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Extensively managed grasslands are recognized globally for their high biodiversity and their social and cultural values. However, their capacity to deliver multiple ecosystem services (ES) as parts of agricultural systems is surprisingly understudied compared to other production systems. We undertook a comprehensive overview of ES provided by natural and semi‐natural grasslands, using southern Africa (SA) and northwest Europe as case studies, respectively. We show that these grasslands can supply additional non‐agricultural services, such as water supply and flow regulation, carbon storage, erosion control, climate mitigation, pollination, and cultural ES. While demand for ecosystems services seems to balance supply in natural grasslands of SA, the smaller areas of semi‐natural grasslands in Europe appear to not meet the demand for many services. We identified three bundles of related ES from grasslands: water ES including fodder production, cultural ES connected to livestock production, and population‐based regulating services (e.g., pollination and biological control), which also linked to biodiversity. Greenhouse gas emission mitigation seemed unrelated to the three bundles. The similarities among the bundles in SA and northwestern Europe suggest that there are generalities in ES relations among natural and semi‐natural grassland areas. We assessed trade‐offs and synergies among services in relation to management practices and found that although some trade‐offs are inevitable, appropriate management may create synergies and avoid trade‐offs among many services. We argue that ecosystem service and food security research and policy should give higher priority to how grasslands can be managed for fodder and meat production alongside other ES. By integrating grasslands into agricultural production systems and land‐use decisions locally and regionally, their potential to contribute to functional landscapes and to food security and sustainable livelihoods can be greatly enhanced.

Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000  S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales. Whole genome sequencing is increasingly being adopted for Shigella sonnei outbreak investigation and surveillance, but there is no global classification standard. Here, the authors develop and validate a genomic framework implemented using open-source software, and demonstrate its application using surveillance data.

Objectives Prostate volume (PV) in combination with prostate specific antigen (PSA) yields PSA density which is an increasingly important biomarker. Calculating PV from MRI is a time-consuming, radiologist-dependent task. The aim of this study was to assess whether a deep learning algorithm can replace PI-RADS 2.1 based ellipsoid formula (EF) for calculating PV. Methods Eight different measures of PV were retrospectively collected for each of 124 patients who underwent radical prostatectomy and preoperative MRI of the prostate (multicenter and multi-scanner MRI’s 1.5 and 3 T). Agreement between volumes obtained from the deep learning algorithm (PV DL ) and ellipsoid formula by two radiologists (PV EF1 and PV EF2 ) was evaluated against the reference standard PV obtained by manual planimetry by an expert radiologist (PV MPE ). A sensitivity analysis was performed using a prostatectomy specimen as the reference standard. Inter-reader agreement was evaluated between the radiologists using the ellipsoid formula and between the expert and inexperienced radiologists performing manual planimetry. Results PV DL showed better agreement and precision than PV EF1 and PV EF2 using the reference standard PV MPE (mean difference [95% limits of agreement] PV DL : −0.33 [−10.80; 10.14], PV EF1 : −3.83 [−19.55; 11.89], PV EF2 : −3.05 [−18.55; 12.45]) or the PV determined based on specimen weight (PV DL : −4.22 [−22.52; 14.07], PV EF1 : −7.89 [−30.50; 14.73], PV EF2 : −6.97 [−30.13; 16.18]). Inter-reader agreement was excellent between the two experienced radiologists using the ellipsoid formula and was good between expert and inexperienced radiologists performing manual planimetry. Conclusion Deep learning algorithm performs similarly to radiologists in the assessment of prostate volume on MRI. Key Points • A commercially available deep learning algorithm performs similarly to radiologists in the assessment of prostate volume on MRI. • The deep-learning algorithm was previously untrained on this heterogenous multicenter day-to-day practice MRI data set.

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei . We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri , and that the HIV epidemic may have promoted Shigella population expansion. As a leading cause of diarrhoeal mortality and morbidity, authors examine the epidemiology and genome dynamics of shigellosis in South Africa, utilising whole genome sequence analysis.

CONTEXT: Hemipteran pests cause significant yield losses in European cereal fields. It has been suggested that local management interventions to promote natural enemies are most successful in simple landscapes that are dominated by large arable fields. OBJECTIVES: We study how farming category (conventional, new and old organic fields) and landscape complexity affect pests, natural enemies and biological control services in spring barley. We further analyse if yields are related to pest infestation or biological control services. METHODS: The amount of pasture and the length of field borders were used to define landscape complexity around barley fields in Southern Sweden. Arthropods were sampled with an insect suction sampler and predation and parasitism services were estimated by field observations and inspections of pest individuals. RESULTS: Pest infestation was affected by landscape complexity, with higher aphid, but lower leafhopper numbers in more complex landscapes. Aphid predation was higher under organic farming and affected by effects on predator abundance and community composition independent of landscape complexity. Auchenorrhyncha parasitism was neither significantly affected by landscape complexity nor by farming category. Higher aphid predation rates and lower aphid densities were characteristic for organically managed fields with higher barley yields. CONCLUSIONS: Our results suggest that it is possible to increase both aphid biological control services and barley yield via local management effects on predator communities independent of landscape complexity. However, the success of such management practices is highly dependent on the pest and natural enemy taxa and the nature of the trophic interaction.

Lawsonia intracellularis is an obligate intracellular bacterial pathogen that causes proliferative enteropathy (PE) in pigs. L. intracellularis infection causes extensive intestinal crypt cell proliferation and inhibits secretory and absorptive cell differentiation. However, the affected host upstream cellular pathways leading to PE are still unknown. β-catenin/Wnt signalling is essential in maintaining intestinal stem cell (ISC) proliferation and self-renewal capacity, while Notch signalling governs differentiation of secretory and absorptive lineage specification. Therefore, in this report we used immunofluorescence (IF) and quantitative reverse transcriptase PCR (RTqPCR) to examine β-catenin/Wnt and Notch-1 signalling levels in uninfected and L. intracellularis infected pig ileums at 3, 7, 14, 21 and 28 days post challenge (dpc). We found that while the significant increase in Ki67+ nuclei in crypts at the peak of L. intracellularis infection suggested enhanced cell proliferation, the expression of c-MYC and ASCL2, promoters of cell growth and ISC proliferation respectively, was down-regulated. Peak infection also coincided with enhanced cytosolic and membrane-associated β-catenin staining and induction of AXIN2 and SOX9 transcripts, both encoding negative regulators of β-catenin/Wnt signalling and suggesting a potential alteration to β-catenin/Wnt signalling levels, with differential regulation of the expression of its target genes. We found that induction of HES1 and OLFM4 and the down-regulation of ATOH1 transcript levels was consistent with the increased Notch-1 signalling in crypts at the peak of infection. Interestingly, the significant down-regulation of ATOH1 transcript levels coincided with the depletion of MUC2 expression at 14 dpc, consistent with the role of ATOH1 in promoting goblet cell maturation. The lack of significant change to LGR5 transcript levels at the peak of infection suggested that the crypt hyperplasia was not due to the expansion of ISC population. Overall, simultaneous induction of Notch-1 signalling and the attenuation of β-catenin/Wnt pathway appear to be associated with the inhibition of goblet cell maturation and enhanced crypt cell proliferation at the peak of L. intracellularis infection. Moreover, the apparent differential regulation of apoptosis between crypt and lumen cells together with the strong induction of Notch-1 signalling and the enhanced SOX9 expression along crypts 14 dpc suggest an expansion of actively dividing transit amplifying and/or absorptive progenitor cells and provide a potential basis for understanding the development and maintenance of PE.

Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated, and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans ( n  = 83) and birds ( n  = 79) isolated in Great Britain between 2000 and 2021 and analysed these alongside a broader public dataset ( n  = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98–35.45 p  = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii . Escherichia albertii is an emerging gastrointestinal pathogen that causes disease in humans and animals, notably birds. In this genomic epidemiology study, the authors investigate characteristics of isolates sampled from humans and birds in Great Britain and find that they tend to cluster separately.

Disruption of the homeostatic balance of intestinal dendritic cells (DCs) and macrophages (MQs) may contribute to inflammatory bowel disease. We characterized DC and MQ populations, including their ability to produce retinoic acid, in clinical material encompassing Crohn's ileitis, Crohn's colitis and ulcerative colitis (UC) as well as mesenteric lymph nodes (MLNs) draining these sites. Increased CD14+DRint MQs characterized inflamed intestinal mucosa while total CD141+ or CD1c+ DCs numbers were unchanged. However, CD103+ DCs, including CD141+CD103+ and CD1c+CD103+ DCs, were reduced in inflamed intestine. In MLNs, two CD14− DC populations were identified: CD11cintHLADRhi and CD11chiHLADRint cells. A marked increase of CD11chiHLADRint DC, particularly DRintCD1c+ DCs, characterized MLNs draining inflamed intestine. The fraction of DC and MQ populations expressing aldehyde dehydrogenase (ALDH) activity, reflecting retinoic acid synthesis, in UC colon, both in active disease and remission, were reduced compared to controls and inflamed Crohn's colon. In contrast, no difference in the frequency of ALDH+ cells among blood precursors was detected between UC patients and non-inflamed controls. This suggests that ALDH activity in myeloid cells in the colon of UC patients, regardless of whether the disease is active or in remission, is influenced by the intestinal environment.

Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri . Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data. An increase in shigellosis cases among men who have sex with men in the United Kingdom has been linked to an extensively drug-resistant strain of Shigella sonnei . In this genomic epidemiology study, the authors investigate the genetic basis, evolutionary history, and international dissemination of the outbreak strain.