Integrative taxonomy of platygastrine wasps of Germany

In the context of the sixth mass extinction, our understanding of insect decline is severely limited by a lack of information on biodiversity. Many highly abundant and diverse insect groups remain unidentifiable to species or even to genus. The parasitoid wasp superfamily Platygastroidea is one such dark taxon. The taxonomic impediment is especially severe in the Palearctic Platygastrinae due to the proliferation of names with vague concepts. Platygastrine wasps parasitize the hyper-diverse Cecidomyiidae (Diptera), suggesting that their species richness may be correspondingly high. Revisionary work is needed to identify named species and to discover new ones. This work applies integrative taxonomic methods to address the most pressing problems within the subfamily. The research presented in this dissertation focuses on Europe, particularly Germany, which is the current center of insect decline research as well as a historical center of platygastrine taxonomy. As part of this work, historical descriptions and their associated type material were examined and clarified so that further revisionary work can occur. The dissertation is structured in five chapters, of which two are published and three are unpublished. The first chapter reviews 18 genera of Platygastridae described by Arnold Förster (1856), most of which represent distinct and recognizable lineages. The study provides their taxonomic history, diagnostic remarks, English translations, and illustrations of important specimens from the Förster collection in the Natural History Museum Vienna. The collection also includes original exemplar specimens of European species whose types have been lost. Potential neotypes and lectotypes from this material are noted, with the aim of improving nomenclatural stability in the group. Potential neotypes were found for Amblyaspis forticornis (Nees, 1834), Isocybus grandis (Nees, 1834), Platygaster striolata Nees, 1834, and Trichacis tristis (Nees, 1834). Lectotypes will be designated for Platygaster spinigera Nees, 1834, which will be transferred to Leptacis, and for Platygaster corvina Förster, 1861, with Platygaster henkvlugi Buhl, 1996 treated as a junior synonym. Synopeas mutica (Nees, 1834) should be transferred back to Platygaster. The second chapter addresses generic concepts within Platygastrinae sensu Ashmead. Part of Platygastrinae (former Inostemmatinae sensu Ashmead) was reviewed and keyed by Masner & Huggert (1989). However, more than half of the genera in the subfamily, including the vast majority of species, have not been revised. A working key to 14 major world genera, the first of its kind, is provided. An additional six genera and three subgenera of uncertain placement are discussed. The third chapter focuses on nomenclatural problems in the genus Platygaster Latreille, which is the type genus for its subfamily, family, and superfamily. It is also the largest genus in Platygastroidea with nearly 700 species, and recent evidence indicates that it is not monophyletic. It is necessary to establish the identity of the type specimen, as well as the identities of the 13 generic junior synonyms and four subgenera, in order to proceed with taxonomic divisions. The type specimen Scelio ruficornis Latreille, 1805, lost to science for 192 years, was rediscovered. However, it does not belong to the prevailing concept of Platygaster, but to Isocybus Förster, which has extreme taxonomic ramifications. The proposed solution would replace the type species of each genus in order to retain prevailing usage and prevent widespread confusion. A petition is presented to designate Epimeces ensifer Westwood as the type of Platygaster and Scelio ruficornis as the type of Isocybus. In the fourth chapter, the genus Trichacis Förster is revised for Europe. Examination of historical and modern collections combined with DNA barcoding revealed the presence of only a single species in Europe, Trichacis tristis (Nees, 1834), redescribed here. The results suggest that T. tristis has 14 junior synonyms: T. abdominalis (Thomson, 1859); T. bidentiscutum Szabó, 1981; T. didas (Walker, 1835); T. fusciala Szabó, 1981; T. hajduica Szabó, 1981; T. illusor Kieffer, 1916; T. nosferatus Buhl, 1997; T. pisis (Walker, 1835); T. persicus Asadi & Buhl, 2021; T. pulchricornis Szelényi, 1953; T. quadriclava Szabó, 1981; T. remulus (Walker, 1835); T. vitreus Buhl, 1997; and T. weiperti Buhl, 2019. Four species should be transferred to Amblyaspis Förster: T. afurcata Szabó, 1977, T. hungarica Szabó, 1977, T. pannonica Szabó, 1977, and T. tatika Szabó, 1977. Intraspecific variation, biological associations, and taxonomic history are discussed. DNA barcodes are provided and analyzed in the context of worldwide Trichacis and its sister genus Isocybus Förster. The fifth chapter examines platygastrid diversity in Germany in the context of insect decline. DNA barcodes indicate the presence of 178 observed species, with an estimated total of 290. GBOL sampling captured an estimated 93.7% of total species richness, but only 45.8% of rare species. A case study from Isocybus compares historical specimens, DNA barcode vouchers, and ecological data to illustrate the possible decline of a wetland parasitoid species. Altogether, the research demonstrates the importance of historical material, especially type specimens, in understanding biodiversity through time, and provides an essential taxonomic foundation for much-needed modern identification resources for Platygastrinae in the western Palearctic and beyond.Mitten im sechsten Massensterben ist unser Verständnis des Insektenrückgangs durch mangelhafte Informationen über die biologische Vielfalt noch immer stark eingeschränkt. Viele der häufigen und artenreichen Insektengruppen lassen sich nicht bis zur Art oder Gattung bestimmen, verweilen daher im Dunkeln. Platygastroidea, eine Überfamilie parasitoider Wespen, stellt ein solches "dark Taxon" dar. Bei paläarktischen Platygastrinae ist die taxonomische Bearbeitung besonders schwer, da es in einer Vielzahl von Taxa Unklarheiten gibt. Platygastrinae parasitieren die sehr artenreichen Cecidomyiidae (Diptera), was darauf schließen lässt, dass ihr Artenreichtum ebenfalls entsprechend groß sein könnte. Taxonomische Revisionen sind erforderlich, um beschriebene Arten zu identifizieren und neue zu entdecken. Die vorliegende Arbeit nutzt integrative Taxonomie, um die dringendsten Probleme dieser Unterfamilie anzugehen. Der Forschungsschwerpunkt liegt auf Europa, insbesondere Deutschland, das aktuelle Zentrum der Erforschung des Insektensterben, sowie ein historisches Zentrum der Platygastrinen-Taxonomie. Die Dissertation ist in fünf Kapitel unterteilt, von denen zwei veröffentlich und drei unveröffentlicht sind. Das erste Kapitel liefert einen Überblick über die 18 von Arnold Förster (1856) beschriebenen Gattungen der Platygastridae. Informationen über ihre Taxonomie, Anmerkungen zur Diagnose, Übersetzungen sowie Abbildungen wichtiger Exemplare aus der Förster-Sammlung im Naturhistorischen Museum Wien werden bereitgestellt. Die Sammlung Förster enthält zudem wichtige Original-Exemplare europäischer Arten, deren Typen unauffindbar sind. Potenzielle Neotypen und Lectotypen aus diesem Material sind vermerkt, um die nomenklatorische Stabilität der Gruppe zu verbessern. Potenzielle Neotypen wurden für Amblyaspis forticornis (Nees, 1834), Isocybus grandis (Nees, 1834), Platygaster striolata Nees, 1834, und Trichacis tristis (Nees, 1834) gefunden. Lectotypen werden für P. spinigera Nees, 1834, die zu Leptacis gestellt wird, und für P. corvina Förster, 1861, bestimmt, wobei Platygaster henkvlugi Buhl, 1996 als jüngeres Synonym zur letztgenannten Art behandelt wird. Synopeas mutica (Nees, 1834) sollte zurück zu Platygaster gestellt werden. Das zweite Kapitel befasst sich mit Gattungskonzepten innerhalb der Platygastrinae sensu Ashmead. Ein Teil der Platygastrinae (früher Inostemmatinae sensu Ashmead) wurde von Masner & Huggert (1989) überarbeitet und ein Bestimmungsschlüssel bereitgestellt. Viele Gattungen dieser Unterfamilie, einschließlich der meisten Arten, wurden jedoch nicht überarbeitet. Ein Bestimmungsschlüssel für 14 wichtige Gattungen der Welt wird vorgelegt. Weitere sechs Gattungen und drei Untergattungen mit unsicherer Stellung werden diskutiert. Das dritte Kapitel stellt die nomenklatorischen Probleme in der Gattung Platygaster Latreille dar, die Typusgattung der Überfamilie. Mit fast 700 Arten ist sie die größte Gattung der Platygastroidea, die nach neueren Erkenntnissen nicht monophyletisch ist. Das Aufklären der Identitäten des Typusexemplars, 13 jüngerer Synonyme und vier Untergattungen ist wichtig, um mit der taxonomischen Aufarbeitung fortzufahren. Das Typusexemplar von Scelio ruficornis, das 192 Jahre lang für die Wissenschaft als verschollen galt, wurde wiederentdeckt. Der Typus passt jedoch nicht zum vorherrschenden Konzept von Platygaster, sondern von Isocybus. Dies hat bedeutende taxonomische Auswirkungen. Als Lösung wird empfohlen, die Typusarten der einzelnen Gattungen zu ersetzen, um die aktuelle Namensnutzung beizubehalten und Verwirrung zu verhindern. Die Designation von Epimeces ensifer Westwood als Typusart von Platygaster und Scelio ruficornis als Typusart von Isocybus wird vorgeschlagen. In Kapitel vier wird die Gattung Trichacis Förster für Europa überarbeitet. Eine Untersuchung von historischem und neuem Sammlungsmaterial in Kombination mit DNA-Barcoding offenbarte das Vorhandensein einer einzigen Art in Europa, Trichacis tristis (Nees, 1834), die hier neu beschrieben wird. Die Ergebnisse zeigen, dass T. tristis 14 jüngere Synonyme hat: T. abdominalis (Thomson, 1859); T. bidentiscutum Szabó, 1981; T. didas (Walker, 1835); T. fusciala Szabó, 1981; T. hajduica Szabó, 1981; T. illusor Kieffer, 1916; T. nosferatus Buhl, 1997; T. pisis (Walker, 1835); T. persicus Asadi & Buhl, 2021; T. pulchricornis Szelényi, 1953; T. quadriclava Szabó, 1981; T. remulus (Walker, 1835); T. vitreus Buhl, 1997; und T. weiperti Buhl, 2019. Vier Arten sollten zu Amblyaspis Förster gestellt werden: T. afurcata Szabó, 1977, T. hungarica Szabó, 1977, T. pannonica Szabó, 1977 und T. tatika Szabó, 1977. Intraspezifische Variationen, biologische Assoziationen und die taxonomische Geschichte werden diskutiert. DNA-Barcodes werden bereitgestellt und im Kontext der weltweiten Arten von Trichacis und ihrer Schwestergattung Isocybus Förster analysiert. Im fünften Kapitel wird die Diversität der Platygastriden in Deutschland im Hinblick auf das Insektensterben untersucht. DNA-Barcodes weisen auf das Vorhandensein von 178 Arten hin, bei einer geschätzten Gesamtzahl von 290 Arten. Die Studie erfasste geschätzt 93,7 % des gesamten Artenreichtums, aber nur 45,8 % der seltenen Arten. Eine Untersuchung der Gattung Isocybus mittels historischer Belege, DNA-Barcodes und ökologischer Daten zeigt den potentiellen Rückgang einer Parasitoidenart. Diese Arbeit demonstriert, wie wichtig Sammlungen, insbesondere Typusexemplare, für das Verständnis der Artenvielfalt im Laufe der Zeit sind und liefert die taxonomische Grundlage für die dringend benötigten modernen Bestimmungshilfen der Platygastrinae in der westlichen Paläarktis und darüber hinaus

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.Gordon and Betty Moore Foundation (Grant GBMR #495.01)National Science Foundation (U.S.) (Grant OCE-1153588)National Science Foundation (U.S.) (Grant OCE-0425602)National Science Foundation (U.S.) (Grant DBI-0424599)Center for Microbial Oceanography: Research and Educatio

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Acquired Resistance to KRAS (G12C) Inhibition in Cancer

BACKGROUND: Clinical trials of the KRAS inhibitors adagrasib and sotorasib have shown promising activity in cancers harboring KRAS glycine-to-cysteine amino acid substitutions at codon 12 (KRAS(G12C)). The mechanisms of acquired resistance to these therapies are currently unknown. METHODS: Among patients with KRAS(G12C) -mutant cancers treated with adagrasib monotherapy, we performed genomic and histologic analyses that compared pretreatment samples with those obtained after the development of resistance. Cell-based experiments were conducted to study mutations that confer resistance to KRAS(G12C) inhibitors. RESULTS: A total of 38 patients were included in this study: 27 with non-small-cell lung cancer, 10 with colorectal cancer, and 1 with appendiceal cancer. Putative mechanisms of resistance to adagrasib were detected in 17 patients (45% of the cohort), of whom 7 (18% of the cohort) had multiple coincident mechanisms. Acquired KRAS alterations included G12D/R/V/W, G13D, Q61H, R68S, H95D/Q/R, Y96C, and high-level amplification of the KRAS(G12C) allele. Acquired bypass mechanisms of resistance included MET amplification; activating mutations in NRAS, BRAF, MAP2K1, and RET; oncogenic fusions involving ALK, RET, BRAF, RAF1, and FGFR3; and loss-of-function mutations in NF1 and PTEN. In two of nine patients with lung adenocarcinoma for whom paired tissue-biopsy samples were available, histologic transformation to squamous-cell carcinoma was observed without identification of any other resistance mechanisms. Using an in vitro deep mutational scanning screen, we systematically defined the landscape of KRAS mutations that confer resistance to KRAS(G12C) inhibitors. CONCLUSIONS: Diverse genomic and histologic mechanisms impart resistance to covalent KRAS(G12C) inhibitors, and new therapeutic strategies are required to delay and overcome this drug resistance in patients with cancer. (Funded by Mirati Therapeutics and others; ClinicalTrials.gov number, NCT03785249.)

The khmer software package: enabling efficient nucleotide sequence analysis

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Global disparities in surgeons’ workloads, academic engagement and rest periods: the on-calL shIft fOr geNEral SurgeonS (LIONESS) study

: The workload of general surgeons is multifaceted, encompassing not only surgical procedures but also a myriad of other responsibilities. From April to May 2023, we conducted a CHERRIES-compliant internet-based survey analyzing clinical practice, academic engagement, and post-on-call rest. The questionnaire featured six sections with 35 questions. Statistical analysis used Chi-square tests, ANOVA, and logistic regression (SPSS® v. 28). The survey received a total of 1.046 responses (65.4%). Over 78.0% of responders came from Europe, 65.1% came from a general surgery unit; 92.8% of European and 87.5% of North American respondents were involved in research, compared to 71.7% in Africa. Europe led in publishing research studies (6.6 ± 8.6 yearly). Teaching involvement was high in North America (100%) and Africa (91.7%). Surgeons reported an average of 6.7 ± 4.9 on-call shifts per month, with European and North American surgeons experiencing 6.5 ± 4.9 and 7.8 ± 4.1 on-calls monthly, respectively. African surgeons had the highest on-call frequency (8.7 ± 6.1). Post-on-call, only 35.1% of respondents received a day off. Europeans were most likely (40%) to have a day off, while African surgeons were least likely (6.7%). On the adjusted multivariable analysis HDI (Human Development Index) (aOR 1.993) hospital capacity &gt; 400 beds (aOR 2.423), working in a specialty surgery unit (aOR 2.087), and making the on-call in-house (aOR 5.446), significantly predicted the likelihood of having a day off after an on-call shift. Our study revealed critical insights into the disparities in workload, access to research, and professional opportunities for surgeons across different continents, underscored by the HDI

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P &lt; 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

Measurement of the top quark mass using charged particles in pp collisions at root s=8 TeV

Peer reviewe