Ex situ living plant collections play a crucial role in providing nature-based solutions to twenty-first century global challenges. However, the complex dynamics of these artificial ecosystems are poorly quantified and understood, affecting biodiversity storage, conservation and utilization. To evaluate the management of ex situ plant diversity, we analysed a century of data comprising 2.2 million records, from a meta-collection currently holding 500,000 accessions and 41

Conservation Horticulture (1) is an essential, central aspect of modern botanic garden culture and operations, (2) cannot be separated from botanic gardens and (3) produces positive outcomes in every other programme with which it intersects. Here, given the inseparable nature of each, a definition for Conservation Horticulture is provided along with an aligned definition of Botanic Garden. The concept of Conservation Horticulture is illustrated with examples.

Copernicia macroglossa Schaedtler, the CUBAN PETTICOAT PALM, is endemic to the lowlands of Cuba, and is one of the palms from this island most attractive to tropical gardens. Here, the species is illustrated from individuals cultivated at Montgomery Botanical Center (city of Coral Gables, Florida) and Florida International University (Miami‐Dade, Florida). We neotypify this name, review its conservation status, and construct maps with current distribution and a potential geographical range based on models. Its botanical illustration history is reviewed and photographs of the species in habitat and in botanic gardens are included, as well as anatomical images and descriptions of leaf‐segment sections.

Background: Detecting healthcare-associated transmission and outbreaks often relies on reactive whole-genome sequencing (WGS), which occurs after the suspected transmission has occurred. Additionally, reactive WGS frequently misidentifies transmission and misses transmission when it has occurred. We initiated weekly real-time WGS to detect bacterial transmission and direct infection prevention interventions. We describe our experience after 1 year of real-time WGS surveillance at the University of Pittsburgh Medical Center–Presbyterian Hospital, a large, tertiary-care facility. Methods: Weekly WGS surveillance was performed from November 1, 2021, to October 31, 2022. Cultured isolates of select bacterial pathogens from patients who were hospitalized for ≥3 days or had a recent healthcare exposure in the prior 30 days were collected and sequenced. Isolates that were ≤15 single-nucleotide polymorphisms (SNPs) were considered genetically related clusters except for Clostridioides difficile (≤2 SNPs). Genetically related clusters were investigated for epidemiological links and interventions to interrupt transmission were implemented at the discretion of the infection prevention team. We analyzed subsequent infections that occurred within an outbreak after an intervention was in place. Results: In total, 1,909 isolates were sequenced. Of 1,633 unique patient isolates clustered by sequence type, 74 clusters were identified comprising 210 (12.9%) patient isolates (Table 1). The median time from culture date to sequencing was 14 days (IQR, 5.25). The median cluster size was 2 (IQR, 1) (Table 2). Overall, 118 patient isolates (56.2%) had an epidemiological link to a prior isolate, indicating potential transmission. Of 74 clusters, 66 (89.2%) received infection prevention interventions after notification based upon epidemiological data. The infection prevention team performed 69 total interventions, which included unit education (n = 28), hand hygiene observations (n = 16), enhanced cleaning (n = 16), environmental cultures or removal of endoscope (n = 7), and enhanced microbiology surveillance (n = 2). The 59 subsequent infections after infection prevention notification included 17 (28.8%) with no clear epidemiological link, and 41 (69.5%) with an epidemiological link either to a new transmission route (n = 37) or the same route prior to infection prevention intervention (n = 4). Only 1 (1.7%) subsequent infection within a cluster occurred after an infection prevention intervention from the same potential route, which was a suspected unit-based transmission of vancomycin-resistant Enterococcus faecium . Conclusions: Real-time WGS was effective at detecting genetically related clusters, finding potential sources, and halting further transmission after interventions by the infection prevention team. Quick turnaround times from patient culture to sequencing and analysis were vital for successful WGS surveillance. Real-time WGS surveillance has the potential to substantially shift the infection prevention paradigm for outbreak detection. Disclosure: None

Systematic study of the palm (Arecaceae) flora from the Leeward Antilles marked both Sabal antillensis and Sabal lougheediana as endemic to Curaçao and Bonaire respectively. Although both species are emergent, obvious and charismatic elements of the Antillean flora, they were only described within the last decade. Sabal lougheediana is in demographic crisis as a result of constant ungulate pressure prohibiting seedling establishment, while S. antillensis is thriving as a result of careful management. Given the surprisingly recent discovery of these two species, and the severity of the conservation concern, genomic data can help inform whether these taxa are in fact well-circumscribed species, and help to guide further conservation actions. To investigate genomic diversity, we employed RADSeq data from samples throughout the range of both species. Results show significant genetic distance and fixation between the two taxa as currently circumscribed, as well as reduced genetic diversity and increased inbreeding in both species. Multivariate analysis of genetic distance and Bayesian clustering analysis both show clear and significant separation of the two taxa. Parallel assay of ex situ collections informs how future development of germplasm reserves can help support conservation of both species. We provide recommendations to help conserve these two unique and distinct species.

During the present biodiversity crisis, rare and endangered plants can be conserved ex situ in botanic gardens or seed banks. Ex situ collections distributed among multiple locations—“metacollections”—can safeguard against extinction but must represent adequate genetic diversity to be resilient to changing environments. Previous analyses have revealed strategies to create genetically diverse metacollections of plants with diverse life histories. However, past work has neglected important aspects of metacollection conservation: rare alleles, redundancy (duplication of alleles to be resilient to loss), geographic coverage, and relatedness. Therefore, we assessed two existing large metacollections (>250 individuals) of two International Union for Conservation of Nature (IUCN) Red List threatened plant species—Quercus acerifolia, a wind-pollinated oak, and Zamia integrifolia, an insect-pollinated cycad—for these previously neglected aspects of metacollection genetic conservation. We found that large metacollections of both species conserved genetic diversity well: over 80% of all alleles were conserved in at least one copy, and ∼70% of alleles were represented in five to 10 copies. Metacollections, however, could still be improved. The rare genetic diversity of Z. integrifolia was less well conserved than that of Q. acerifolia, and several wild populations of both species are precariously undersampled. Ex situ collections also contained high relatedness, which may hamper restoration efforts. Although large metacollections are commendable for their size and breadth, examining metacollections for these facets allowed a more holistic evaluation of genetic diversity conservation.

We utilized 10 microsatellite loci to examine the genetic diversity, genetic structure, and demographic history of Zamia decumbens Calonje, Meerman, M.P. Griff. & Hoese, an endangered cycad species occurring in small populations on karst topography within the Maya Mountains of Belize. Four populations in two distinct habitats were sampled: three inside dolines (one at a cave entrance and two at the bottom of sinkholes) and one on a rocky hilltop. Genetic variation in the species reflects the demographic history of the sampled populations which appears closely linked to the karstification of the limestone bedrock on which it occurs rather than being structured geographically or by habitat type. Contemporary gene flow between populations is low, with the cave population facilitating most of the genetic connectivity in the region as a source of migrants to other populations. Coalescent-based modeling revealed that the two sinkhole populations were established first, and the hilltop and cave populations were more recently founded from a common ancestral population. All populations were in Hardy-Weinberg equilibrium and moderately heterozygous, yet signatures for recent bottleneck events were recovered for the doline populations. Furthermore, a high inbreeding coefficient and high average pairwise relatedness were found for the hilltop population, the latter possibly the result of recent illegal harvesting activities.

Cycadales is highly endangered and one of the oldest dioecious gymnosperm lineages, making their reproductive biology highly relevant to conservation efforts and our understanding of the impact of dioecy, yet cycad reproductive ecophysiology is poorly understood. We examined how the costs associated with reproduction may impact basic physiological variation in cycad species. Specifically, we measured traits related to functional morphology and photosynthetic physiology in sterile and fertile staminate plants ('males') of Zamia portoricensis. Light response curves showed that sterile plants had greater light-use efficiency and maximum photosynthetic capacity per area compared with fertile plants. However, fertile and sterile plants exhibited similar respiration rates. We found significantly more nitrogen in leaves of fertile individuals, but similar nitrogen isotope composition and no differences in carbon content between sterile and fertile individuals. Despite having lower leaf-level photosynthetic rates, fertile plants had greater canopy-level photosynthesis than sterile plants, which was achieved by increasing leaf number and total leaf area. Our data suggest that sterile individuals may have greater light demands relative to fertile individuals, and fertile individuals may have greater nitrogen demands, which may be critical for successful reproductive events in staminate plants of the endangered cycad, Z. portoricensis.

Botanic garden collections are increasingly seeking to quantify and improve the value of their collections for science, horticulture, conservation and other uses. Quantifying the value of a collection depends on the mission of the institution. Many botanic gardens are prioritising the conservation of rare and threatened species towards preventing plant extinctions. In doing so, botanic gardens must make decisions about which plants should remain, be replaced or be added to their collections, and how to allocate staff and resources to care for individual plants, while considering funding and space limits. So, how can curators make the biggest impact towards conserving plant species? We present a promising method to quantitatively assess which plant species might be higher or lower conservation priority to an ex situ collection, using what we term ‘endangerment value’ – the value of collections for preventing plant extinction. We apply this method to four genera of high importance at The Morton Arboretum and showcase advantages of this approach as well as pitfalls. We found this method useful for priority setting, but note that the inclusion and exclusion of different data and how they are weighted impacts the ranking of priority species – an important lesson for any prioritisation method. We hope this method will inspire and help other botanic gardens to evaluate their current and future endangerment value and set priorities for maintaining and growing ex situ collections globally.

Background: Identifying and interrupting transmission of severe acute respiratory syndrome coronavirus 2 and resulting disease (COVID-19) in acute-care settings can be challenging due to incubation period, asymptomatic infection, and prevalent community disease. To elucidate routes of infection and interrupt COVID-19 outbreaks with uncertain epidemiological chains of transmission, UPMC utilized reactive whole-genome sequencing (WGS) of viral specimens. Methods: UPMC infection prevention teams identified healthcare-associated COVID-19 clusters with uncertain transmission pathways among patients and/or healthcare personnel (HCP) in acute-care hospitals. Nasopharyngeal samples preserved in viral transport media were obtained for genetic analyses. Nucleic acids were extracted and WGS libraries were prepared by targeted enrichment or multiplex PCR methodologies. Resulting sequencing reads were aligned to the Wuhan-1 reference genome, followed by identification of single-nucleotide polymorphisms (SNPs) among the genomes and construction of a phylogenetic tree. Specimens were considered genetically similar if there were ≤2 SNP differences between viral genomes within a cluster. Results: Between May 2020 until August 2022, infection prevention teams requested WGS for 17 healthcare-associated clusters of COVID-19 involving 182 individuals across 8 UPMC facilities (median outbreak size, 9 individuals; range, 2–26). Of the 182 individuals, 36 lacked clinical specimens and 30 did not pass WGS quality-control criteria of ≥95% of the reference genome with a minimum of 10× coverage. Of the 116 sequenced genomes, 94 (81%) had virus genetically similar to ≥1 other specimen, including 87 (83.6%) of 104 patient viruses and 7 (58.3%) of 12 HCP viruses, comprising 22 clusters (Fig. 1). The remaining 22 (20.6%) specimens were genetically unrelated. In total, 16 (94.1%) of the 17 epidemiologically identified clusters had 2 or more individuals with a genetically similar virus. Also, 7 (41.1%) of these clusters had genetically similar viral genomes for every individual within each cluster. Also, 9 (52.9%) clusters contained both genetically related and unrelated specimens: 5 of these had more complex genomic profiles (including 4 clusters containing 2 distinct subclusters of ≥2 genetically related viruses) and 1 cluster contained 3 subclusters of ≥2 genetically related viruses. In the outbreak with 3 clusters, 3 SNPs separated specimens from 2 temporally proximal clusters, suggesting possible propagation between clusters (cluster B-3 in Fig. 1). Conclusions: WGS can complement traditional epidemiological investigations of healthcare-associated COVID-19 outbreaks, revealing complex transmission dynamics. Future investigations will characterize the impact of WGS on determining specific transmission pathways in acute-care facilities.Disclosures: None

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Heterocyte-forming cyanobacteria form symbiotic relationships with several lineages of plants. Here, twenty (20) strains of endosymbiotic cyanobacteria (cyanobionts) with Nostoc-like morphologies were isolated from the highly specialized coralloid roots of five host species in Cycadales—Cycas debaoensis, C. fairylakea, C. elongata, Ceratozamia robusta, and Macrozamia moorei. Molecular phylogeny based on the 16S rRNA gene placed these strains into seven different taxa within the Nostocaceae, specifically under the genera Desmonostoc and Dendronalium. The percent dissimilarity and unique patterns in the secondary structures of the D1-D1′, Box-B, V2, and V3 helices, which were based on the 16S–23S rRNA internal transcribed spacer (ITS) regions, supported three distinct species in Desmonostoc. These three morphologically distinct novel species are described in this report: Desmonostoc debaoense sp. nov., Desmonostoc meilinense sp. nov., and Desmonostoc xianhuense sp. nov. Other investigated strains were phylogenetically identified as members of the recently discovered genus Dendronalium and represent the first report of association of that genus with cycads. Our findings suggest that the order Cycadales hosts diverse species of cyanobionts in their coralloid roots and that many potential unreported or novel taxa are present in cycads occurring in their natural habitat and await discovery.

Climate change will alter natural areas on a global scale within the next century, especially in low-lying coastal areas where sea-level rise is predicted to severely degrade or destroy many ecosystems. As sea-level rise continues, it is expected that salinity due to saltwater intrusion will impact soil health and agricultural production, this is of even greater importance in areas such as South Florida where the surface and groundwater resources are hydrologically connected due to the shallow and highly permeable limestone soils. The chlorophyll concentrations in leaf tissue were chosen as the primary health indicator to assess whether this is a valuable factor to consider for plant health risk assessment and whether optical sensor technology such as the SPAD and NDVI, are valuable tools when understanding the impact seawater encroachment has on plant nitrogen uptake. Therefore, the aim of this study was to evaluate the effects of salt concentrations on plant growth and health of four palm species. The treatments were from pure reverse osmosis water, Fresh water, brackish water, seawater and hypersaline water (0, 0.5, 5, 10, 15, 25, and 50 ppt). Control treatment that received reverse osmosis filtrated water with a salinity concentration of 0 ppt had the highest health-indicator averages compared to treatment 50 ppt. As the salinity increased, all health indicators gradually declined or remained rather constant and declined as they approached the greater salinity concentrations. The growth parameters and chlorophyll content were reduced over time, particularly at higher salt concentrations for all palm species studied. The chlorophyll content by SPAD and the normalized difference vegetation index (NDVI) can be used as health indicators of the palm species studied, as it was observed in this study a decline in the chlorophyll content as there was an increase in salt concentrations. It is important to emphasize that leaf chlorosis and subsequent decline of palm species were observed in the treatment with higher salt concentration, thus highlighting the importance of chlorophyll content as an indicator of plant health. The species Roystonea regia was very susceptible to salinity, and the palm Sabal palmetto is more susceptible to salinity than the Thrinax radiata and Pseudophoenix sargentii palms.

Background: Current guidelines recommend contact precautions to prevent transmission of methicillin-resistant Staphylococcus aureus (MRSA) in acute-care hospitals. Prior literature demonstrates that discontinuation of contact precautions for MRSA has not been associated with an increase in carriage rates including surveillance-defined healthcare-associated infection (HAI) while horizontal infection prevention strategies are implemented. Objective: To analyze the impact of discontinuation of contact precautions on the rate of MRSA infections, including surveillance-defined HAI and transmission events identified through whole-genome sequencing (WGS) surveillance. Methods: In this single tertiary-care center, retrospective, observational, quality improvement analysis, we measured 2 MRSA HAI outcomes before and after discontinuation of contact precautions (ie, gown and gloves no longer required for care of patients with prior or current MRSA infections or colonization, effective December 2, 2020). First, we conducted a time-series analysis using linear regression modelling of NHSN reported MRSA HAI rates (January 2019–November 2022). We also calculated the frequency of WGS-confirmed MRSA transmission events before in the discontinuation of contact precautions (January 2019–August 2019) and after the discontinuation of contact precautions (January 2022–November 2022) periods. Surveillance HAI events were determined using NHSN definitions; MRSA transmission events were defined as an isolate identified ≥3 days after hospitalization or within 30 days of a healthcare exposure, genetically related by ≤15 single-nucleotide polymorphisms compared to ≥1 previously sequenced MRSA isolate. Results: We identified 171 MRSA HAIs in the 23 months before discontinuation of contact precautions, corresponding to 4.24 HAI per 10,000 patient days, and 129 HAIs in the 24 months after discontinuation of contact precautions, corresponding to 3.01 HAI per 10,000 patient days (Fig.). We detected a nonsignificant change in the trend in HAI rate before and after discontinuation of contact precautions ( P = .22) as well as a significant immediate decrease in the MRSA HAI rate ( P < 0 .001) at the time of discontinuation of contact precautions. In the WGS analysis 8 months before discontinuation of contact precautions, 11 MRSA transmission events were confirmed, comprising 4 clusters (0.75 per 10,000 patient days). In the WGS for the 11-month analysis period after discontinuation of contact precautions, there were 23 confirmed MRSA transmission events comprising 10 clusters (1.22 per 10,000 patient days; incidence rate ratio, 1.61; 95% CI, 0.75–3.66; P = .19). Conclusions: After discontinuation of contact precautions, there was no significant increase in MRSA HAI or transmission events. Further evaluation of the individual WGS transmission clusters will be helpful to determine whether discontinuation of contact precautions led to MRSA transmission in this facility in the period after discontinuation of contact precautions. Disclosure: None

With only 24 plants located in the wild in 2017, the Haitian endemic Attalea crassispatha (Mart.) Burret (Arecaceae) is one of the major priorities for palm conservation in the Caribbean Island Biodiversity Hotspot and is the only member of the genus (~ 30 species) that occurs in the region. A project of ex situ conservation and field surveys published in 1994 involved Fairchild Tropical Botanic Garden (FTBG) as a major distributor of wild collected germplasm with other botanic gardens/institutions from South Florida and the tropics in 1989 and 1991. Part of this material was also grown in FTBG. Over 25 years after this conservation initiative was established, new field surveys were made in 2017 where the species occurs in Peninsule de Tiburon, southern Haiti. The number of living plants recorded in this new inventory was 24 (vs 25 reported in 1994). DNA microsatellite data (SSRs) were used to compare levels of genetic variation in the FTBG ex situ conservation collections and the wild. We found that the FTBG genotypes did not capture most of the already limited genetic diversity found in the wild. Cluster analyses based on Bayesian statistics recognized three major genetic groups in the wild, and three of them were found in plants occurring mostly in the northern slopes of Peninsule de Tiburon; in contrast, only two of the genetic clusters were predominant in the southern portion of this peninsula mostly in the Cavaillon area. Our results concur with those recently published based on Single-nucleotide polymorphisms (SNPs) molecular markers for ex situ collections of this palm species conserved in five botanic gardens/research institutes.

Imperiled plant species can benefit from ex situ cultivation to safeguard against loss of genetic diversity and possible extinction in the wild. Few studies use genetic monitoring in endangered plant species to evaluate how well current management practices maintain genetic diversity and limit inbreeding and relatedness after plants are brought into cultivation. We examine this question using Attalea crassispatha, a palm species with fewer than 100 palms surviving worldwide, and only 25 remaining in their native habitat. We sampled all accessible palms of this species (both in situ and ex situ) to (1) investigate how well garden collections capture in situ genetic diversity, (2) evaluate how well genetic diversity is carried forward into subsequent generations ex situ, (3) determine the number of wild and founding individuals contributing to ex situ breeding efforts, and (4) identify optimal breeding pairs that would maximize diversity and limit inbreeding. We found higher genetic diversity in situ and that current propagation practices lead to self-fertilization in the ex situ population and therefore fail to adequately steward genetic diversity in the conservation collection. Using relatedness analyses, we identified optimal breeding pairs in collections at different locations, highlighting the need for coordinated breeding efforts to maximize diversity ex situ. We also identified putative A. crassispatha that are genetically unrelated to the rest of the study cohort and are likely mislabeled. This study highlights the utility of genetic monitoring and the importance of careful coordination and record keeping within and among collections to ensure genetic diversity is maintained for future conservation efforts.

SummaryZamia decumbens Calonje, Meerman, M.P.Griff. & Hoese, a threatened cycad species from Belize, is showcased and illustrated based on field observations as well as plants cultivated in the ex situ conservation living collections of Montgomery Botanical Center (MBC) in Coral Gables, Florida. This once obscure species was described in 2009, studied in the field, and introduced into ex situ conservation collections at MBC and other botanical gardens around the world. At MBC, the living collection of Z. decumbens plants has been used to conduct additional research to advance further our knowledge about cycads and to develop guidelines for building living plant collections in support of conservation. In this contribution we discuss this species and its cultivation at the ex situ conservation collection at MBC, using it to illustrate the important role botanical gardens can play in protecting threatened species and advancing our knowledge about them.

At the Montgomery Botanical Center (MBC), Miami, Florida, USA, a graduate course on Plant Taxonomy and Nomenclature, administered by the Florida International University (FIU)-Biology Department, was held April 25–29, 2022.

Summary Background Healthcare-associated bacterial pathogens frequently carry plasmids that contribute to antibiotic resistance and virulence. The horizontal transfer of plasmids in healthcare settings has been previously documented, but genomic and epidemiologic methods to study this phenomenon remain underdeveloped. The objectives of this study were to develop a method to systematically resolve and track plasmids circulating in a single hospital, and to identify epidemiologic links that indicated likely horizontal plasmid transfer. Methods We derived empirical thresholds of plasmid sequence similarity from comparisons of plasmids carried by bacterial isolates infecting individual patients over time, or involved in hospital outbreaks. We then applied those metrics to perform a systematic screen of 3,074 genomes of nosocomial bacterial isolates from a single hospital for the presence of 89 plasmids. We also collected and reviewed data from electronic health records for evidence of geotemporal associations between patients infected with bacteria encoding plasmids of interest. Findings Our analyses determined that 95% of analyzed genomes maintained roughly 95% of their plasmid genetic content at a nucleotide identity at least 99·985%. Applying these similarity thresholds to identify horizontal plasmid transfer identified 45 plasmids circulating among clinical isolates. Ten plasmids met criteria for geotemporal links associated with horizontal transfer. Several plasmids with shared backbones also encoded different additional mobile genetic element content, and these elements were variably present among the sampled clinical isolate genomes. Interpretation The horizontal transfer of plasmids among nosocomial bacterial pathogens is frequent within hospitals and can be monitored with whole genome sequencing and comparative genomics approaches. These approaches should incorporate both nucleotide identity and reference sequence coverage to study the dynamics of plasmid transfer in the hospital. Funding This research was supported by the US National Institute of Allergy and Infectious Disease (NIAID) and the University of Pittsburgh School of Medicine. RESEARCH IN CONTEXT Evidence before this study A search of PubMed for research articles containing the search terms “plasmid”, “transfer”, “epidemiology”, “hospital”, and “patients” identified 115 peer-reviewed manuscripts published before 01 January 2022. Twenty-four manuscripts documented the dissemination of one or more plasmids by horizontal transfer in a hospital setting. Most of these prior studies focused on a single plasmid, outbreak, antibiotic resistance gene or pathogen species, and none established an a priori approach to identify plasmids circulating among non-clonal bacterial genomes. While prior studies have quantified plasmid preservation and nucleotide identity, similarity thresholds to infer horizontal transfer were neither uniform across studies nor systematically derived from empirical data. Added value of this study This study advances the field of genomic epidemiology by proposing and demonstrating the utility of empirically derived thresholds of plasmid sequence similarity for inferring horizontal transfer in healthcare settings. It also advances the field by tracking horizontal plasmid transfer within a single hospital at a hitherto unprecedented scale, examining the evidence of horizontal transfer of 89 plasmids among thousands of clinical bacterial isolates sampled from a single medical center. Our systematic review of patient healthcare data related to horizontal transfer also occurred at a breadth not previously undertaken in hospital epidemiology. Implications of all the available evidence When successfully integrated into contemporary methods for surveillance of nosocomial pathogens, comparative genomics can be used to track and intervene directly against the dissemination of plasmids that exacerbate virulence and antimicrobial resistance in healthcare-associated bacterial infections. Standardized thresholds of plasmid identity benefit epidemiologic investigations of horizontal transfer similar to those offered by establishing uniform thresholds of genome identity for investigations of bacterial transmission.