| 1. |
- Ahlinder, Jon, et al.
(författare)
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Chemometrics comes to court: evidence evaluation of chem–bio threat agent attacks
- 2015
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Ingår i: Journal of Chemometrics. - : John Wiley & Sons. - 0886-9383 .- 1099-128X. ; 29:5, s. 267-276
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Tidskriftsartikel (refereegranskat)abstract
- Forensic statistics is a well-established scientific field whose purpose is to statistically analyze evidence in order to support legal decisions. It traditionally relies on methods that assume small numbers of independent variables and multiple samples. Unfortunately, such methods are less applicable when dealing with highly correlated multivariate data sets such as those generated by emerging high throughput analytical technologies. Chemometrics is a field that has a wealth of methods for the analysis of such complex data sets, so it would be desirable to combine the two fields in order to identify best practices for forensic statistics in the future. This paper provides a brief introduction to forensic statistics and describes how chemometrics could be integrated with its established methods to improve the evaluation of evidence in court.The paper describes how statistics and chemometrics can be integrated, by analyzing a previous know forensic data set composed of bacterial communities from fingerprints. The presented strategy can be applied in cases where chemical and biological threat agents have been illegally disposed.
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| 2. |
- Ahlinder, Jon, et al.
(författare)
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Increased knowledge of Francisella genus diversity highlights the benefits of optimised DNA-based assays
- 2012
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 12, s. 220-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Recent advances in sequencing technologies offer promising tools for generating large numbers of genomes, larger typing databases and improved mapping of environmental bacterial diversity. However, DNA-based methods for the detection of Francisella were developed with limited knowledge about genetic diversity. This, together with the high sequence identity between several Francisella species, means there is a high risk of false identification and detection of the highly virulent pathogen Francisella tularensis. Moreover, phylogenetic reconstructions using single or limited numbers of marker sequences often result in incorrect tree topologies and inferred evolutionary distances. The recent growth in publicly accessible whole-genome sequences now allows evaluation of published genetic markers to determine optimal combinations of markers that minimise both time and laboratory costs. Results: In the present study, we evaluated 38 previously published DNA markers and the corresponding PCR primers against 42 genomes representing the currently known diversity of the genus Francisella. The results highlight that PCR assays for Francisella tularensis are often complicated by low specificity, resulting in a high probability of false positives. A method to select a set of one to seven markers for obtaining optimal phylogenetic resolution or diagnostic accuracy is presented. Conclusions: Current multiple-locus sequence-typing systems and detection assays of Francisella, could be improved by redesigning some of the primers and reselecting typing markers. The use of only a few optimally selected sequence-typing markers allows construction of phylogenetic topologies with almost the same accuracy as topologies based on whole-genome sequences.
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| 3. |
- Ahlinder, Jon, et al.
(författare)
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Life stage-specific inbreeding depression in long-lived Pinaceae species depends on population connectivity
- 2021
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.
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| 4. |
- Ahlinder, Jon, et al.
(författare)
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Oligotyping reveals divergent responses of predation resistant bacteria to aquatic productivity and plankton composition
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Predation-resistance has been suggested to be a key for persistence of pathogenic bacteria in aquatic environments. Little is known about driving factors for different types of protozoa resistant bacteria (PRB). We studied if presence of PRB is linked to specific plankton taxa, the aquatic nutrient state, or predation pressure on bacteria. Nineteen freshwater systems were sampled and analyzed for PRB, plankton composition and physicochemical variables. Three PRB genera were identified; Pseudomonas, Mycobacterium and Rickettsia. Use of minimum entropy decomposition algorithm and phylogenetic analysis showed that different nodes (representing OTUs of high taxonomic resolution) matched to environmental isolates of the three genera. Links between the PRB genera and specific plankton taxa were found, but showed different relationships depending on if 18S rRNA OTU or microscopy data were used in the analysis. Mycobacterium spp. was negatively correlated to aquatic nutrient state, while Pseudomonas showed the opposite pattern. Rickettsia spp. was positively related to predation pressure on bacteria. Both Mycobacterium and Rickettsia were more abundant in systems with high eukaryotic diversity, while Pseudomonas occurred abundantly in waters with low prokaryotic diversity. The different drivers may be explained by varying ecological strategies, where Mycobacterium and Rickettsia are slow growing and have an intracellular life style, while Pseudomonas is fast growing and opportunistic. Here we give an insight to the possibilities of newly advanced methods such as sequencing and oligotyping to link potential pathogens with biomarkers. This as a tool to assist predictions of the occurrence and persistence of environmental pathogens.
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| 5. |
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| 6. |
- Ahlinder, Jon, et al.
(författare)
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Upstream land use with microbial downstream consequences : iron and humic substances link to Legionella spp
- 2024
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Ingår i: Water Research. - : Elsevier. - 0043-1354 .- 1879-2448. ; 256
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Tidskriftsartikel (refereegranskat)abstract
- Intensified land use can disturb water quality, potentially increasing the abundance of bacterial pathogens, threatening public access to clean water. This threat involves both direct contamination of faecal bacteria as well as indirect factors, such as disturbed water chemistry and microbiota, which can lead to contamination. While direct contamination has been well described, the impact of indirect factors is less explored, despite the potential of severe downstream consequences on water supply. To assess direct and indirect downstream effects of buildings, farms, pastures and fields on potential water sources, we studied five Swedish lakes and their inflows. We analysed a total of 160 samples in a gradient of anthropogenic activity spanning four time points, including faecal and water-quality indicators. Through species distribution modelling, Random Forest and network analysis using 16S rRNA amplicon sequencing data, our findings highlight that land use indirectly impacts lakes via inflows. Land use impacted approximately one third of inflow microbiota taxa, in turn impacting ∌20–50 % of lake taxa. Indirect effects via inflows were also suggested by causal links between e.g. water colour and lake bacterial taxa, where this influenced the abundance of several freshwater bacteria, such as Polynucleobacter and Limnohabitans. However, it was not possible to identify direct effects on the lakes based on analysis of physiochemical- or microbial parameters. To avoid potential downstream consequences on water supply, it is thus important to consider possible indirect effects from upstream land use and inflows, even when no direct effects can be observed on lakes. Legionella (a genus containing bacterial pathogens) illustrated potential consequences, since the genus was particularly abundant in inflows and was shown to increase by the presence of pastures, fields, and farms. The approach presented here could be used to assess the suitability of lakes as alternative raw water sources or help to mitigate contaminations in important water catchments. Continued broad investigations of stressors on the microbial network can identify indirect effects, avoid enrichment of pathogens, and help secure water accessibility.
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| 7. |
- Andersson, Agneta, et al.
(författare)
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Aquatic ecosystems at risk for occurrence of pathogenic bacteria
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Pathogenic bacteria occur naturally in aquatic systems. Co-existence of bacteria and protozoa has led to development of predation resistance strategies, which is suggested to serve as a driver for evolution of pathogenic bacteria. However, the ecological mechanisms for selection for different types of predation resistant and pathogenic bacteria are poorly known. To disentangle effects from nutrient availability and protozoan predation pressure on the occurrence of varying predation resistant bacterial genera, an enrichment-dilution experiment was performed where an aquatic bacterial community was exposed to protozoa. Operational taxonomical units, specific for three predation resistant bacterial genera were identified; Pseudomonas, Rickettsia and Mycobacterium. These genera are also known to harbor species that are potentially pathogenic to mammals. Rickettsia and Mycobacterium were promoted where protozoa were abundant and the predation pressure high, while Pseudomonas dominated the bacterial community at the highest nutrient level where the predation pressure on bacteria were low. Our study thus indicates that waters of all nutrient states can harbor pathogenic bacteria, but that bacteria with different ecological strategies occur depending on nutrient level and perturbation. The generative model approach presented here provide a possibility to integrate environmental data in prediction models of pathogens in complex environments.
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| 8. |
- Dwibedi, Chinmay Kumar, et al.
(författare)
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Biological amplification of low frequency mutations unravels laboratory culture history of the bio-threat agent Francisella tularensis
- 2020
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Ingår i: Forensic Science International. - : Elsevier. - 1872-4973 .- 1878-0326. ; 45
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Tidskriftsartikel (refereegranskat)abstract
- Challenges of investigating a suspected bio attack include establishing if microorganisms have been cultured to produce attack material and to identify their source. Addressing both issues, we have investigated genetic variations that emerge during laboratory culturing of the bacterial pathogen Francisella tularensis. Key aims were to identify genetic variations that are characteristic of laboratory culturing and explore the possibility of using biological amplification to identify genetic variation present at exceedingly low frequencies in a source sample. We used parallel serial passage experiments and high-throughput sequencing of F. tularensis to explore the genetic variation. We found that during early laboratory culture passages of F. tularensis, gene duplications emerged in the pathogen genome followed by single-nucleotide polymorphisms in genes for bacterial capsule synthesis. Based on a biological enrichment scheme and the use of high-throughput sequencing, we identified genetic variation that likely pre-existed in a source sample. The results support that capsule synthesis gene mutations are common during laboratory culture, and that a biological amplification strategy is useful for linking a F. tularensis sample to a specific laboratory variant among many highly similar variants.
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| 9. |
- Eriksson, Karolina Ida Anna, et al.
(författare)
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Association between Legionella species and humic substances during early summer in the northern Baltic Sea
- 2023
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is projected to cause alterations in northern coastal systems, including humification and intensified nutrient loads, which can lead to ecosystem imbalances and establishment of new bacterial species. Several potential pathogens, such as different species of Legionella, hide in the environment between infections, some by living inside protozoan host cells. Knowledge about the occurrence of Legionella in natural waters is missing, which disable risk assessments of exposure. We performed a study of the species diversity of Legionella in the northern Baltic Sea (Gulf of Bothnia) during early summer to map their occurrence and to identify possible environmental drivers. We detected Legionella and potential protozoan hosts along gradients of the Gulf of Bothnia. We also for the first time present third generation full-length 16S rRNA amplicon sequencing (Nanopore) to resolve environmental species classification of Legionella, with a method suitable to study all bacteria. Our data show that full length 16S rRNA sequences is sufficient to resolve Legionella while the standard short Illumina sequences did not capture the entire diversity. For accurate species classification of Legionella, harmonization between the Nanopore classification methods is still needed and the bias toward the well-studied Legionella pneumophila need to be resolved. Different Legionella species occurred both in the Bothnian Sea and in the Bothnian Bay and their abundance were linked to humic substances and low salinity. The relative abundance of Legionella was higher in the humic-rich northern waters of the Bothnian Bay. The link between Legionella species and humic substances may be indirect via promotion of the heterotrophic microbial food web, allowing Legionella species and similar bacteria to establish. Humic substances are rich in iron, which has been shown crucial for growth of Legionella species and other pathogens. Considering climate change projections in this regional area, with increased humification and freshwater inflow, this bacterial niche containing potential pathogens might become more widespread in the future Baltic Sea. This study demonstrates the significance of DNA sequencing to monitor public health relevant bacteria like Legionella species in the environment. Including sequencing of bacteria and protozoa in the environmental monitoring programs could be used to identify ecosystem imbalances, which enable appropriate responses to emerging diseases.
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| 10. |
- Eriksson, Karolina I. A., 1991-
(författare)
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Bacteria that escape predation : waterborne pathogens and their relatives
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The hidden presence of opportunistic bacterial pathogens in the environment evokes concerns about emerging diseases, especially in the light of climate change. The co-evolution of bacteria and their predators (protozoa) has led to bacterial defence strategies of which some contribute to the ability of bacteria to cause disease. To increase our understanding of the interplay between bacteria, protozoa, land use, and climate scenarios in Nordic brackish and freshwater, four studies were designed. The first study explored the co-occurrence patterns between predation resistant bacteria (PRB) and bacterivorous protozoa in a coastal area in the northern Baltic Sea. The results showed higher PRB diversity in the bays and freshwater inlets, than in the offshore waters. Further, genotype specific interactions between protozoa and bacteria were identified. The second study focused on Legionella species diversity and their association with humic substances and low salinity, potentially facilitated through the promotion of the heterotrophic microbial food web or by iron availability. The third study examined the impact of intensified land use on bacterial taxa abundance and community composition in lake inflows, demonstrating indirect downstream effects on water quality. Factors such as pastures, fields, farms, aluminium, iron, and humic substances were linked to increased Legionella abundance. The fourth study exposed aquatic organisms to climate change scenarios, causing eutrophication or brownification with elevated iron levels. Pseudomonas aeruginosa were found to be especially persistent to iron, likely linked to the same mechanism that enables survival in protozoan cells. This trait was shared with other observed intracellular pathogens and uncultured species, who showed elevated resilience to brownification and ability to survive outside host cells. These findings identified complex relationships, which improve our understanding of the intricate dynamics that shape aquatic ecosystems, and highlight the importance of considering multiple factors in managing water resources and maintaining ecosystem health. Human activities including intensified land use can have far-reaching consequences, jeopardizing the pristine nature of water bodies and escalate the presence of environmental and opportunistic bacterial pathogens.
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