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Mahtani-Williams S, Fulton W, Desvars-Larrive A, Lado S, Elbers JP, Halpern B, Herczeg D, Babocsay G, Lauš B, Nagy ZT, Jablonski D, Kukushkin O, Orozco-terWengel P, Vörös J, Burger PA. Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia. Genes (Basel) 2020; 11:genes11101218. [PMID: 33080926 PMCID: PMC7603136 DOI: 10.3390/genes11101218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/02/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022] Open
Abstract
Across the distribution of the Caspian whipsnake (Dolichophis caspius), populations have become increasingly disconnected due to habitat alteration. To understand population dynamics and this widespread but locally endangered snake’s adaptive potential, we investigated population structure, admixture, and effective migration patterns. We took a landscape-genomic approach to identify selected genotypes associated with environmental variables relevant to D. caspius. With double-digest restriction-site associated DNA (ddRAD) sequencing of 53 samples resulting in 17,518 single nucleotide polymorphisms (SNPs), we identified 8 clusters within D. caspius reflecting complex evolutionary patterns of the species. Estimated Effective Migration Surfaces (EEMS) revealed higher-than-average gene flow in most of the Balkan Peninsula and lower-than-average gene flow along the middle section of the Danube River. Landscape genomic analysis identified 751 selected genotypes correlated with 7 climatic variables. Isothermality correlated with the highest number of selected genotypes (478) located in 41 genes, followed by annual range (127) and annual mean temperature (87). We conclude that environmental variables, especially the day-to-night temperature oscillation in comparison to the summer-to-winter oscillation, may have an important role in the distribution and adaptation of D. caspius.
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Affiliation(s)
- Sarita Mahtani-Williams
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
- Fundación Charles Darwin, Avenida Charles Darwin s/n, Casilla 200144, Puerto Ayora EC-200350, Ecuador
| | - William Fulton
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
| | - Amelie Desvars-Larrive
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Institute of Food Safety, Food Technology and Veterinary Public Health, Vetmeduni Vienna, Veterinaerplatz 1, A-1210 Vienna, Austria
- Complexity Science Hub Vienna, Josefstädter Straße 39, A-1080 Vienna, Austria
| | - Sara Lado
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
| | - Jean Pierre Elbers
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
| | - Bálint Halpern
- MME Birdlife Hungary, Költő utca 21., H-1121 Budapest, Hungary; (B.H.); (G.B.)
| | - Dávid Herczeg
- Lendület Evolutionary Ecology Research Group, Centre for Agricultural Research, Plant Protection Institute, Herman Ottó út 15., H-1022 Budapest, Hungary;
| | - Gergely Babocsay
- MME Birdlife Hungary, Költő utca 21., H-1121 Budapest, Hungary; (B.H.); (G.B.)
- Mátra Museum of the Hungarian Natural History Museum, Kossuth Lajos utca 40., H-3200 Gyöngyös, Hungary
| | - Boris Lauš
- Association HYLA, Lipocac I., No. 7, C-10000 Zagreb, Croatia;
| | - Zoltán Tamás Nagy
- Independent Researcher, Hielscherstraße 25, D-13158 Berlin, Germany;
| | - Daniel Jablonski
- Department of Zoology, Comenius University in Bratislava, Ilkovičova 6, Mlynská Dolina, S-84215 Bratislava, Slovakia;
| | - Oleg Kukushkin
- Department of Biodiversity Studies and Ecological Monitoring, T. I. Vyazemsky Karadag Scientific Station–Nature Reserve–Branch of Institute of Biology of the Southern Seas of the Russian Academy of Sciences, Nauki Street 24, R-298188 Theodosia, Crimea;
- Department of Herpetology, Zoological Institute of the Russian Academy of Sciences, Universitetskaya Embankment 1, R-199034 Saint Petersburg, Russia
| | - Pablo Orozco-terWengel
- Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Ave, Cardiff CF103AX, UK;
| | - Judit Vörös
- Department of Zoology, Hungarian Natural History Museum, Baross u. 13., H-1088 Budapest, Hungary
- Molecular Taxonomy Laboratory, Hungarian Natural History Museum, Ludovika tér 2-6., H-1083 Budapest, Hungary
- Correspondence: (J.V.); (P.A.B.)
| | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstrasse 1, A-1160 Vienna, Austria; (S.M.-W.); (W.F.); (A.D.-L.); (S.L.); (J.P.E.)
- Correspondence: (J.V.); (P.A.B.)
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Pour SH, Wahab AKA, Shahid S. Spatiotemporal changes in precipitation indicators related to bioclimate in Iran. THEORETICAL AND APPLIED CLIMATOLOGY 2020; 141:99-115. [DOI: 10.1007/s00704-020-03192-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 03/22/2020] [Indexed: 09/02/2023]
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Kim J, Shin H, Park H, Jung H, Kim J, Cho S, Ryu S, Jeon B. Microbiota Analysis for the Optimization of Campylobacter Isolation From Chicken Carcasses Using Selective Media. Front Microbiol 2019; 10:1381. [PMID: 31293537 PMCID: PMC6598470 DOI: 10.3389/fmicb.2019.01381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 06/03/2019] [Indexed: 01/01/2023] Open
Abstract
Since contaminated poultry meat is the major source of transmitting Campylobacter jejuni to humans, the isolation of Campylobacter from poultry carcasses is frequently performed in many countries as a baseline survey to ensure food safety. However, existing isolation methods have technical limitations in isolating this fastidious bacterium, such as a growth competition with indigenous bacteria in food samples. In this study, we compared the differences in microbiota compositions between Bolton and Preston selective media, two most common selective media to isolate Campylobacter, and investigated how different microbiota compositions resulting from different enrichment methods may affect isolation frequencies. A next-generation sequencing (NGS) analysis of 16S rRNA demonstrated that Bolton and Preston-selective enrichments generated different microbiota structures that shared only 31.57% of Operating Taxonomic Unit (OTU) types. Particularly, Escherichia was highly prevalent in Bolton selective media, and the enrichment cultures that increase Escherichia negatively affected the efficacy of Campylobacter isolation. Furthermore, the combination of the selective media made a significant difference in the isolation frequency. The Bolton broth and Preston agar combination exhibited the highest (60.0%) frequencies of Campylobacter isolation, whereas the Bolton broth and Bolton agar combination showed the lowest (2.5%). These results show that each selective medium generates a unique microbiota structure and that the sequence of combining the selective media also critically affects the isolation frequency by altering microbiota compositions. In this study, we demonstrated how a microbiota analysis using NGS can be utilized to optimize a protocol for bacterial isolation from food samples.
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Affiliation(s)
- Jinshil Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
| | - Hyeeun Park
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hayan Jung
- Department of Food Science and Biotechnology, College of Life Science, Sejong University, Seoul, South Korea
| | - Junhyung Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byeonghwa Jeon
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Spatial Pattern of the Unidirectional Trends in Thermal Bioclimatic Indicators in Iran. SUSTAINABILITY 2019. [DOI: 10.3390/su11082287] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Changes in bioclimatic indicators can provide valuable information on how global warming induced climate change can affect humans, ecology and the environment. Trends in thermal bioclimatic indicators over the diverse climate of Iran were assessed in this study to comprehend their spatio-temporal changes in different climates. The gridded temperature data of Princeton Global Meteorological Forcing with a spatial resolution of 0.25° and temporal extent of 1948–2010 was used for this purpose. Autocorrelation and wavelets analyses were conducted to assess the presence of self-similarity and cycles in the data series. The modified version of the Mann–Kendall (MMK) test was employed to estimate unidirectional trends in 11 thermal bioclimatic indicators through removing the influence of natural cycles on trend significance. A large decrease in the number of grid points showing significant trends was noticed for the MMK in respect to the classical Mann–Kendall (MK) test which indicates that the natural variability of the climate should be taken into consideration in bioclimatic trend analyses in Iran. The unidirectional trends obtained using the MMK test revealed changes in almost all of the bioclimatic indicators in different parts of Iran, which indicates rising temperature have significantly affected the bioclimate of the country. The semi-dry region along the Persian Gulf in the south and mountainous region in the northeast were found to be more affected in terms of the changes in a number of bioclimatic indicators.
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Kim J, Oh E, Banting GS, Braithwaite S, Chui L, Ashbolt NJ, Neumann NF, Jeon B. An Improved Culture Method for Selective Isolation of Campylobacter jejuni from Wastewater. Front Microbiol 2016; 7:1345. [PMID: 27617011 PMCID: PMC4999441 DOI: 10.3389/fmicb.2016.01345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/15/2016] [Indexed: 01/30/2023] Open
Abstract
Campylobacter jejuni is one of the leading foodborne pathogens worldwide. C. jejuni is isolated from a wide range of foods, domestic animals, wildlife, and environmental sources. The currently available culture-based isolation methods are not highly effective for wastewater samples due to the low number of C. jejuni in the midst of competing bacteria. To detect and isolate C. jejuni from wastewater samples, in this study, we evaluated a few different enrichment conditions using five different antibiotics (i.e., cefoperazone, vancomycin, trimethoprim, polymyxin B, and rifampicin), to which C. jejuni is intrinsically resistant. The selectivity of each enrichment condition was measured with Ct value using quantitative real-time PCR, and multiplex PCR to determine Campylobacter species. In addition, the efficacy of Campylobacter isolation on different culture media after selective enrichment was examined by growing on Bolton and Preston agar plates. The addition of polymyxin B, rifampicin, or both to the Bolton selective supplements enhanced the selective isolation of C. jejuni. The results of 16S rDNA sequencing also revealed that Enterococcus spp. and Pseudomonas aeruginosa are major competing bacteria in the enrichment conditions. Although it is known to be difficult to isolate Campylobacter from samples with heavy contamination, this study well exhibited that the manipulation of antibiotic selective pressure improves the isolation efficiency of fastidious Campylobacter from wastewater.
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Affiliation(s)
- Jinyong Kim
- School of Public Health, University of Alberta, Edmonton, AB Canada
| | - Euna Oh
- School of Public Health, University of Alberta, Edmonton, AB Canada
| | - Graham S Banting
- School of Public Health, University of Alberta, Edmonton, ABCanada; Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, ABCanada
| | - Shannon Braithwaite
- School of Public Health, University of Alberta, Edmonton, ABCanada; Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, ABCanada
| | - Linda Chui
- Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, ABCanada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, ABCanada
| | - Nicholas J Ashbolt
- School of Public Health, University of Alberta, Edmonton, ABCanada; Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, ABCanada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, ABCanada; Provincial Laboratory for Public Health, Alberta Health Services, Edmonton, ABCanada
| | - Byeonghwa Jeon
- School of Public Health, University of Alberta, Edmonton, AB Canada
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Henry R, Schang C, Chandrasena GI, Deletic A, Edmunds M, Jovanovic D, Kolotelo P, Schmidt J, Williamson R, McCarthy D. Environmental monitoring of waterborne Campylobacter: evaluation of the Australian standard and a hybrid extraction-free MPN-PCR method. Front Microbiol 2015; 6:74. [PMID: 25709604 PMCID: PMC4321596 DOI: 10.3389/fmicb.2015.00074] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 01/21/2015] [Indexed: 11/13/2022] Open
Abstract
Campylobacter is the leading agent of diarrheal disease worldwide. This study evaluates a novel culture-PCR hybrid (MPN-PCR) assay for the rapid enumeration of Campylobacter spp. from estuarine and wastewater systems. To first evaluate the current, culture-based, Australian standard, an inter-laboratory study was conducted on 69 subsampled water samples. The proposed Most-Probable Number (MPN)-PCR method was then evaluated, by analysing 147 estuarine samples collected over a 2 year period. Data for 14 different biological, hydrological and climatic parameters were also collated to identify pathogen-environment relationships and assess the potential for method specific bias. The results demonstrated that the intra-laboratory performance of the MPN-PCR was superior to that of AS/NZS (σ = 0.7912, P < 0.001; κ = 0.701, P < 0.001) with an overall diagnostic accuracy of ~94%. Furthermore, the analysis of both MPN-PCR and AS/NZS identified the potential for the introduction of method specific bias during assessment of the effects of environmental parameters on Campylobacter spp. numbers.
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Affiliation(s)
- Rebekah Henry
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | - Christelle Schang
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | - Gayani I. Chandrasena
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | - Ana Deletic
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | - Mark Edmunds
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | - Dusan Jovanovic
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | - Peter Kolotelo
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | | | - Richard Williamson
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
| | - David McCarthy
- Environmental and Public Health Laboratory, Department of Civil Engineering, Monash UniversityClayton, VIC, Australia
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Lévesque S, Fournier E, Carrier N, Frost E, Arbeit RD, Michaud S. Campylobacteriosis in urban versus rural areas: a case-case study integrated with molecular typing to validate risk factors and to attribute sources of infection. PLoS One 2013; 8:e83731. [PMID: 24386265 PMCID: PMC3873381 DOI: 10.1371/journal.pone.0083731] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 11/15/2013] [Indexed: 11/26/2022] Open
Abstract
Campylobacter infection is a leading cause of bacterial gastroenteritis worldwide, and most clinical cases appear as isolated, sporadic infections for which the source is rarely apparent. From July 2005 to December 2007 we conducted a prospective case-case study of sporadic, domestically-acquired Campylobacter enteritis in rural versus urban areas and a prevalence study of Campylobacter in animal and environmental sources in the Eastern Townships, Quebec. Isolates were typed using Multilocus Sequence Typing (MLST) to reinforce the case-case findings and to assign a source probability estimate for each human isolate. The risk of human campylobacteriosis was 1.89-fold higher in rural than urban areas. Unconditional multivariate logistic regression analysis identified two independent risk factors associated with human Campylobacter infections acquired in rural area: occupational exposure to animals (OR = 10.6, 95% CI: 1.2–91, p = 0.032), and household water coming from a private well (OR = 8.3, 95% CI: 3.4–20.4, p<0.0001). A total of 851 C. jejuni isolates (178 human, 257 chicken, 87 bovine, 266 water, 63 wild bird) were typed using MLST. Among human isolates, the incidence rates of clonal complexes (CC) CC-21, CC-45, and CC-61 were higher in rural than urban areas. MLST-based source attribution analysis indicated that 64.5% of human C. jejuni isolates were attributable to chicken, followed by cattle (25.8%), water (7.4%), and wild birds (2.3%). Chicken was the attributable source for the majority of cases, independent of residential area, sex and age. The increased incidence in rural compared to urban areas was associated with occupational exposure to animals, particularly cattle among those aged 15–34 years, and with consumption of private well water. Both bovine and water exposure appeared to contribute to the seasonal variation in campylobacteriosis. These results provide a basis for developing public education and preventive programs targeting the risk factors identified.
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Affiliation(s)
- Simon Lévesque
- Department of Microbiology and Infectious Diseases, Faculté de Médecine de l'Université de Sherbrooke, Québec, Canada
| | - Eric Fournier
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada
| | - Nathalie Carrier
- Centre de Recherche Clinique Étienne-Le Bel du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric Frost
- Department of Microbiology and Infectious Diseases, Faculté de Médecine de l'Université de Sherbrooke, Québec, Canada
- Centre de Recherche Clinique Étienne-Le Bel du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, Canada
| | - Robert D. Arbeit
- Infectious Diseases Section, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Sophie Michaud
- Department of Microbiology and Infectious Diseases, Faculté de Médecine de l'Université de Sherbrooke, Québec, Canada
- * E-mail:
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Effect of incubation temperature on the detection of thermophilic campylobacter species from freshwater beaches, nearby wastewater effluents, and bird fecal droppings. Appl Environ Microbiol 2013; 79:7639-45. [PMID: 24077717 DOI: 10.1128/aem.02324-13] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This large-scale study compared incubation temperatures (37°C versus 42°C) to study the detection of thermophilic Campylobacter species, including Campylobacter jejuni, C. coli, and C. lari, in various surface water samples and bird fecal droppings around Hamilton Harbor, Lake Ontario. The putative culture isolates obtained from incubation temperatures of 37 and 42°C were confirmed by Campylobacter genus- and species-specific triplex PCR assays targeting the 16S rRNA gene and the 16S-23S rRNA gene internal transcribed spacer (ITS) region. A total of 759 water, wastewater, and bird fecal dropping samples were tested. Positive amplification reactions for the genus Campylobacter were found for 454 (60%) samples incubated at 37°C, compared to 258 (34%) samples incubated at 42°C. C. jejuni (16%) and C. lari (12%) were detected significantly more frequently at the 42°C incubation temperature than at 37°C (8% and 5%, respectively). In contrast, significantly higher rates of C. coli (14%) and other Campylobacter spp. (36%) were detected at the 37°C incubation temperature than at 42°C (8% and 7%, respectively). These results were consistent across surface water, wastewater, and bird fecal dropping samples. At times, Campylobacter spp. were recovered and detected at 37°C (3% for C. jejuni, 10% for C. coli, and 3% for C. lari) when the same samples incubated at 42°C were negative. A significantly higher rate of other Campylobacter spp. was detected only at 37°C (32%) than only at 42°C (3%). These results indicate that incubation temperature can significantly influence the culturability and detection of thermophilic and other fastidious Campylobacter spp. and that a comprehensive characterization of the Campylobacter spp. in surface water, wastewaters, or bird fecal droppings will require incubation at both 37 and 42°C.
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