Biology subjects

Battisti, A.

Publications and source records attributed to Battisti, A..

9 recordsLinked to original sources

bioRxiv2025

A minimal model of Norway spruce - bark beetle outbreak dynamics

Bark beetles pose a growing threat to coniferous forests worldwide, with outbreaks increasingly linked to environmental stress and host vulnerability. Most mechanistic models focus on equilibrium states, neglecting the dynamical nature of outbreaks triggered by environmental perturbations. Using Ips typographus as focal species, we present a minimal model capturing key processes such as threshold-driven mass attacks, with parameters adaptable to different environmental conditions. Under current conditions, the model predicts a stable endemic state that is reactive, meaning environmental shocks trigger isolated, transient outbreaks. Under altered conditions, reflecting potential climate change scenarios, the system undergoes a regime shift, producing recurrent outbreaks that arise spontaneously from insect-host feedbacks. Finally, we examine repeated environmental disturbances and forest management, showing that the effectiveness of outbreak mitigation depends on the interplay between management frequency and intensity. Overall, we provide a mechanistic framework for understanding outbreak dynamics and guiding management strategies under changing environmental conditions.

ecology↗

bioRxiv2024

Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance

Sewage metagenomics has risen to prominence in urban population surveillance of pathogens and antimicrobial resistance (AMR). Unknown species with similarity to known genomes cause database bias in reference-based metagenomics. To improve surveillance, we designed this study to recover sewage genomes and develop a quantification and correlation workflow for these genomes and AMR over time. We used longitudinal sewage sampling in seven treatment plants from five major European cities to explore the utility of catch-all sequencing of these population-level samples. Using metagenomic assembly methods, we recovered 2,332 metagenome-assembled genomes (MAGs) from prokaryotic species, 1,334 of which were previously undescribed. These genomes account for [~]69% of sequenced DNA and provide insight into sewage microbial dynamics. Rotterdam (Netherlands) and Copenhagen (Denmark) showed strong seasonal microbial community shifts, while Bologna, Rome, (Italy) and Budapest (Hungary) had occasional blooms of Pseudomonas-dominated communities, accounting for up to [~]95% of sample DNA. Seasonal shifts and blooms present challenges for effective sewage surveillance. We find that bacteria of known shared origin, like human gut microbiota, form communities, suggesting the potential for source-attributing novel species and their ARGs through network community analysis. This could significantly improve AMR tracking in urban environments.

microbiology↗

bioRxiv2023

The bacterial community of the European spruce bark beetle in space and time

The European spruce bark beetle Ips typographus is a pest causing severe damages in forests dominated by the Norway spruce in Europe. Microorganisms play an essential role in the host species performance, including nutrition, fitness as well as in overcoming host defenses. Here, we performed high-throughput 16S rRNA metabarcoding of I. typographus across different populations in Europe, to assess its bacterial community. We investigated four postglacial refugial areas in Europe and focused specifically on a current bark beetle hot spot in the Dolomites where we compared populations with different epidemiological phases (outbreaking vs. non-outbreaking) and across different seasons (pre-overwintering vs. overwintering). Our results show that the bacterial community structure varied among populations from the refugial areas and between different regions within the Dolomites. We found a significant difference in the bacterial community between pre-overwintering and overwintering individuals, but we did not find differences between epidemic and endemic populations. The prevalence of the genus Erwinia which was present in every individual and Pseudoxanthomonas in almost every individual across all populations, suggests that these taxa form the core bacterial community of I. typographus. Furthermore, several additional bacterial taxa occurred in all populations, but with variable frequencies. This study highlights a complex interaction of I. typographus and various bacterial taxa across different regions and ecological phases of I. typographus populations and provides new insights into the role of microorganisms in the biology of this important pest species.

ecology↗

bioRxiv2023

Drivers of asymmetrical insect invasions between three world regions

The geographical exchange of non-native insects can be highly asymmetrical, with some world regions exporting or importing more species than others. Several hypotheses have been proposed to explain such asymmetries, including differences in propagule pressure, environmental features in recipient regions, or biological traits of invaders. We tested aspects of these hypotheses in the context of the exchange of non-native insects between North America, Europe, and Australasia. Europe was the dominant exporter of non-native insect species between the three regions, with most of this asymmetry arising prior to 1950. The European dominance could not be explained by differences in import value, source species pool sizes, or native plant richness in the recipient regions. We identified that the introduction of non-native plants, driven in part by European colonization, best explains the asymmetrical exchange of non-native insects between our focal regions.

ecology↗

bioRxiv2022

Cosmopolitan Scolytinae: strong common drivers but too many singularities for accurate prediction

AimMany scolytine beetle species have been expanding their range in new territories across geographic barriers, traveling with wood, wood products and plants for planting, sometimes with a high impact on plant health. Here we attempt to quantify the mobility of these cosmopolitan species and to identify the biological drivers of mobility and impact. LocationWorld Major taxa studiedColeoptera; Curculionidae; Scolytinae MethodsMobility was estimated by counting the numbers of landmasses (contiguous pieces of land, surrounded by ocean or sea) colonized by each species. A series of potential drivers (taxonomic tribes; feeding habits; polyphagy; reproductive strategy; host taxa; pheromones and primary attractants) as well as impact on host health were recorded. Results163 species were identified, out of 5546 counted in the whole subfamily. Four tribes (Xyleborini; Ipini; Crypturgini; Hylastini) were significantly over-represented, and two others (Corthylini; Hexacolini) were under-represented. 53% of the 163 species are inbreeding, a very significant excess as compared to the whole subfamily (29%). The inbreeders colonized more landmasses than the outbreeders. There is a significant relationship between the number of host families attacked by a species and the number of colonized landmasses. Species restricted to conifers colonized fewer landmasses than hardwood generalists. Species attacking both types of hosts are the most mobile. Most of the invasive species respond to host primary attractants, only one quarter respond to pheromones. All very mobile species respond to primary attractants, and none responds to pheromones. Very mobile species are all associated with a high or moderate impact. Main conclusionsThe most mobile species belong for a large part to a limited number of subtribes. They are often inbreeding, polyphagous and respond to primary attractants but do not produce pheromones. However, many species that do not, or only partly, belong to these categories, have established in several landmasses, sometimes with a high impact. For example, the outbreeding Scolytus multistriatus, that attacks only 3 host families and produces aggregation pheromones, has established in thirteen landmasses, with a high impact. Therefore, risk prediction needs to assess diversity of species-specific biological traits beyond the few routinely analyzed in literature.

ecology↗

bioRxiv2021

Evidence of structural rearrangements and variability in pESI(like) megaplasmids of S.Infantis by resolving the pESI-like-blaCTX-M-1 positive variant.

The increasing prevalence of pESI(like)-positive, multidrug-resistant (MDR) S. Infantis in Europe is a cause of major concern. As previously demonstrated, the pESI(like) megaplasmid is not only a carrier of antimicrobial resistant (AMR) genes (at least tet, dfr and sul genes), but also harbours several virulence and fitness genes, and toxin/antitoxin systems that enhance its persistence in the S. Infantis host. In this study, five prototype pESI(like) plasmids, of either CTX-M-1 or CTX-M-65 ESBL producing strains, were long-read sequenced using Oxford Nanopore Technology (ONT) and their complete sequences were resolved. Comparison of the structure and gene content of the five sequenced plasmids, and further comparison with previously published pESI(like) sequences, indicated that although the sequence of such pESI(like) "mosaic" plasmids remains almost identical, their structures appear different and composed of regions inserted or transposed after different events. The results obtained in this study are essential to better understand the plasticity and the evolution of the pESI(like) megaplasmid, and therefore to better address risk management options and policy decisions to fight against AMR and MDR in Salmonella and other food-borne pathogens.

microbiology↗

bioRxiv2018

Complex responses of global insect pests to climate change

Insect pests strongly affect the productivity and profitability of agriculture and forestry. Despite the well-known sensitivity of insects to abiotic effects such as temperature, their potential responses to ongoing climate change remain unclear. Here we compile and review documented climate change responses of 31 of the globally most impactful phytophagous insect pests, focussing on species for which long-term, high-quality data are available. Most of the selected species show at least one response affecting their severity as pests, including changes in geographic range, population dynamics, life-history traits, and/or trophic interactions. Of the studied pests, 41% only show responses that are linked to increased pest severity, 4% only show responses of decreased severity, whereas importantly 55%, the majority of studied pests, show mixed responses including both increased and decreased severity under ongoing climate change. Variability in impact is further supported by a thermal sensitivity analysis showing little benefit of climate warming in relation to the optimal developmental temperatures for the majority of these pests under both current climate and future projections. Overall the results show that calculating the net effect of climate change on phytophagous insect pest impact is far from straightforward. The documented variation in responses, e.g. between agricultural and forest pests, indicates that efforts to mitigate undesirable climate change effects must target individual species, taking into account the complex ecological and evolutionary mechanisms underlying their responses.

ecology↗

bioRxiv2018

Core Genome Multi Locus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections

The use of whole genome sequencing (WGS) using next generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through Single Nucleotide Polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis, whereas gene-by-gene comparison through core-genome Multilocus Sequence Typing (cgMLST) has not been explored so far. The current study developed an allele-based method cgMLST and compared its performance to the genome-wide SNP approach and the traditional MLVA on a defined sample collection. The dataset comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 epidemiologically unrelated human and animal isolates collected in Italy. The cgMLST scheme generated in this study contained 2,687 targets of the B. melitensis 16M reference genome (75.4% of the complete genome). We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be [≤]4 loci in the cgMLST and [≤]10 in WGS SNP analysis. CgMLST and SNP analysis provided much higher phylogenetic distance resolution than MLVA, particularly for strains belonging to the same lineage thus allowing diverse and unrelated genotypes to be identified with greater confidence. The application of this cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.

microbiology↗

bioRxiv2017

Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

EFFORT groupHaitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie David, Antonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzynska, Magdalena Zajac, Hristo Daskalov, Helmut W Saatkamp, Katharina D.C. Stark.\n\nAbstractAntimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. Use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (www.effort-against-amr.eu), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 gigabases of DNA sequence, using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and countries. We found that the total acquired AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. Novel, functionally-determined AMR genes were, however, not associated with total drug use.

microbiology↗