica and L. monocytogenes, indicating that water type may influence the agreement of these results. IMPORTANCE Detecting foodborne pathogens in irrigation water can inform interventions and management strategies to reduce risk of contamination and illness associated with fresh and fresh-cut fruits and vegetables. The use of non-culture methods like qPCR has the potential to accelerate the testing process. Results indicated that pond and reclaimed water showed higher levels of agreement between culture and qPCR methods than river water, perhaps due to specific physiochemical characteristics of the water. These findings also show that season and sample volume affect the agreement of qPCR and culture results. Overall, qPCR methods could be more confidently utilized to determine the absence of Salmonella enterica and Listeria monocytogenes in irrigation water samples examined in this study.
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Affiliation(s)
- Chanelle L. Acheamfour
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
- Department of Biological Sciences, Delaware State University, Dover, Delaware, USA
| | - Salina Parveen
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Alan Gutierrez
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Eric T. Handy
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Sara Behal
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Donghyun Kim
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Seongyun Kim
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
- Department of Environmental System Engineering, Chonnam National University, Yeosu, Republic of Korea
| | - Cheryl East
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
| | - Ray Xiong
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
| | - Joseph R. Haymaker
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Shirley A. Micallef
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland, USA
| | - Rachel E. Rosenberg Goldstein
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Kalmia E. Kniel
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware, USA
| | - Amy R. Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Maryland, USA
| | - Fawzy Hashem
- Department of Natural Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA
| | - Manan Sharma
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Environmental Microbial and Food Safety Laboratory, Beltsville, Maryland, USA
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Opmeer L, Gazzoli I, Ballmann M, Willemsen M, Voshol GP, Grudniewska-Lawton M, Havenga M, Yallop C, Hamidi A, Gillissen G, Bakker WAM. High throughput AS LNA qPCR method for the detection of a specific mutation in poliovirus vaccine strains. Vaccine 2024; 42:2475-2484. [PMID: 38503660 PMCID: PMC11007389 DOI: 10.1016/j.vaccine.2024.01.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/21/2023] [Accepted: 01/30/2024] [Indexed: 03/21/2024]
Abstract
Sabin Inactivated Poliovirus Vaccine (sIPV) has become one of the preferred vaccination options for the last step in the Poliovirus eradication program. Sequencing of poliovirus samples is needed during the manufacturing of poliovirus vaccines to assure the safety and immunogenicity of these vaccines. Next-generation sequencing analysis is the current costly and time-consuming gold standard for monitoring the manufacturing processes. We developed a low-cost and quick, highly sensitive, and allele-specific locked nucleic acid-probe-based reverse transcription quantitative PCR alternative that can accurately detect mutations in poliovirus vaccine samples during process development, scaling up, and release. Using the frequently in vitro occurring and viral replication-impacting VP1-E295K mutation as a showcase, we show that this technology can accurately detect E295K mutations in poliovirus 2 samples to similar levels as NGS. The qPCR technology was developed employing a synthetic dsDNA fragment-based standard curve containing mixes of E295K-WT (wildtype) and Mut (mutant) synthetic dsDNA fragments ranging from 1 × 107 copies/µL to 1 × 102 copies/µL to achieve a linear correlation with R2 > 0.999, and PCR efficiencies of 95-105 %. Individual standard concentration levels achieved accuracies of ≥92 % (average 96 %) and precisions of ≤17 % (average 3.3 %) RSD. Specificity of locked nucleic acid (LNA)-probes was confirmed in the presence and absence of co-mutations in the probe-binding region. Application of the developed assay to Sabin Poliovirus type 2 production run samples, illustrated a linear relationship with an R2 of 0.994, and an average accuracy of 97.2 % of the variant (allele)-specific AS LNA qPCR result, compared to NGS. The assay showed good sensitivity for poliovirus samples, containing E295K mutation levels between 0 % and 95 % (quantification range). In conclusion, the developed AS LNA qPCR presents a valuable low-cost, and fast tool, suitable for the process development and quality control of polio vaccines.
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Affiliation(s)
- Lizet Opmeer
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Isabella Gazzoli
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Mónika Ballmann
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Marieke Willemsen
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Gerben P Voshol
- GenomeScan B.V., Plesmanlaan 1d, 2333 BZ Leiden, The Netherlands
| | | | - Menzo Havenga
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Christopher Yallop
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Ahd Hamidi
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Gert Gillissen
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands
| | - Wilfried A M Bakker
- Batavia Biosciences B.V., Bioscience Park Leiden, Zernikedreef 16, 2333CL Leiden, The Netherlands.
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48
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Lameira I, Pinto AS, Lima Â, Muzny CA, Cerca N. Optimized bacterial absolute quantification method by qPCR using an exogenous bacterial culture as a normalization strategy in triple-species BV-like biofilms. J Microbiol Methods 2024; 219:106895. [PMID: 38331102 DOI: 10.1016/j.mimet.2024.106895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/04/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Quantitative Polymerase Chain Reaction (qPCR) is a widely used method in molecular biology to quantify target DNA sequences. Despite its accuracy, there are important experimental controls that should be considered to avoid biased results. One of them is gDNA loss during extraction, which is higher among samples with lower bacterial concentrations. Improvement in qPCR quantification procedures is mandatory to obtain reproducible and accurate results. Herein, we report an improved qPCR method for bacterial quantification of Gardnerella vaginalis, Prevotella bivia, and Fannyhessea vaginae, three key-bacterial vaginosis (BV)-associated bacteria (BVAB) thought to play important roles in the pathogenesis of this common vaginal infection. The formation of a mature biofilm on vaginal epithelial cells is an unique feature of BV and, despite over 60 years of research, the exact etiology of BV remains unknown. Here, we optimized a qPCR method that accurately quantified triple-species biofilms containing these key BVAB, after the addition of an exogenous bacterial control containing a fixed concentration of Escherichia coli, prior to gDNA extraction. This improved method minimized and normalized the inherent losses associated with bacterial centrifugation, which allows better sensitivity at lower bacterial concentrations.
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Affiliation(s)
- Inês Lameira
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Ana S Pinto
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Ângela Lima
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal
| | - Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Nuno Cerca
- Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho, Campus de Gualtar, Braga, Portugal; LABBELS -Associate Laboratory, Braga, Guimarães, Portugal.
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49
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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50
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Leutenegger CM, Evason MD, Willcox JL, Rochani H, Richmond HL, Meeks C, Lozoya CE, Tereski J, Loo S, Mitchell K, Andrews J, Savard C. Benzimidazole F167Y polymorphism in the canine hookworm, Ancylostoma caninum: Widespread geographic, seasonal, age, and breed distribution in United States and Canada dogs. Int J Parasitol Drugs Drug Resist 2024; 24:100520. [PMID: 38237210 PMCID: PMC10825515 DOI: 10.1016/j.ijpddr.2024.100520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024]
Abstract
Surveillance data for Ancylostoma spp. and the A. caninum benzimidazole treatment resistance associated F167Y polymorphism using molecular diagnostics was obtained in a large population of dogs from the United States and Canada. Real-time PCR (qPCR) for Ancylostoma spp. and allele-specific qPCR detecting a single nucleotide polymorphism (SNP) F167Y was used in 262,872 canine stool samples collected between March and December of 2022. Ancylostoma spp. was found at an overall prevalence of 2.5% (6538/262,872), with the highest prevalence in the Southern US, 4.4% (4490/103,095), and the lowest prevalence in Canada 0.6% (101/15,829). The A. caninum F167Y polymorphism was found with the highest prevalence (13.4%, n = 46/343) in the Western US and the lowest in Canada at 4.1% (4/97). The F167Y polymorphism was detected every month over the 10-month collection period. Seasonal distribution showed a peak in June for both Ancylostoma spp. (3.08%, 547/17,775) and A. caninum F167Y (12.25%, 67/547). However, the A. caninum F167Y polymorphism prevalence was highest in September (13.9%, 119/856). Age analysis indicates a higher prevalence of both hookworm infections and occurrence of resistant isolates in puppies. The breeds with the highest F167Y polymorphism prevalence in Ancylostoma spp. detected samples were poodles (28.9%), followed by Bernese Mountain dogs (25%), Cocker spaniels (23.1%), and greyhounds (22.4%). Our data set describes widespread geographic distribution of the A. caninum benzimidazole resistance associated F167Y polymorphism in the United States and Canada, with no clear seasonality compared to the Ancylostoma spp. prevalence patterns. The F167 polymorphism was present in all geographic areas with detected hookworms, including Canada. Our study highlights that the F167Y polymorphism is represented in many dog breeds, including greyhounds.
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Affiliation(s)
| | | | | | | | | | - Cathy Meeks
- Antech Diagnostics, Fountain Valley, CA, USA
| | | | | | | | | | - Jan Andrews
- Antech Diagnostics, Fountain Valley, CA, USA
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