1
|
Evaluating the Bacterial Diversity from the Southwest Coast of India Using Fatty Acid Methyl Ester Profiles. Curr Microbiol 2021; 78:649-658. [PMID: 33392676 DOI: 10.1007/s00284-020-02315-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
The fatty acid composition of bacterial isolates remains stable under standardized culture conditions, which makes it a useful taxonomic marker. The present study aims to characterize the diversity and quantity of fatty acid methyl esters (FAME) profiles of cultivable bacterial isolates collected along the southwest coast of India. Based on the similarity indices (range > 0.3-0.7) of the FAME profiles, the isolates were aggregated into 10 families, 11 genera and 19 species of cultured isolates. The following classes of bacteria were found: Bacilli, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Actinobacteria, which also included a few pathogens such as Pseudomonas, Staphylococcus and Bacillus sp. The hydroxyl FAMEs 2-hydroxydodecanoic acid (C12:0 2OH), 2-hydroxypentadecanoic acid (C15:0 2OH),3-hydroxy 14-methylpentadecanoic acid (C16:0iso 3OH), 3 hydroxy hexadecenoic acid (C16:0 3OH) and 3-hydroxy 15-methylhexadecanoic acid (C17:0iso 3OH), as well as the unsaturated FAMEs (11Z)-11-hexadecenoic acid (C16:1 ɷ5c), were exclusively associated with the isolates from Mangalore samples. Similarly, FAMEs 2-hydroxydecanoic acid (C10:0 2OH), 9-methyldecanoic acid (C11:0iso), undecanoic acid (C11:0), tridecanoic acid (C13:0), 10-methylhexadecanoic acid (C16:0 10-CH3) and (7Z)-7-hexadecenoic acid (C16:1 ɷ9c) occurred only in the isolates from Trivandrum samples. However, the isolates from Goa did not possess a signature FAME profile. The reproducibility of the GC-MIDI bacterial identification system was evaluated using 16S rRNA gene sequencing techniques for selected isolates.
Collapse
|
2
|
Harvey JE, Smiljanić M, Scharnweber T, Buras A, Cedro A, Cruz-García R, Drobyshev I, Janecka K, Jansons Ā, Kaczka R, Klisz M, Läänelaid A, Matisons R, Muffler L, Sohar K, Spyt B, Stolz J, van der Maaten E, van der Maaten-Theunissen M, Vitas A, Weigel R, Kreyling J, Wilmking M. Tree growth influenced by warming winter climate and summer moisture availability in northern temperate forests. GLOBAL CHANGE BIOLOGY 2020; 26:2505-2518. [PMID: 31860143 DOI: 10.1111/gcb.14966] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/30/2019] [Indexed: 05/22/2023]
Abstract
The role of future forests in global biogeochemical cycles will depend on how different tree species respond to climate. Interpreting the response of forest growth to climate change requires an understanding of the temporal and spatial patterns of seasonal climatic influences on the growth of common tree species. We constructed a new network of 310 tree-ring width chronologies from three common tree species (Quercus robur, Pinus sylvestris and Fagus sylvatica) collected for different ecological, management and climate purposes in the south Baltic Sea region at the border of three bioclimatic zones (temperate continental, oceanic, southern boreal). The major climate factors (temperature, precipitation, drought) affecting tree growth at monthly and seasonal scales were identified. Our analysis documents that 20th century Scots pine and deciduous species growth is generally controlled by different climate parameters, and that summer moisture availability is increasingly important for the growth of deciduous species examined. We report changes in the influence of winter climate variables over the last decades, where a decreasing influence of late winter temperature on deciduous tree growth and an increasing influence of winter temperature on Scots pine growth was found. By comparing climate-growth responses for the 1943-1972 and 1973-2002 periods and characterizing site-level growth response stability, a descriptive application of spatial segregation analysis distinguished sites with stable responses to dominant climate parameters (northeast of the study region), and sites that collectively showed unstable responses to winter climate (southeast of the study region). The findings presented here highlight the temporally unstable and nonuniform responses of tree growth to climate variability, and that there are geographical coherent regions where these changes are similar. Considering continued climate change in the future, our results provide important regional perspectives on recent broad-scale climate-growth relationships for trees across the temperate to boreal forest transition around the south Baltic Sea.
Collapse
Affiliation(s)
- Jill E Harvey
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
- Natural Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, AB, Canada
| | - Marko Smiljanić
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Tobias Scharnweber
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Allan Buras
- Department of Ecology and Ecosystem Management, TUM School of Life Sciences Weihenstephan, Freising, Germany
| | - Anna Cedro
- Faculty of Geosciences, Szczecin University, Szczecin, Poland
| | - Roberto Cruz-García
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Igor Drobyshev
- Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Institut de recherche sur les forêts, Université du Québec en Abitibi-Témiscamingue (UQAT), Val-d'Or, QC, Canada
| | - Karolina Janecka
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Āris Jansons
- Latvian State Forest Research Institute, Salaspils, Latvia
| | - Ryszard Kaczka
- Faculty of Earth Sciences, University of Silesia, Sosnowiec, Poland
| | - Marcin Klisz
- Department of Silviculture and Forest Tree Genetics, Forest Research Institute, Raszyn, Poland
| | - Alar Läänelaid
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | | | - Lena Muffler
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
- Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Göttingen, Germany
| | - Kristina Sohar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Barbara Spyt
- Faculty of Earth Sciences, University of Silesia, Sosnowiec, Poland
| | - Juliane Stolz
- Chair of Forest Growth and Woody Biomass Production, Dresden, Germany
| | | | | | - Adomas Vitas
- Centre of Environmental Research, Vytautas Magnus University, Kaunas, Lithuania
| | - Robert Weigel
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
- Albrecht von Haller Institute for Plant Sciences, University of Goettingen, Göttingen, Germany
| | - Jürgen Kreyling
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Martin Wilmking
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| |
Collapse
|
3
|
Cheng N, Yang Z, Wang W, Wang X, Xu W, Luo Y. A Variety of Bio-nanogold in the Fabrication of Lateral Flow Biosensors for the Detection of Pathogenic Bacteria. Curr Top Med Chem 2019; 19:2476-2493. [DOI: 10.2174/1568026619666191023125020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/15/2019] [Accepted: 09/13/2019] [Indexed: 12/19/2022]
Abstract
Pathogenic bacteria constitute one of the most serious threats to human health. This has led
to the development of technologies for the rapid detection of bacteria. Bio-nanogold-based lateral flow
biosensors (LFBs) are a promising assay due to their low limit of detection, high sensitivity, good selectivity,
robustness, low cost, and quick assay performance ability. The aim of this review is to provide
a critical overview of the current variety of bio-nanogold LFBs and their targets, with a special focus on
whole-cell and DNA detection of pathogenic bacteria. The challenges of bio-nanogold-based LFBs in
improving their performance and accessibility are also comprehensively discussed.
Collapse
Affiliation(s)
- Nan Cheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhansen Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Weiran Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinxian Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| |
Collapse
|
4
|
Elson R, Davies TM, Jenkins C, Vivancos R, O'Brien SJ, Lake IR. Application of kernel smoothing to estimate the spatio-temporal variation in risk of STEC O157 in England. Spat Spatiotemporal Epidemiol 2019; 32:100305. [PMID: 32007279 DOI: 10.1016/j.sste.2019.100305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 01/27/2023]
Abstract
Identifying geographical areas with significantly higher or lower rates of infectious diseases can provide important aetiological clues to inform the development of public health policy and interventions designed to reduce morbidity. We applied kernel smoothing to estimate the spatial and spatio-temporal variation in risk of STEC O157 infection in England between 2009 and 2015, and to explore differences between the residential locations of cases reporting travel and those not reporting travel. We provide evidence that the distribution of STEC O157 infection in England is non-uniform with respect to the distribution of the at-risk population; that the spatial distribution of the three main genetic lineages infecting humans (I, II and I/II) differs significantly and that the spatio-temporal risk is highly dynamic. Our results also indicate that cases of STEC O157 reporting travel within or outside the UK are more likely to live in the south/south-east of the country, meaning that their residential location may not reflect the location of exposure that led to their infection. We suggest that the observed variation in risk reflects exposure to sources of STEC O157 that are geographically prescribed. These differences may be related to a combination of changes in the strains circulating in the ruminant reservoir, animal movements (livestock, birds or wildlife) or the behavior of individuals prior to infection. Further work to identify the importance of behaviours and exposures reported by cases relative to residential location is needed.
Collapse
Affiliation(s)
- Richard Elson
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; School of Environmental Sciences, University of East Anglia, United Kingdom.
| | - Tilman M Davies
- Department of Mathematics & Statistics, University of Otago, Dunedin, New Zealand
| | - Claire Jenkins
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom
| | - Roberto Vivancos
- National Infection Service, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Emerging and Zoonotic Infections, United Kingdom
| | - Sarah J O'Brien
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; Institute of Population Health Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Iain R Lake
- National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections, United Kingdom; School of Environmental Sciences, University of East Anglia, United Kingdom
| |
Collapse
|
5
|
Tarr GAM, Stokowski T, Shringi S, Tarr PI, Freedman SB, Oltean HN, Rabinowitz PM, Chui L. Contribution and Interaction of Shiga Toxin Genes to Escherichia coli O157:H7 Virulence. Toxins (Basel) 2019; 11:toxins11100607. [PMID: 31635282 PMCID: PMC6832461 DOI: 10.3390/toxins11100607] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 01/17/2023] Open
Abstract
Escherichia coli O157:H7 is the predominant cause of diarrhea-associated hemolytic uremic syndrome (HUS) worldwide. Its cardinal virulence traits are Shiga toxins, which are encoded by stx genes, the most common of which are stx1a, stx2a, and stx2c. The toxins these genes encode differ in their in vitro and experimental phenotypes, but the human population-level impact of these differences is poorly understood. Using Shiga toxin-encoding bacteriophage insertion typing and real-time polymerase chain reaction, we genotyped isolates from 936 E. coli O157:H7 cases and verified HUS status via chart review. We compared the HUS risk between isolates with stx2a and those with stx2a and another gene and estimated additive interaction of the stx genes. Adjusted for age and symptoms, the HUS incidence of E. coli O157:H7 containing stx2a alone was 4.4% greater (95% confidence interval (CI) −0.3%, 9.1%) than when it occurred with stx1a. When stx1a and stx2a occur together, the risk of HUS was 27.1% lower (95% CI −87.8%, −2.3%) than would be expected if interaction were not present. At the population level, temporal or geographic shifts toward these genotypes should be monitored, and stx genotype may be an important consideration in clinically predicting HUS among E. coli O157:H7 cases.
Collapse
Affiliation(s)
- Gillian A M Tarr
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada.
| | - Taryn Stokowski
- Department of Laboratory Medicine and Pathology, University of Alberta and Alberta Public Labs, Edmonton, AB T6G 2J2, Canada.
| | - Smriti Shringi
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99163, USA.
| | - Phillip I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Stephen B Freedman
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada.
| | - Hanna N Oltean
- Washington State Department of Health, Shoreline, WA 98155, USA.
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA.
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta and Alberta Public Labs, Edmonton, AB T6G 2J2, Canada.
| |
Collapse
|
6
|
Tarr GAM, Shringi S, Oltean HN, Mayer J, Rabinowitz P, Wakefield J, Tarr PI, Besser TE, Phipps AI. Importance of case age in the purported association between phylogenetics and hemolytic uremic syndrome in Escherichia coli O157:H7 infections. Epidemiol Infect 2018; 146:1550-1555. [PMID: 29914582 PMCID: PMC6092231 DOI: 10.1017/s0950268818001632] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/13/2018] [Accepted: 05/18/2018] [Indexed: 11/05/2022] Open
Abstract
Escherichia coli O157:H7 is the largest cause of hemolytic uremic syndrome (HUS). Previous studies proposed that HUS risk varies across the E. coli O157:H7 phylogenetic tree (hypervirulent clade 8), but the role of age in the association is unknown. We determined phylogenetic lineage of E. coli O157:H7 isolates from 1160 culture-confirmed E. coli O157:H7 cases reported in Washington State, 2004-2015. Using generalised estimating equations, we tested the association between phylogenetic lineage and HUS. Age was evaluated as an effect modifier. Among 1082 E. coli O157:H7 cases with both phylogenetic lineage and HUS status (HUS n = 76), stratified analysis suggested effect modification by age. Lineages IIa and IIb, relative to Ib, did not appear associated with HUS in children 0-9-years-old. For cases 10-59-years-old, lineages IIa and IIb appeared to confer increased risk of HUS, relative to lineage Ib. The association reversed in ⩾60-year-olds. Results were similar for clade 8. Phylogenetic lineage appears to be associated with HUS risk only among those ⩾10-years-old. Among children <10, the age group most frequently affected, lineage does not explain progression to HUS. However, lineage frequency varied across age groups, suggesting differences in exposure and/or early disease manifestation.
Collapse
Affiliation(s)
- G. A. M. Tarr
- Department of Pediatrics, University of Calgary Cumming School of Medicine, Calgary, Alberta, CA
| | - S. Shringi
- Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - H. N. Oltean
- Washington State Department of Health, Shoreline, Washington, USA
| | - J. Mayer
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Geography, University of Washington, Seattle, Washington, USA
| | - P. Rabinowitz
- Department of Environmental and Occupational Health Sciences and Center for One Health Research, University of Washington, Seattle, Washington, USA
| | - J. Wakefield
- Departments of Biostatistics and Statistics, University of Washington, Seattle, Washington, USA
| | - P. I. Tarr
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - T. E. Besser
- Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - A. I. Phipps
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| |
Collapse
|