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Suwannapoom C, Osathanunkul M. Distinguishing fanged frogs (Limnonectes) species (Amphibia: Anura: Dicroglossidae), from Thailand using high resolution melting analysis. Sci Rep 2023; 13:18615. [PMID: 37903792 PMCID: PMC10616069 DOI: 10.1038/s41598-023-43637-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/26/2023] [Indexed: 11/01/2023] Open
Abstract
Morphologically, species of fanged frogs (Limnonectes) are exceedingly similar, making it difficult to distinguish them within the complex. In Thailand, it has been difficult to distinguish between the sympatric species L. bannaensis and L. taylori, particularly among tadpoles, adolescents, and adult females. A precise identification contributes to a greater understanding of biodiversity, particularly for assessing distributions and population dynamics. Therefore, a novel approach is required. The objective of this study was to develop a high resolution melting analysis (HRM) for the rapid and accurate identification of six species of Limnonectes of the L. kuhlii complex found in Thailand, particularly the two sympatric fanged frogs. Here, HRM assays using 16S rRNA mitochondrial primers were designed and developed. There was as much as a 25.3% variation in the nucleotide sequence of the fragment amplified by HRM16S primers among the six species of Limnonectes. Prior to conducting an in vitro HRM, the DNA sequences were used in a simulation HRM, uMELT Quartz, to predict the melting curve for each species of Limnonectes. There were discrepancies between the predicted melting curves of each species generated by the programme. Consequently, in vitro HRM tests were conducted. The obtained melting curve and Tm values were consistent with those predicted, albeit with a slightly different Tm value and a more distinct melting curve. All evaluated species of Limnonectes could be easily distinguished from one another by comparing the melting curve shapes. The HRM assay was then used to confirm the species of 18 Limnonectes samples in comparison to the reference samples (confidence interval > 90%). In addition, the results of HRM were consistent with those of experts who used morphological analysis to identify species. The HRM was found to be useful, and therefore the method would also contribute to future ecological and systematic studies on the target species.
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Affiliation(s)
- Chatmongkon Suwannapoom
- School of Agriculture and Natural Resources, University of Phayao, Muang District, Phayao, Thailand
| | - Maslin Osathanunkul
- Department of Biology, Faculty of Science, Chiang Mai University, Muang District, Chiang Mai, 50200, Thailand.
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2
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Pakbin B, Basti AA, Khanjari A, Brück WM, Azimi L, Karimi A. Development of high-resolution melting (HRM) assay to differentiate the species of Shigella isolates from stool and food samples. Sci Rep 2022; 12:473. [PMID: 35013489 PMCID: PMC8748861 DOI: 10.1038/s41598-021-04484-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/23/2021] [Indexed: 11/09/2022] Open
Abstract
Shigella species, a group of intracellular foodborne pathogens, are the main causes of bacillary dysentery and shigellosis in humans worldwide. It is essential to determine the species of Shigella in outbreaks and food safety surveillance systems. The available immunological and molecular methods for identifying Shigella species are relatively complicated, expensive and time-consuming. High resolution melting (HRM) assay is a rapid, cost-effective, and easy to perform PCR-based method that has recently been used for the differentiation of bacterial species. In this study, we designed and developed a PCR-HRM assay targeting rrsA gene to distinguish four species of 49 Shigella isolates from clinical and food samples and evaluated the sensitivity and specificity of the assay. The assay demonstrated a good analytical sensitivity with 0.01–0.1 ng of input DNA template and an analytical specificity of 100% to differentiate the Shigella species. The PCR-HRM assay also was able to identify the species of all 49 Shigella isolates from clinical and food samples correctly. Consequently, this rapid and user-friendly method demonstrated good sensitivity and specificity to differentiate species of the Shigella isolates from naturally contaminated samples and has the potential to be implemented in public health and food safety surveillance systems.
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Affiliation(s)
- Babak Pakbin
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Sierre, Switzerland.,Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box: 14155-6453, Tehran, Iran
| | - Afshin Akhondzadeh Basti
- Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box: 14155-6453, Tehran, Iran.
| | - Ali Khanjari
- Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box: 14155-6453, Tehran, Iran
| | - Wolfram Manuel Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Sierre, Switzerland
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute of Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute of Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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3
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Pakbin B, Basti AA, Khanjari A, Azimi L, Brück WM, Karimi A. RAPD and ERIC-PCR coupled with HRM for species identification of non-dysenteriae Shigella species; as a potential alternative method. BMC Res Notes 2021; 14:345. [PMID: 34479650 PMCID: PMC8414663 DOI: 10.1186/s13104-021-05759-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
Objective Species identification of Shigella isolates are so prominent for epidemiological studies and infection prevention strategies. We developed and evaluated RAPD and ERIC-PCR coupled with HRM for differentiation of non-dysenteriae Shigella species as potential alternative methods. After isolation of eighteen Shigella strains from faecal specimens collected from children under 2 years of age with diarrhea (n = 143), the species of the isolates were identified by slide agglutination assay. Also, species were identified using developed RAPD-PCR-HRM and ERIC-PCR-HRM techniques. Differentiation of the data sets was measured by principal component analysis as a dimension reduction method. Then, sensitivity and specificity of the methods were evaluated. Results We found RAPD-PCR-HRM method with high sensitivity and specificity (100 and 85% respectively) to identify non-dysenteriae Shigella species in clinical specimens. However, sensitivity and specificity of ERIC-PCR-HRM were evaluated 33 and 46% respectively and significantly lower than that of RAPD-PCR-HRM assay. Regardless of inherent poor reproducibility of DNA fingerprinting-based methods, RAPD-PCR-HRM assay can be considered as a potential alternative method to identify non-dysenteriae species of Shigella in clinical specimens. As we observed in the current study, HRM technique is more rapid, inexpensive, and sensitive than gel electrophoresis method to characterize PCR amplicons.
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Affiliation(s)
- Babak Pakbin
- Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box 14155-6453, Tehran, Iran.,Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Sierre, Switzerland
| | - Afshin Akhondzadeh Basti
- Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box 14155-6453, Tehran, Iran.
| | - Ali Khanjari
- Department of Food Hygiene and Quality of Control, Faculty of Veterinary Medicine, University of Tehran, P.O. Box 14155-6453, Tehran, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute of Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Wolfram Manuel Brück
- Institute for Life Technologies, University of Applied Sciences Western Switzerland Valais-Wallis, 1950 Sion 2, Sierre, Switzerland
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute of Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Gazali FM, Nuhamunada M, Nabilla R, Supriyati E, Hakim MS, Arguni E, Daniwijaya EW, Nuryastuti T, Haryana SM, Wibawa T, Wijayanti N. Detection of SARS-CoV-2 spike protein D614G mutation by qPCR-HRM analysis. Heliyon 2021; 7:e07936. [PMID: 34514180 PMCID: PMC8420086 DOI: 10.1016/j.heliyon.2021.e07936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES Monitoring the spread of the G614 in specific locations is critical as this variant is highly transmissible and can trigger the emergence of other mutations. Therefore, a rapid and accurate method that can reliably detect the D614G mutation will be beneficial. This study aims to analyze the potential use of the two-step Reverse Transcriptase quantitative polymerase chain reaction - high resolution melting analysis (RT-qPCR-HRM) to detect a specific mutation in the SARS-CoV-2 genome. METHODS Six SARS-CoV-2 RNA samples were synthesized into cDNA and analyzed with the qPCR-HRM method in order to detect the D614G mutation in Spike protein of SARS-CoV-2. The primers are designed to target the specific Spike region containing the D614G mutation. The qPCR-HRM analysis was conducted simultaneously, and the identification of the SARS-CoV-2 variant was confirmed by conventional PCR and Sanger sequencing methods. RESULTS The results showed that the melting temperature (Tm) of the D614 variant was 79.39 ± 0.03 °C, which was slightly lower than the Tm of the G614 variant (79.62 ± 0.015 °C). The results of the HRM analysis, visualized by the normalized melting curve and the difference curve were able to discriminate the D614 and G614 variant samples. All samples were identified as G614 variants by qPCR-HRM assay, which was subsequently confirmed by Sanger sequencing. CONCLUSIONS This study demonstrated a sensitive method that can identify the D614G mutation by a simple two-step RT-qPCR-HRM assay procedure analysis, which can be useful for active surveillance of the transmission of a specific mutation.
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Affiliation(s)
- Faris Muhammad Gazali
- Master Program in Biotechnology Study Program, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Diagnostic Laboratory of World Mosquito Program (WMP), Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Edwin Widyanto Daniwijaya
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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Unnikrishnan R, Dev SA, Jayaraj R. Pitfalls and promises of raw drug identification techniques in the ayurvedic industry: an overview. 3 Biotech 2020; 10:497. [PMID: 33150123 DOI: 10.1007/s13205-020-02482-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/13/2020] [Indexed: 11/26/2022] Open
Abstract
India, with a rich heritage of floral diversity, is well-known for its medicinal plant wealth and is the largest producer of medicinal herbs in the world. Ethnobiological Survey of Ministry of Environment and Forests (MOEF) could identify 8000 plant species utilized in various systems of medicine with approximately 25,000 effective herbal formulations. The extensive consumption to meet demand-supply ratio exerts a heavy strain on the existing resources. This subsequently led to the adulteration and substitution of medicinal plants with look-alike species. The consumer's faith on herbal medicine is in the phase of decline due to the extremities in adulteration/substitution and ensuing consequences. It is imperative to bring forth universally acceptable standard tools to authenticate raw drugs before being processed further into formulations. A vast array of techniques such as physical, chemical (analytical), biochemical, anatomical, organoleptic, and recently emerged DNA based molecular methods are widely used for plant species authentication. In recent years, DNA barcoding has made remarkable progress in the field of medicinal plants research. DNA metabarcoding is the latest development for qualitative evaluation of the herbal formulations, whereas for quantitative analysis, combination of pharmacognostic, pharmacovigilance and analytical methods are inevitable for authentication. This review addresses the overall strengths and shortcomings of the existing as well as recently emerged techniques in authenticating ayurvedic raw drugs.
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Affiliation(s)
- Remya Unnikrishnan
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
- Cochin University of Science & Technology, Kochi, Kerala India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
| | - R Jayaraj
- Forest Ecology and Biodiversity Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala India
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6
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A high-resolution melting analysis method for the effective discrimination of three Sepia species. J Verbrauch Lebensm 2020. [DOI: 10.1007/s00003-020-01289-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Cai S, Xu J, Shao Y, Gong J, Zhao F, He L, Shan X. Rapid identification of the Candida glabrata species complex by high-resolution melting curve analysis. J Clin Lab Anal 2020; 34:e23226. [PMID: 32048348 PMCID: PMC7307358 DOI: 10.1002/jcla.23226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/13/2019] [Accepted: 01/07/2020] [Indexed: 02/02/2023] Open
Abstract
Background Candida glabrata is a common pathogen that causes invasive candidiasis. Among non‐albicans Candida infections, C glabrata infections are associated with the highest fatality rates. Candida glabrata sensu stricto, Candida nivariensis, and Candida bracarensis have been identified and together form the C glabrata species complex. It is difficult to detect the two rare species by traditional laboratory methods. This study established a method for the rapid identification of members of the C glabrata species complex based on high‐resolution melting curve (HRM) analysis and evaluated its practical application. Methods The internal transcribed spacer (ITS) region was used as target gene region to design specific primers. HRM analysis was performed with three subspecies of the C glabrata species complex and negative controls to test its specificity and sensitivity. To evaluate its practical application, the HRM technique was tested with clinical isolates, and the results were compared with the DNA sequencing results. Results Differences were detected among the melting profiles of the members of the C glabrata species complex. The negative controls were not amplified, indicating the high specificity of the method. The minimum detection limits of C glabrata sensu stricto, C nivariensis, and C bracarensis were approximately 1 × 101 copies/µL or less. The results of the HRM analysis of the clinical isolates were consistent with the DNA sequencing results. Conclusions The HRM method is sensitive and can be used to rapidly identify the members of the C glabrata species complex. The method can allow early and targeted treatment of patients with invasive candidiasis.
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Affiliation(s)
- Shuqian Cai
- Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Zhejiang, China.,State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Juan Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,School of Public Health, Wuhan University of Science and Technology, Hubei, China
| | - Yakun Shao
- Department of Dermatology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jie Gong
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fei Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lihua He
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoyun Shan
- Department of Clinical Laboratory, Jinhua Municipal Central Hospital, Zhejiang, China
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8
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Ahani Azari A, Amanollahi R, Jafari Jozani R, Trott DJ, Hemmatzadeh F. High-resolution melting curve analysis: a novel method for identification of Mycoplasma species isolated from clinical cases of bovine and porcine respiratory disease. Trop Anim Health Prod 2019; 52:1043-1047. [PMID: 31673887 PMCID: PMC7222993 DOI: 10.1007/s11250-019-02098-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/24/2019] [Accepted: 09/23/2019] [Indexed: 11/22/2022]
Abstract
Mycoplasma species cause wide ranges of infectious diseases in human and animals. The aim of the present study was to evaluate a real-time polymerase chain reaction (RT-PCR) followed by a high-resolution melting curve assay (HRM) for rapid differentiation of Mycoplasma species isolated from clinical cases of bovine and porcine respiratory disease. Lung samples from suspected cases to respiratory infections from cows and pigs were cultured on specific media, and the extracted DNA were tested by conventional polymerase chain reaction (PCR) assays for Mycoplasma. A set of universal primers specific for the 16S ribosomal RNA gene was designed and used for RT-PCR and HRM. The HRM analysis was able to differentiate between five different species of Mycoplasmas, namely, M. hyopneumoniae, M. bovis, M. hyorhinis, M. hyosynoviae and other uncultured Mycoplasma. All results were confirmed based on 16S rRNA gene sequencing. This rapid and reliable assay was as a simple alternative to PCR and sequencing, differentiating bovine and porcine mycoplasmas in species level.
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Affiliation(s)
- Ania Ahani Azari
- Department of Microbiology, Gorgan branch, Islamic Azad University, Gorgan, Iran.
| | - Reza Amanollahi
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | | | - Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, South Australia, Australia.,School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Farhid Hemmatzadeh
- Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, South Australia, Australia.,School of Animal and Veterinary Sciences, Roseworthy Campus, The University of Adelaide, Roseworthy, South Australia, Australia
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9
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Evaluation of a Novel Mitochondrial Pan-Mucorales Marker for the Detection, Identification, Quantification, and Growth Stage Determination of Mucormycetes. J Fungi (Basel) 2019; 5:jof5040098. [PMID: 31614610 PMCID: PMC6958370 DOI: 10.3390/jof5040098] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 02/06/2023] Open
Abstract
Mucormycosis infections are infrequent yet aggressive and serious fungal infections. Early diagnosis of mucormycosis and its discrimination from other fungal infections is required for targeted treatment and more favorable patient outcomes. The majority of the molecular assays use 18 S rDNA. In the current study, we aimed to explore the potential of the mitochondrial rnl (encoding for large-subunit-ribosomal-RNA) gene as a novel molecular marker suitable for research and diagnostics. Rnl was evaluated as a marker for: (1) the Mucorales family, (2) species identification (Rhizopus arrhizus, R. microsporus, Mucor circinelloides, and Lichtheimia species complexes), (3) growth stage, and (4) quantification. Sensitivity, specificity, discriminatory power, the limit of detection (LoD), and cross-reactivity were evaluated. Assays were tested using pure cultures, spiked clinical samples, murine organs, and human paraffin-embedded-tissue (FFPE) samples. Mitochondrial markers were found to be superior to nuclear markers for degraded samples. Rnl outperformed the UMD universal® (Molyzm) marker in FFPE (71.5% positive samples versus 50%). Spiked blood samples highlighted the potential of rnl as a pan-Mucorales screening test. Fungal burden was reproducibly quantified in murine organs using standard curves. Identification of pure cultures gave a perfect (100%) correlation with the detected internal transcribed spacer (ITS) sequence. In conclusion, mitochondrial genes, such as rnl, provide an alternative to the nuclear 18 S rDNA genes and deserve further evaluation.
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Buchheister S, Roegener F, Zschemisch NH, Talbot SR, Christensen H, Bleich A. One for two: A novel and highly sensitive virulence factor-based quantitative polymerase chain reaction assay for the simultaneous detection of Rodentibacter pneumotropicus and Rodentibacter heylii in environmental sample material. Lab Anim 2019; 54:239-250. [PMID: 31195883 DOI: 10.1177/0023677219853600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hygienic monitoring of laboratory rodents has focused more and more on the analysis of environmental sample material by quantitative polymerase chain reaction (qPCR) assays. This approach requires profound knowledge of specific genetic sequences of the agents to be monitored and the assays need to be permanently adapted to take the latest research into account. [Pasteurella] pneumotropica was recently reclassified into the new genus Rodentibacter, with Rodentibacter (R.) pneumotropicus and R. heylii as the most commonly detected species in laboratory mouse colonies. This study aimed at the development of a specific qPCR assay for the simultaneous detection of both agents. A novel primer probe set, based on detection of the specific virulence factor' 'inclusion body protein A' gene (ibpA), was confirmed by testing the assay on currently described Rodentibacter type species and other Pasteurellaceae. Furthermore, it was validated within four different barrier units and results were compared with the cultural analysis of sentinel mice. The assay was suitable to specifically detect R. pneumotropicus and R. heylii and discriminate them from other murine Rodentibacter spp. In addition, it revealed high sensitivity for the detection of both agents in environmental sampling material including exhaust air dust in individually ventilated cage systems. Altogether, higher pathogen prevalence was detected via qPCR of environmental samples compared with cultural diagnostics of sentinel mice. This study describes a qPCR assay for the simultaneous detection of R. pneumotropicus and R. heylii. This assay was demonstrated to be beneficial during routine health monitoring, especially with regard to environmental sampling strategies.
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Affiliation(s)
| | - Florian Roegener
- Institute of Laboratory Animal Science, Hannover Medical School, Germany
| | | | - Steven R Talbot
- Institute of Laboratory Animal Science, Hannover Medical School, Germany
| | - Henrik Christensen
- Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - André Bleich
- Institute of Laboratory Animal Science, Hannover Medical School, Germany
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11
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Design of Melting Curve Analysis (MCA) by Real-Time Polymerase Chain Reaction Assay for Rapid Distinction of Staphylococci and Antibiotic Resistance. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.81604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Adhikary S, Bisgaard M, Boot R, Benga L, Nicklas W, Christensen H. Development of multi locus sequence typing (MLST) of Rodentibacter pneumotropicus. Vet Microbiol 2019; 231:11-17. [PMID: 30955797 DOI: 10.1016/j.vetmic.2019.02.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/04/2019] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
The aim of the investigation was to develop a definitive typing system for Rodentibacter pneumotropicus. A total of 79 strains including the type strain of R. pneumotropicus, all associated with rodents were used to develop a multi-locus sequence typing scheme (MLST). Primers were designed for conserved regions of seven house-keeping genes (atpG, frdB, gdh, pgi, pmi, recA, zwf) and internal fragments of 399-839 bp were sequenced for all strains. The genes were also extracted in full length from whole genomic sequences of 14 strains of which 10 were sequenced in the current study. The number of alleles at the different loci ranged from 5 to 7 and a total of 20 allelic profiles or sequence types were recognized amongst the 79 strains. Analysis of the MLST data showed that some STs have been stable over many years probably circulating in the same colonies and probably transferred between colonies. We assume that this MLST scheme may provide a high level of resolution and might be an excellent tool for studying the population structure and epidemiology of R. pneumotropicus. Further development of the scheme is expected by including more genes and more strains and involve whole genomic sequencing.
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Affiliation(s)
- Sadhana Adhikary
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Ron Boot
- mr. Tripkade 51, 3571SW Utrecht, the Netherlands
| | - Laurentiu Benga
- Central Unit for Animal Research and Animal Welfare Affairs, University Hospital, Heinrich - Heine - University, Duesseldorf, Germany
| | - Werner Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Henrik Christensen
- Department of Veterinary and Animal Science, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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13
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Fingas F, Volke D, Hassert R, Fornefett J, Funk S, Baums CG, Hoffmann R. Sensitive and immunogen-specific serological detection of Rodentibacter pneumotropicus infections in mice. BMC Microbiol 2019; 19:43. [PMID: 30777007 PMCID: PMC6380038 DOI: 10.1186/s12866-019-1417-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/08/2019] [Indexed: 02/02/2023] Open
Abstract
Background Rodentibacter (R.) pneumotropicus colonizes the respiratory and urogenital tracts of laboratory mice with a reported moderate serological prevalence from 4 to 13%. Thus, regular tests to identify this pathogen in mice are recommended for animal facilities. However, a recent study indicated that current serological assays are partly insensitive, as C57BL/6 and BALB/c mice infected with R. pneumotropicus were incorrectly screened as seronegative. Results Here, we report a systematic analysis of protein and lipopolysaccharides antigens by immunoblot and ELISA that allowed establishing a sensitive test system able to differentiate between R. pneumotropicus and the closely related species R. heylii. Furthermore, the main immunogen, designated as ‘characteristic antigen for Rodentibacter of laboratory origin 1’ (CARLO-1), was identified by two-dimensional gel electrophoresis followed by immunoblot and tandem mass spectrometry in a preparation of outer membrane proteins. An indirect ELISA relying on the recombinantly expressed protein provided high sensitivity, specificity, and selectivity. The corresponding carlo1 gene was highly conserved (> 97%) among 21 isolates of R. pneumotropicus and R. heylii. Conclusion The newly identified protein CARLO-1 is well suited for the sensitive and specific serological detection of Rodentibacter infections in mice. Indirect differentiation of R. pneumotropicus and R. heylii infections may be possible using an ELISA based on a whole-cell antigen preparation. All four established ELISA systems using a whole-cell preparation, lipopolysaccharides, outer-membrane proteins and protein CARLO-1 as antigen, respectively, outperformed a commercial ELISA in terms of sensitivity. Electronic supplementary material The online version of this article (10.1186/s12866-019-1417-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Felix Fingas
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.,GVG Diagnostics GmbH, Leipzig, Germany
| | - Daniela Volke
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
| | - Rayk Hassert
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
| | - Juliane Fornefett
- Institute for Bacteriology and Mycology, Faculty of Veterinary Medicine, Universität Leipzig, Leipzig, Germany
| | - Sophie Funk
- Institute for Bacteriology and Mycology, Faculty of Veterinary Medicine, Universität Leipzig, Leipzig, Germany
| | - Christoph Georg Baums
- Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany.,Institute for Bacteriology and Mycology, Faculty of Veterinary Medicine, Universität Leipzig, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany. .,Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany. .,Biotechnologisch-Biomedizinisches Zentrum, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany.
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14
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Dafni H, Greenfeld L, Oren R, Harmelin A. The Likelihood of Misidentifying Rodent Pasteurellaceae by Using Results from a Single PCR Assay. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE 2019; 58:201-207. [PMID: 30651159 DOI: 10.30802/aalas-jaalas-18-000049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The precise identification of rodent Pasteurellaceae is known to be highly challenging. An unknown strain of Pasteurellaceae appeared and rapidly spread throughout our animal facilities. Standard microbiology, combined with biochemical analysis, suggested that the bacteria strain was Rodentibacter pneumotropicus or R. heylii. We submitted samples of the unknown bacteria and known isolates of R. pneumotropicus, R. heylii, and Muribacter muris, to 2 service laboratories that provide animal health monitoring. Results of microbiology tests performed by both laboratories, species-specific PCR analysis performed by one laboratory, and independent 16S rRNA gene sequencing yielded identical identification of the unknown bacteria as Pasteurellaceae (Pasteurella spp.) and not R. pneumotropicus or R. heylii. In contrast, the similarly intended PCR assay performed by the other laboratory identified the bacteria as R. heylii. Careful evaluation of all of the results led us to conclude that the correct identification of the bacteria is Pasteurellaceae. From our experience, we recommend that a combination of several methods should be used to achieve correct identification of rodent Pasteurellaceae. Specifically, we advise that all primer sets used should be disclosed when reporting PCR test results, including in health reports provided by service laboratories and animal vendors. Careful, correct, and informative health monitoring reports are most beneficial to animal researchers and caretakers who might encounter the presence and effects of rodent Pasteurellaceae.
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Affiliation(s)
- Hagit Dafni
- Department of Veterinary Resources, The Weizmann Institute of Science, Rehovot, Israel.
| | - Lea Greenfeld
- Department of Veterinary Resources, The Weizmann Institute of Science, Rehovot, Israel
| | - Roni Oren
- Department of Veterinary Resources, The Weizmann Institute of Science, Rehovot, Israel
| | - Alon Harmelin
- Department of Veterinary Resources, The Weizmann Institute of Science, Rehovot, Israel
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15
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Benga L, Sager M, Christensen H. From the [ Pasteurella ] pneumotropica complex to Rodentibacter spp.: an update on [ Pasteurella ] pneumotropica. Vet Microbiol 2018; 217:121-134. [DOI: 10.1016/j.vetmic.2018.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/14/2018] [Accepted: 03/10/2018] [Indexed: 01/08/2023]
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16
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Carraro R, Dalla Rovere G, Ferraresso S, Carraro L, Franch R, Toffan A, Pascoli F, Patarnello T, Bargelloni L. Development of a real-time PCR assay for rapid detection and quantification of Photobacterium damselae subsp. piscicida in fish tissues. JOURNAL OF FISH DISEASES 2018; 41:247-254. [PMID: 28857188 DOI: 10.1111/jfd.12703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 06/07/2023]
Abstract
The availability of a rapid and accurate method for the diagnosis of Photobacterium damselae subsp. piscicida (Phdp), able to discriminate its strictly correlated subsp. damselae (Phdd), formally known as Vibrio damsela, is essential for managing fish pasteurellosis outbreaks in farmed fish. A single-step, high-sensitivity real-time PCR assay for simultaneous detection and quantification of P. damselae was designed targeting partial of the sequence of the bamB gene and tested for specificity and sensitivity on laboratory-generated samples as well as on experimentally infected seabream tissue samples. With a limit of detection (LOD) of one copy in pure bacterial DNA, the sensitivity was higher than all methods previously reported. Validation in target and non-target bacterial species proved the assay was able to discriminate Phdd-Phdp subspecies from diverse hosts/geographical origins and between non-target species. In addition, two SNPs in the target amplicon region determine two distinctive qPCR dissociation curves distinguishing between Phdp-Phdd. This is the first time that a molecular method for P. damselae diagnosis combines detection, quantification and subspecies identification in one step. The assay holds the potential to improve the knowledge of infection dynamics and the development of better strategies to control an important fish disease.
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Affiliation(s)
- R Carraro
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - G Dalla Rovere
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - S Ferraresso
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - L Carraro
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - R Franch
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - A Toffan
- Fish Virology Department, National Reference Laboratory for Fish, Crustacean and Mollusc Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - F Pascoli
- Fish Virology Department, National Reference Laboratory for Fish, Crustacean and Mollusc Diseases, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - T Patarnello
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - L Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
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17
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Rao D, Wu M, Wang J, Yuan W, Zhu Y, Cong F, Xu F, Lian Y, Huang B, Wu Q, Chen M, Zhang Y, Huang R, Guo P. Differentiation of minute virus of mice and mouse parvovirus by high resolution melting curve analysis. J Virol Methods 2017; 250:41-46. [PMID: 28947147 DOI: 10.1016/j.jviromet.2017.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 09/21/2017] [Accepted: 09/21/2017] [Indexed: 11/30/2022]
Abstract
Murine parvovirus is one of the most prevalent infectious pathogens in mouse colonies. A specific primer pair targeting the VP2 gene of minute virus of mice (MVM) and mouse parvovirus (MPV) was utilized for high resolution melting (HRM) analysis. The resulting melting curves could distinguish these two virus strains and there was no detectable amplification of the other mouse pathogens which included rat parvovirus (KRV), ectromelia virus (ECT), mouse adenovirus (MAD), mouse cytomegalovirus (MCMV), polyoma virus (Poly), Helicobactor hepaticus (H. hepaticus) and Salmonella typhimurium (S. typhimurium). The detection limit of the standard was 10 copies/μL. This study showed that the PCR-HRM assay could be an alternative useful method with high specificity and sensitivity for differentiating murine parvovirus strains MVM and MPV.
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Affiliation(s)
- Dan Rao
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Miaoli Wu
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Jing Wang
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510633, China
| | - Wen Yuan
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510633, China
| | - Yujun Zhu
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Feng Cong
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Fengjiao Xu
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510633, China
| | - Yuexiao Lian
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Bihong Huang
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Qiwen Wu
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China; South China Agricultural University, Guangzhou 510642, China
| | - Meili Chen
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510633, China
| | - Yu Zhang
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Ren Huang
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510633, China.
| | - Pengju Guo
- Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China.
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18
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Resistin-like molecule β is a bactericidal protein that promotes spatial segregation of the microbiota and the colonic epithelium. Proc Natl Acad Sci U S A 2017; 114:11027-11033. [PMID: 28973871 DOI: 10.1073/pnas.1711395114] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The mammalian intestine is colonized by trillions of bacteria that perform essential metabolic functions for their hosts. The mutualistic nature of this relationship depends on maintaining spatial segregation between these bacteria and the intestinal epithelial surface. This segregation is achieved in part by the presence of a dense mucus layer at the epithelial surface and by the production of antimicrobial proteins that are secreted by epithelial cells into the mucus layer. Here, we show that resistin-like molecule β (RELMβ) is a bactericidal protein that limits contact between Gram-negative bacteria and the colonic epithelial surface. Mouse and human RELMβ selectively killed Gram-negative bacteria by forming size-selective pores that permeabilized bacterial membranes. In mice lacking RELMβ, Proteobacteria were present in the inner mucus layer and invaded mucosal tissues. Another RELM family member, human resistin, was also bactericidal, suggesting that bactericidal activity is a conserved function of the RELM family. Our findings thus identify the RELM family as a unique family of bactericidal proteins and show that RELMβ promotes host-bacterial mutualism by regulating the spatial segregation between the microbiota and the intestinal epithelium.
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19
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Identification and differentiation of Campylobacter species by high-resolution melting curve analysis. Microb Pathog 2017; 108:109-113. [DOI: 10.1016/j.micpath.2017.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 04/28/2017] [Accepted: 05/02/2017] [Indexed: 11/24/2022]
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20
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Adhikary S, Bisgaard M, Dagnæs-Hansen F, Christensen H. Clonal outbreaks of [ Pasteurella] pneumotropica biovar Heyl in two mouse colonies. Lab Anim 2017; 51:613-621. [PMID: 28358244 DOI: 10.1177/0023677217698503] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of this study was to document the pathogenic role of biovar Heyl of [ Pasteurella] pneumotropica in mouse colonies. Fifty-three isolates associated with mastitis and orbital, cutaneous and vaginal abscesses as well as isolates from the nose and vagina of healthy mice were investigated. According to phenotypic characteristics and rpoB sequencing, the isolates were identified as [ P.] pneumotropica biovar Heyl. Pulsed-field gel electrophoresis (PFGE) revealed five closely related profiles separated by only one to four fragments. The outbreak strains diverged from epidemiologically unrelated strains with the same rpoB sequence type, as shown by the PFGE profiles. The investigation documented that members of biovar Heyl of [ P.] pneumotropica caused disease outbreaks in mouse colonies since the clonality indicated a primary role of [ P.] pneumotropica biovar Heyl in the infections observed.
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Affiliation(s)
- Sadhana Adhikary
- 1 Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Henrik Christensen
- 1 Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Miller M, Ritter B, Zorn J, Brielmeier M. Exhaust Air Dust Monitoring is Superior to Soiled Bedding Sentinels for the Detection of Pasteurella pneumotropica in Individually Ventilated Cage Systems. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2016; 55:775-781. [PMID: 27931316 PMCID: PMC5113879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/04/2016] [Accepted: 04/27/2016] [Indexed: 06/06/2023]
Abstract
Reliable detection of unwanted organisms is essential for meaningful health monitoring in experimental animal facilities. Currently, most rodents are housed in IVC systems, which prevent the aerogenic transmission of pathogens between cages. Typically soiled-bedding sentinels (SBS) exposed to soiled bedding collected from a population of animals within an IVC rack are tested as representatives, but infectious agents often go undetected due to inefficient transmission. Pasteurellaceae are among the most prevalent bacterial pathogens isolated from experimental mice, and the failure of SBS to detect these bacteria is well established. In this study, we investigated whether analysis of exhaust air dust (EAD) samples by using a sensitive and specific real-time PCR assay is superior to conventional SBS monitoring for the detection of Pasteurella pneumotropica (Pp) infections. In a rack with a known prevalence of Pp-positive mice, weekly EAD sampling was compared with the classic SBS method over 3 mo. In 6 rounds of testing, with a prevalence of 5 infected mice in each of 7 cages in a rack of 63 cages, EAD PCR detected Pp at every weekly time point; SBS failed to detect Pp in all cases. The minimal prevalence of Pp-infected mice required to obtain a reliable positive result by EAD PCR testing was determined to be 1 in 63 cages. Reliable detection of Pp was achieved after only 1 wk of exposure. Analysis of EAD samples by real-time PCR assay provides a sensitive, simple, and reliable approach for Pp identification in laboratory mice.
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Affiliation(s)
- Manuel Miller
- Research Unit for Comparative Medicine, Helmholtz Zentrum Mnchen, German Research Center for Environmental Health, Neuherberg, Germany;,
| | - Brbel Ritter
- Research Unit for Comparative Medicine, Helmholtz Zentrum Mnchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Julia Zorn
- Research Unit for Comparative Medicine, Helmholtz Zentrum Mnchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Markus Brielmeier
- Research Unit for Comparative Medicine, Helmholtz Zentrum Mnchen, German Research Center for Environmental Health, Neuherberg, Germany
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