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Yamanouchi K, Arima H, Sakamoto Y, Kanto K, Itoh K, Tsujiguchi T. Isolation and habitat analysis of Balamuthia mandrillaris from soil. Parasitol Res 2024; 123:163. [PMID: 38499865 DOI: 10.1007/s00436-024-08182-5] [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: 12/28/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Balamuthia mandrillaris is a free-living amoeba that causes meningoencephalitis in mammals. Over 200 cases of infection were reported worldwide, with a fatality rate of over 95%. A clear route of infection was unknown for a long time until a girl died of granulomatous amoebic encephalitis (GAE) in California, USA, in 2003 due to infection with B. mandrillaris detected in a potted plant. Since then, epidemiological studies were conducted worldwide to detect B. mandrillaris in soil and other environmental samples. We previously reported the isolation of B. mandrillaris from the soil in Japan; however, the existing B. mandrillaris culture method with BM3 medium and COS-7 cells was unsuccessful. Therefore, in this study, we aimed to conduct soil analysis to determine the growth conditions of B. mandrillaris. B. mandrillaris-positive soils were defined as soils from which B. mandrillaris was isolated and environmental DNA was PCR-positive. Soils inhabited by B. mandrillaris were alkaline, with high electrical conductivity and characteristics of nutrient-rich soils of loam and clay loam. The results of this study suggest a possible reason for the high prevalence of GAE caused by B. mandrillaris among individuals employed in agriculture-related occupations.
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Affiliation(s)
- Kanako Yamanouchi
- Department of Bioscience and Laboratory Medicine, Graduate School of Health Sciences, Hirosaki University, 66-1 Hon-Cho, Hirosaki, 036-8564, Japan.
| | - Hiroaki Arima
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Yamato Sakamoto
- Department of Bioscience and Laboratory Medicine, Graduate School of Health Sciences, Hirosaki University, 66-1 Hon-Cho, Hirosaki, 036-8564, Japan
| | - Kazuki Kanto
- Department of Bioscience and Laboratory Medicine, Graduate School of Health Sciences, Hirosaki University, 66-1 Hon-Cho, Hirosaki, 036-8564, Japan
| | - Katsuhiro Itoh
- Education Center for Disaster and Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-Cho, Hirosaki, 036-8564, Japan
| | - Takakiyo Tsujiguchi
- Education Center for Disaster and Radiation Emergency Medicine, Hirosaki University, 66-1 Hon-Cho, Hirosaki, 036-8564, Japan
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Caron K, Craw P, Richardson MB, Bodrossy L, Voelcker NH, Thissen H, Sutherland TD. The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance. SENSORS 2021; 21:s21196625. [PMID: 34640944 PMCID: PMC8513014 DOI: 10.3390/s21196625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 12/11/2022]
Abstract
Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.
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Affiliation(s)
- Karine Caron
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
| | - Pascal Craw
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Mark B. Richardson
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Levente Bodrossy
- CSIRO Oceans & Atmosphere, Hobart, TAS 7004, Australia; (P.C.); (L.B.)
| | - Nicolas H. Voelcker
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, VIC 3168, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Helmut Thissen
- CSIRO Manufacturing, Clayton, VIC 3168, Australia; (M.B.R.); (N.H.V.); (H.T.)
| | - Tara D. Sutherland
- CSIRO Health & Biosecurity, Canberra, ACT 2602, Australia;
- Correspondence:
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Tagliapietra V, Boniotti MB, Mangeli A, Karaman I, Alborali G, Chiari M, D’Incau M, Zanoni M, Rizzoli A, Pacciarini ML. Mycobacterium microti at the Environment and Wildlife Interface. Microorganisms 2021; 9:microorganisms9102084. [PMID: 34683407 PMCID: PMC8539169 DOI: 10.3390/microorganisms9102084] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
An unexpected high presence of Mycobacterium microti in wild boar in Northern Italy (Garda Lake) has been reported since 2003, but the factors contributing to the maintenance of this pathogen are still unclear. In this study, we investigated the presence of M. microti in wild rodents and in water and soil samples collected at wild boar aggregation areas, such as watering holes, with the aim of clarifying their role in M. microti transmission. In total, 8 out of 120 captured animals tested positive for the Mycobacterium tuberculosis complex (MTBC) as assessed by real-time PCR, and six samples were confirmed to be M. microti. A strain with a genetic profile similar to those previously isolated in wild boars in the same area was isolated from one sample. Of the 20 water and 19 mud samples, 3 and 1, respectively, tested positive for the presence of MTBC, and spacer oligotype SB0118 (vole type) was detected in one sample. Our study suggests that wild rodents, in particular Apodemus sylvaticus, Microtus sp. and Apodemus flavicollis, play roles in the maintenance of M. microti infections in wild boar through ingestion or by contact with either infected excreta or a contaminated environment, such as at animal aggregation sites.
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Affiliation(s)
- Valentina Tagliapietra
- Departemt of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098 San Michele all’Adige, Italy;
- Correspondence:
| | - Maria Beatrice Boniotti
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Anna Mangeli
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Iyad Karaman
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Giovanni Alborali
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Mario Chiari
- Direzione Generale Welfare, U.O. Veterinaria, Regione Lombardia, Piazza Città di Lombardia 1, 20124 Milano, Italy;
| | - Mario D’Incau
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Mariagrazia Zanoni
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Annapaola Rizzoli
- Departemt of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098 San Michele all’Adige, Italy;
| | - Maria Lodovica Pacciarini
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
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Wnuk E, Waśko A, Walkiewicz A, Bartmiński P, Bejger R, Mielnik L, Bieganowski A. The effects of humic substances on DNA isolation from soils. PeerJ 2020; 8:e9378. [PMID: 32775047 PMCID: PMC7384437 DOI: 10.7717/peerj.9378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/28/2020] [Indexed: 11/20/2022] Open
Abstract
Background Humic substances (HS) are compounds with a complicated structure, present in the humus soil layer, water, lake sediments, peat, brown coal and shales. Due to their similar physicochemical properties to DNA, they may have an adverse effect on the subsequent use of the isolated material. The main aim of this research was to examine the effect of HS on DNA isolation depending on the soil type and land use, taking into account the spectroscopic full characteristics of HS fractions. Methods The research was conducted on eight types of soil sample. Soils represented the most important Soil Reference Groups for temperate climates: Fluvisols, Regosols, Cambisols, Arenosols, Histosols and Luvisols. Soil samples were also collected from areas diversified in terms of use: arable land, grassland and forest. The extraction of HS fractions was performed using the procedure recommended by the International HS Society. The fractional composition of HS was characterized by UV-Vis and fluorescence methods. Soil DNA is extracted by direct cell lysis in the using a CTAB-based method with a commonly-used commercial soil DNA isolation kit. The basis for assessing the quantity and quality of extracted DNA was the Polymerase chain reaction (PCR) reaction since the analysis of soil DNA often relies on the use of PCR to study soil microorganisms. Results Based on the results, it can be concluded that in the presence of a high concentration of HS, the isolated DNA was low quality and the additional purification procedure was necessary. Despite the differentiation of the internal structure of HS fractions, the decisive factor in the efficiency of DNA isolation from soil samples was the total carbon content in HS. Reduced DNA yields can significantly constrain PCR detection limits to levels inadequate for metagenomic analysis, especially from humus-rich soils.
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Affiliation(s)
- Ewa Wnuk
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Adam Waśko
- Faculty of Food Science and Biotechnology, Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences, Lublin, Poland
| | - Anna Walkiewicz
- Institute of Agrophysics, Polish Academy of Sciences, Lublin, Poland
| | - Piotr Bartmiński
- Department of Geology, Soil Science and Geoinformation, Maria Curie-Skłodowska University, Lublin, Poland
| | - Romualda Bejger
- Department of Bioengineering, West Pomeranian University of Technology, Szczecin, Poland
| | - Lilla Mielnik
- Department of Bioengineering, West Pomeranian University of Technology, Szczecin, Poland
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Guerra V, Beule L, Lehtsaar E, Liao HL, Karlovsky P. Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer. Microorganisms 2020; 8:microorganisms8040532. [PMID: 32272709 PMCID: PMC7232467 DOI: 10.3390/microorganisms8040532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 11/23/2022] Open
Abstract
As our understanding of soil biology deepens, there is a growing demand for investigations addressing microbial processes in the earth beneath the topsoil layer, called subsoil. High clay content in subsoils often hinders the recovery of sufficient quantities of DNA as clay particles bind nucleic acids. Here, an efficient and reproducible DNA extraction method for 200 mg dried soil based on sodium dodecyl sulfate (SDS) lysis in the presence of phosphate buffer has been developed. The extraction protocol was optimized by quantifying bacterial 16S and fungal 18S rRNA genes amplified from extracts obtained by different combinations of lysis methods and phosphate buffer washes. The combination of one minute of bead beating, followed by ten min incubation at 65°C in the presence of 1 M phosphate buffer with 0.5% SDS, was found to produce the best results. The optimized protocol was compared with a commonly used cetyltrimethylammonium bromide (CTAB) method, using Phaeozem soil collected from 60 cm depth at a conventional agricultural field and validated on five subsoils. The reproducibility and robustness of the protocol was corroborated by an interlaboratory comparison. The DNA extraction protocol offers a reproducible and cost-effective tool for DNA-based studies of subsoil biology.
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Affiliation(s)
- Victor Guerra
- North Florida Research and Education Center, Soil and Water Sciences Department, University of Florida, Quincy, FL 32351, USA; (V.G.); (H.-L.L.)
| | - Lukas Beule
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37075 Goettingen, Germany; (E.L.); (P.K.)
- Correspondence:
| | - Ena Lehtsaar
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37075 Goettingen, Germany; (E.L.); (P.K.)
| | - Hui-Ling Liao
- North Florida Research and Education Center, Soil and Water Sciences Department, University of Florida, Quincy, FL 32351, USA; (V.G.); (H.-L.L.)
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Faculty of Agricultural Sciences, University of Goettingen, 37075 Goettingen, Germany; (E.L.); (P.K.)
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