A Multilocus Sequence Tying Scheme for Rapid Identification of Xanthomonas citri Based on Whole Genome Sequencing Data

Xanthomonas citri is a plant-pathogenic bacterium associated with a diverse range of plant host species. It has undergone substantial reclassification and currently consists of fourteen different subspecies or pathovars that are responsible for a wide range of plant diseases. Whole genome sequencing (WGS) provides a cutting-edge advantage over other diagnostic techniques in epidemiological and evolutionary studies of X. citri because it has a higher discriminatory power and is replicable across laboratories. Also, WGS allows the improvement of multi-locus sequence typing (MLST) schemes. In this study, we used genome sequences of Xanthomonas isolates from the NCBI RefSeq database to develop a seven-gene MLST scheme that yielded 19 sequence types (STs) that correlated with phylogenetic clades of X. citri subspecies/pathovars. Using this MLST scheme, we examined 2,911 assemblies from NCBI GenBank and identified 15 novel STs from 37 isolates that were misclassified in the NCBI. In total, we identified 545 X. citri assemblies from GenBank with 95% average nucleotide identity to the X. citri type strain and all were classified as one of the 34 STs. All MLST classifications correlated with phylogenetic position inferred from alignments using 92 conserved genes. We observed several instances where strains from different pathovars formed closely related monophyletic clades and shared the same ST, indicating that further investigation of the validity of these pathovars is required. Our MLST scheme described here is a robust tool for rapid classification of X. citri pathovars using WGS and a powerful method for further comprehensive taxonomic revision of X. citri pathovars.

Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses

Campylobacter species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the Campylobacter genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the Campylobacter genus core genome (500 loci) using publicly available Campylobacter complete genomes (n = 498) and constructed a core genome phylogeny using 2,193 publicly available Campylobacter genomes to examine inter-species diversity and species boundaries. Utilizing 8,440 Campylobacter genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated Campylobacter species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had in silico DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool Campylobacter Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%. The ANI genomic species definitions proposed here allow consistent species definition in the Campylobacter genus and will facilitate the detection of novel species in the future.IMPORTANCEIn recent years, Campylobacter has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the Campylobacter genus in public databases. Currently, a standardized Campylobacter species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the Campylobacter genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the Campylobacter species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed Campylobacter Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to Campylobacter genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus Campylobacter.

Emergence of Poultry-Associated Human Salmonella enterica Serovar Abortusovis Infections, New South Wales, Australia

Salmonella enterica serovar Abortusovis is a ovine-adapted pathogen that causes spontaneous abortion. Salmonella Abortusovis was reported in poultry in 2009 and has since been reported in human infections in New South Wales, Australia. Phylogenomic analysis revealed a clade of 51 closely related isolates from Australia originating in 2004. That clade was genetically distinct from ovine-associated isolates. The clade was widespread in New South Wales poultry production facilities but was only responsible for sporadic human infections. Some known virulence factors associated with human infections were only found in the poultry-associated clade, some of which were acquired through prophages and plasmids. Furthermore, the ovine-associated clade showed signs of genome decay, but the poultry-associated clade did not. Those genomic changes most likely led to differences in host range and disease type. Surveillance using the newly identified genetic markers will be vital for tracking Salmonella Abortusovis transmission in animals and to humans and preventing future outbreaks.

Botulinum toxin therapy for management of phantom and residual limb pain following amputation: A systematic review

Chronic pain following amputation is debilitating. Due to its mechanisms in modulating muscle contraction and pain, botulinum toxin has been investigated as a treatment option for phantom limb pain (PLP) and residual limb pain (RLP). The objective of this study was to determine the efficacy of botulinum toxin injection in the management of PLP and RLP following major limb amputation using a systematic review of the literature. The databases Medline, CINAHL, EMBASE, Scopus, Web of Science, and Cochrane were searched from inception through October 30, 2023. The search identified 50 articles; 37 underwent full-text review, and 11 were included in the final review. Eighty-nine individuals with pain were investigated by the included studies; 53 had RLP and 63 had PLP. There was significant variation in botulinum toxin type, injection method, and dosage. Twenty-one (53.9%) and 27 (64.3%) participants had improvement in PLP and RLP following botulinum toxin injection, respectively. Therefore, there is potential for use of botulinum toxin for the treatment of PLP and RLP. However, due to the minimal number of studies, small sample sizes, and heterogenous methodologies, our ability to conclude with certainty the efficacy of botulinum toxin injection on the treatment of PLP and RLP following amputation is limited.

Emergence and genomic insights of non-pandemic O1 Vibrio cholerae in Zhejiang, China

IMPORTANCE

It is well recognized that only Vibrio cholerae O1 causes cholera pandemics. However, not all O1 strains cause pandemic-level disease. In this study, we analyzed non-pandemic O1 V. cholerae isolates from the 1960s to the 1990s from China and found that they fell into three lineages, one of which shared the most recent common ancestor with pandemic O1 strains. Each of these non-pandemic O1 lineages has unique properties that contribute to their capacity to cause cholera. The findings of this study enhanced our understanding of the emergence and evolution of both pandemic and non-pandemic O1 V. cholerae.

Migration and health study: a socio-ecological analysis of sexual health among migrants in Manitoba, Canada

BACKGROUND

To develop effective public health policies, programs, and services tailored to the unique sexual health needs of migrant populations, it is essential to understand the myriad socio-ecological factors that influence their sexual health. This qualitative community-based participatory study aimed to explore factors influencing migrants' sexual health at different socio-ecological levels in a Canadian setting.

METHODS

Participants (n = 34) from African, Caribbean, Black; Latin American; South Asian; Middle Eastern, as well as East and Southeast Asian communities were recruited across Manitoba using printed flyers, community organizations, and social media. Individual interviews, conducted in English, French, Mandarin, Cantonese, Tagalog, Arabic, Swahili, and Tigrinya languages, explored questions relating to sexual health and experiences with service providers. Data were analyzed using reflexive thematic analysis and socio-ecological systems theory.

RESULTS

The study uncovered a range of individual, interpersonal, institutional, and socio-structural factors that affect the sexual health of migrants in Manitoba. Individual factors such as sexual health knowledge and testing practices, interpersonal factors like the type of sexual partnerships, institutional factors such as sexual health information needs, language, and service access barriers, and structural-level factors like gender norms and HIV stigma exerted a significant influence on the sexual health practices of study respondents. Sexual health awareness was influenced by various factors including length of time in Canada and involvement in community-based services. Study respondents identified issues related to access to HIV testing and sexual health information, as well as language barriers, racism in healthcare, and HIV stigma. Gender and social norms played a significant role in discouraging communication about sex and safer sex practices.

CONCLUSIONS

The study highlights the complex interplay of factors that influence the sexual health of migrants, and the need for targeted sexual health awareness campaigns and provision of sexual health information in languages spoken by migrants. Public health interventions focused on improving the sexual health outcomes for migrants should consider the socio-ecological elements identified in this study. These findings can inform public health campaigns to increase access to services and address sexual health inequities among migrant communities in Canada.

Rheumatoid arthritis and older age are associated with lower humoral and cellular immune response to primary series COVID-19 mRNA vaccine

OBJECTIVE

People with autoimmune disease have worse COVID-19 infection-related outcomes, lower antibody responses to COVID-19 vaccine, and higher rates of breakthrough infection. Immunosuppressive medications used to treat rheumatoid arthritis (RA) are associated with lower COVID-19 vaccine responses, though independent contributions of comorbidities, T-cell immunity, and age are less clear. We sought to test the hypothesis that RA, immunosuppressive medications used to treat RA, and older age, contribute to reduced B and T cell response to COVID-19 vaccine.

METHODS

We evaluated serum samples, taken the day of 1st vaccine dose, the day of 2nd dose, 2-6 weeks after 2nd dose, 7-12 weeks after 2nd dose, 13-24 weeks after 2nd dose, and 2-6 weeks after the 3rd dose, for anti-spike IgG and neutralizing antibody levels to Wuhan and Omicron BA.1 and peripheral blood mononuclear cells (PBMC) for spike-specific IFN-γ and IL-2 production by ELISPOT assay in 46 RA and 101 non-autoimmune control participants before and after the primary series COVID-19 mRNA vaccination.

RESULTS

RA participants had lower spike-specific IgG and Wuhan-strain neutralizing antibody levels 2-6 weeks compared to controls after the second dose of primary vaccine series. Neutralizing antibody levels against Omicron BA.1 were low in both groups. IFN-γ production correlated with Wuhan neutralizing antibody levels, while older age negatively correlated with spike-specific IL-2, IFN-γ and IgG. Lower antibody levels were associated with older age, RA status, and medication usage, while lower T cell responses were associated primarily with older age.

CONCLUSIONS

These data indicate lower COVID-19 mRNA vaccine-induced antibody levels in persons with RA compared to individuals without RA, likely partially attributable to immune suppressive medications. At the same time, older age is associated with lower antibody and cellular immune response to COVID-19 vaccines.

"Because of COVID…": The impacts of COVID-19 on First Nation people accessing the HIV cascade of care in Manitoba, Canada

BACKGROUND

The COVID-19 pandemic (March 2020-May 2023) had a profound effect around the world with vulnerable people being particularly affected, including worsening existing health inequalities. This article explores the impact of the pandemic on health services for First Nations people living with HIV (FN-PWLE) in Manitoba, Canada. This study investigated perceptions of both health care providers and FN-PWLE through qualitative interviews occurring between July 2020 and February 2022 to understand their experience and identify lessons learned that could be translated into health system changes.

METHODS

Using a qualitative, participatory-action, intentional decolonizing approach for this study we included an Indigenous knowledge keeper and Indigenous research associates with lived experience as part of the study team. A total of twenty-five [25] in-depth semi-structured interviews were conducted with eleven healthcare providers (HCPs) and fourteen First Nation people with lived HIV experience (FN-PWLE). In total, 18/25 or 72% of the study participants self-identified as First Nation people.

RESULTS

The COVID-19 pandemic negatively impacted health services access for FN-PWLE, a) disrupted relationships between FN-PWLE and healthcare providers, b) disrupted access to testing, in-person appointments, and medications, and c) intersectional stigma was compounded. Though, the COVID-19 pandemic also led to positive effects, including the creation of innovative solutions for the health system overall.

CONCLUSIONS

The COVID-19 pandemic exaggerated pre-existing barriers and facilitators for Manitoba FN-PWLE accessing and using the healthcare system. COVID-19 impacted health system facilitators such as relationships and supports, particularly for First Nation people who are structurally disadvantaged and needing more wrap-around care to address social determinants of health. Innovations during times of crisis, included novel ways to improve access to care and medications, illustrated how the health system can quickly provide solutions to long-standing barriers, especially for geographical barriers. Lessons learned from the COVID-19 pandemic should be considered for improvements to the health system's HIV cascade of care for FN-PWLE and other health system improvements for First Nations people with other chronic diseases and conditions. Finally, this study illustrates the value of qualitative and First Nation decolonizing research methods. Further studies are needed, working together with First Nations organizations and communities, to apply these recommendations and innovations to change health care and people's lives.

Social and structural barriers and facilitators to HIV healthcare and harm reduction services for people experiencing syndemics in Manitoba: study protocol

INTRODUCTION

In Manitoba, Canada, there has been an increase in the number of people newly diagnosed with HIV and those not returning for regular HIV care. The COVID-19 pandemic resulted in increased sex and gender disparities in disease risk and mortalities, decreased harm reduction services and reduced access to healthcare. These health crises intersect with increased drug use and drug poisoning deaths, houselessness and other structural and social factors most acutely among historically underserved groups. We aim to explore the social and structural barriers and facilitators to HIV care and harm reduction services experienced by people living with HIV (PLHIV) in Manitoba.

METHODS AND ANALYSIS

Our study draws on participatory action research design. Guiding the methodological design are the lived experiences of PLHIV. In-depth semi-structured face-to-face interviews and quantitative questionnaires will be conducted with two groups: (1) persons aged ≥18 years living or newly diagnosed with HIV and (2) service providers who work with PLHIV. Data collection will include sex, gender, sociodemographic information, income and housing, experiences with the criminal justice system, sexual practices, substance use practices and harm reduction access, experiences with violence and support, HIV care journey (since diagnosis until present), childhood trauma and a decision-making questionnaire. Data will be analysed intersectionally, employing grounded theory for thematic analysis, sex-based and gender-based analysis and social determinants of health and syndemic framework to understand the experiences of PLHIV in Manitoba.

ETHICS AND DISSEMINATION

We received approval from the University of Manitoba Health Ethics Research Board (HS25572; H2022:218), First Nations Health and Social Secretariat of Manitoba, Nine Circles Community Health Centre, Shared Health Manitoba (SH2022:194) and 7th Street Health Access Centre. Findings will be disseminated using community-focused knowledge translation strategies identified by participants, peers, community members and organisations, and reported in conferences, peer-reviewed journals and a website (www.alltogether4ideas.org).

Genomic epidemiology and multilevel genome typing of Bordetella pertussis

Bordetella pertussis causes pertussis (or whooping cough), a severe respiratory infectious disease in infants, although it can be prevented by whole cell and acellular vaccines. The recent pertussis resurgence in industrialised countries is partly attributed to pathogen adaptation to vaccines, while emergence of antimicrobial resistance, specifically to macrolides in China, has become a concern. Surveillance of current circulating and emerging strains is therefore vital to understand the risks they pose to public health. Although there is increased genomics-based typing, a genomic nomenclature for this pathogen has not been well established. Here, we implemented the Multilevel Genome Typing (MGT) system for B. pertussis with five levels of resolution, which provide targeted typing of relevant lineages and discrimination of closely related strains at the finest scale. The low-resolution levels (MGT2 and MGT3) describe the distribution of major vaccine antigen alleles including ptxP, fim3, fhaB and prn, as well as temporal and spatial trends within the B. pertussis global population. Mid-resolution levels (MGT3 and MGT4) enable typing of antibiotic resistant lineages and Prn deficient lineages within the ptxP3 clade. The high-resolution level (MGT5) can capture finer-scale epidemiology such as outbreaks and local transmission events, with comparable resolution to existing genomic methods of strain relatedness assessment. The scheme offers stable MGT type assignments aiding harmonisation of typing and communication between laboratories. The scheme is available at https://mgtdb.unsw.edu.au/pertussis, is regularly updated from global data repositories and accepts public submissions. The MGT scheme provides a comprehensive, robust, and scalable system for global surveillance of B. pertussis.

Increasing SARS-CoV-2 testing capacity through specimen pooling: An acute care center experience

Innovation in laboratory testing algorithms to address seemingly uncontrollable global supply chain shortages in plastics and other consumables during emergencies such as the current COVID-19 pandemic have been urgently needed. We report our experience with specimen pooling on SARS-CoV-2 testing in an acute care hospital microbiology laboratory during a high testing demand period that exceeded available processing capacity. A fully automated four-in-one pooling algorithm was designed and validated. Correlation and agreement were calculated. A custom Microsoft Excel tool was designed for use by the technologists to aid interpretation, verification and result entry. Cost-per-test impact for pooling was measured in reference to the consumable cost and was denoted as the percentage reduction of cost versus the baseline cost-per-test of testing specimens individually. Validation showed a strong correlation between the signals observed when testing specimens individually versus those that were pooled. Average crossing point difference was 1.352 cycles (95% confidence interval of -0.235 and 2.940). Overall agreement observed between individually and pooled tested specimens was 96.8%. Stratified agreement showed an expected decreased performance of pooling for weakly positive specimens dropping below 60% after a crossing point of 35. Post-implementation data showed the consumable cost-savings achieved through this algorithm was 85.5% after 8 months, creating both testing and resource capacity. Pooling is an effective method to be used for SARS-CoV-2 testing during the current pandemic to address resource shortages and provide quick turnaround times for high test volumes without compromising performance.

Impact of the COVID-19 pandemic on access to HIV testing and condom use among two-spirit, gay, bisexual, and queer (2SGBQ+) men in Manitoba

This cross-sectional online survey (n = 347) examined the impact of the COVID-19 pandemic on access to HIV testing and condom use among Two-Spirit, gay, bisexual, and queer (2SGBQ+) men in Manitoba. Logistic regression assessed the relationship between socio-demographics and the impact of COVID-19 on access to HIV testing and condom use. Among those who answered a question on testing (n = 282), 27.7% reported reduced access to HIV testing. Among those who answered questions on condom use (n = 327), 54.4% reported decreased use of condoms. Compared to living in Winnipeg, living in a medium-sized city (Brandon) and in rural and remote areas were both associated with higher odds of reporting reduced access to HIV testing due to COVID-19. Participants who were dating (vs. married or partnered) were significantly more likely to report reduced access to HIV testing, but less likely to report decreased use of condoms, while younger age was associated with decreased use of condoms. Service providers must be prepared to respond to the impact of COVID-19 on HIV testing and condom use among younger, sexually active 2SGBQ + men, as well as those who live in small, rural, and remote areas in Manitoba.

Association of Cytomegalovirus Serostatus With Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Responsiveness in Nursing Home Residents and Healthcare Workers

Background

Latent cytomegalovirus (CMV) infection is immunomodulatory and could affect mRNA vaccine responsiveness. We sought to determine the association of CMV serostatus and prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with antibody (Ab) titers after primary and booster BNT162b2 mRNA vaccinations in healthcare workers (HCWs) and nursing home (NH) residents.

Methods

Nursing home residents (N = 143) and HCWs (N = 107) were vaccinated and serological responses monitored by serum neutralization activity against Wuhan and Omicron (BA.1) strain spike proteins, and by bead-multiplex immunoglobulin G immunoassay to Wuhan spike protein and its receptor-binding domain (RBD). Cytomegalovirus serology and levels of inflammatory biomarkers were also measured.

Results

Severe acute respiratory syndrome coronavirus 2-naive CMV seropositive (CMV⁺) HCWs had significantly reduced Wuhan-neutralizing Ab (P = .013), anti-spike (P = .017), and anti-RBD (P = .011) responses 2 weeks after primary vaccination series compared with responses among CMV seronegative (CMV^-) HCWs, adjusting for age, sex, and race. Among NH residents without prior SARS-CoV-2 infection, Wuhan-neutralizing Ab titers were similar 2 weeks after primary series but were reduced 6 months later (P = .012) between CMV⁺ and CMV^- subjects. Wuhan-neutralizing Ab titers from CMV⁺ NH residents who had prior SARS-CoV-2 infection consistently trended lower than titers from SARS-CoV-2 experienced CMV^- donors. These impaired Ab responses in CMV⁺ versus CMV^- individuals were not observed after booster vaccination or with prior SARS-CoV-2 infection.

Conclusions

Latent CMV infection adversely affects vaccine-induced responsiveness to SARS-CoV-2 spike protein, a neoantigen not previously encountered, in both HCWs and NH residents. Multiple antigenic challenges may be required for optimal mRNA vaccine immunogenicity in CMV⁺ adults.

Protocol for a randomized controlled trial to assess the effect of Self-Management for Amputee Rehabilitation using Technology (SMART): An online self-management program for individuals with lower limb loss

BACKGROUND

Lower limb loss (LLL) is a distressing experience with psychological, physical, and social challenges. Education is needed to enhance the coping skills and confidence of patients to improve LLL outcomes. However, access to rehabilitation services and education is limited outside of urban centers. To address this service gap, we co-created an eHealth platform, called Self-Management for Amputee Rehabilitation using Technology (SMART).

OBJECTIVES

First, we will test the effect of SMART and usual care compared with usual care only on walking capacity and confidence among individuals with LLL. Second, we will describe key implementation factors for program delivery and adoption at the person- and provider-level.

METHODS

This is a Type 1 Effectiveness-Implementation Hybrid Design, mixed-methods, multi-site (British Columbia and Ontario, Canada), parallel, assessor-blinded randomized controlled trial. Participants will include adults with unilateral LLL, during early prosthetic fitting (<2 years after casting for initial prosthesis). Participants in both groups will receive usual care. The experimental group will receive SMART with weekly support sessions from a trained peer mentor for goal setting and action planning for six weeks. Participants will be encouraged to continue using SMART for an additional four weeks. The control group will receive usual care, and weekly social contacts for six weeks. The primary outcome measure is walking capacity operationalized as the performance based Timed Up and Go test. The secondary outcome is walking confidence using the Ambulatory Self-Confidence Questionnaire. Outcome measures will be assessed at baseline, immediately post-intervention, and four weeks follow-up. We will describe key implementation factors (such as, participant experience, intervention adoption, fidelity) throughout the study using questionnaires, semi-structured interviews, and direct observation.

RESULTS

No participants have been enrolled.

CONCLUSIONS

SMART has the potential to provide knowledge and skill development to augment rehabilitation outcomes for adults with LLL.

TRIAL REGISTRATION

NCT04953364 in Clinical Trial Registry (https://clinicaltrials.gov/).

Relationship between sociodemographics, loss of income, and mental health among two-spirit, gay, bisexual, and queer men in Manitoba during the COVID-19 pandemic

This study examined the relationship between loss of income due to the COVID-19 pandemic and worsening mental health among a sample of 366 Two-Spirit, gay, bisexual, queer (2SGBQ+) men in Manitoba. Data were drawn from a cross-sectional online survey among 2SGBQ+ men in Manitoba. Logistic regression assessed the relationship between sociodemographics, loss of income due to COVID-19 (independent variable) and worsening of mental health (analytic outcome). Among all respondents in the sample (N = 366), 55% indicated worsening of their mental health. In logistic regression, compared to participants who did not experience any loss of income, those who experienced loss of income due to the COVID-19 pandemic were significantly more likely to report worsening mental health (Adjusted Odds Ratio [AOR] = 8.32, 95% Confidence Interval[CI] = 3.54-19.54). Compared to participants who self-identified as gay, bisexual-identifying participants were less likely to report worsening mental health (AOR = .35, 95%CI = 0.13-0.96). Finally, as compared to participants who were married or partnered, participants who were dating (AOR = 3.14, 95%CI = 1.60-6.17), single (AOR = 4.08, 95%CI = 1.75-9.52), and separated/divorced/widowed (AOR = 15.08, 95%CI = 2.22-102.51) were all significantly more likely to report experiencing a worsening of mental health due to the COVID-19 pandemic. This study highlights the need to develop robust public strategies for sub-populations of 2SGBQ+ men (non-gay identified sexual minorities and 2SGBQ+ men who may be more socially isolated). Specific targeted and tailored public health interventions designed with the unique needs of 2SGBQ+ men in Manitoba may be required to increase their access to socio-economic and mental health supports.

Developing a research agenda on exercise and physical activity for people with limb loss in Canada

PURPOSE

There is a lack of high-quality evidence about the effects of exercise or physical activity interventions for adults with lower limb amputations (LLAs). A planning meeting involving stakeholders (i.e., people with LLA, community advocates, health care providers, researchers) was organized to identify key research priorities related to exercise and physical activity for people with LLAs.

METHODS

We used a collaborative prioritized planning process with a pre-meeting survey and 2-day virtual meeting that included: identification and prioritization of challenges or gaps; identification and consolidation of solutions; and action planning. This process integrated a modified Delphi approach, including anonymous feedback in two surveys.

RESULTS

Thirty-five stakeholders participated. Six challenges related to exercise and physical activity for people with LLA were prioritized. One solution was prioritized for each challenge. After consolidation of solutions, participants developed five research action plans for research including: developing an on-line interface; developing and evaluating peer-support programs to support physical activity; examining integration of people with LLA into cardiac rehabilitation; development and evaluation of health provider education; and determining priority outcomes related to physical activity and exercise.

CONCLUSIONS

This collaborative process resulted in an action plan for amputation research and fostered collaborations to move identified priorities into action.IMPLICATIONS FOR REHABILITATIONLower limb amputations impact mobility leading to lower levels of physical activity.There are research gaps in our understanding of the effects of exercise or physical activity interventions for adults with lower limb amputations.Through a collaborative planning process, participants prioritized research directions on physical activity and exercise for people with LLA to advance research in the field.Action plans for research focused on developing online resources, peer support, cardiac rehabilitation for people with LLA, health provider education and determining priority outcomes related to physical activity and exercise.

MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens

Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at multiple precisely defined levels can be used to type isolates at multiple resolutions. The MGT designation for isolates is stable, and the assignment is faster than the existing approaches. MGT’s utility has been demonstrated in multiple species. This paper presents a publicly accessible web service called MGTdb, which enables the assignment of MGT STs to isolates, along with their storage, retrieval and analysis. The MGTdb web service enables upload of genome data as sequence reads or alleles, which are processed and assigned MGT identifiers. Additionally, any newly sequenced isolates deposited in the National Center for Biotechnology Information’s Sequence Read Archive are also regularly retrieved (currently daily), processed, assigned MGT identifiers and made publicly available in MGTdb. Interactive visualization tools are presented to assist analysis, along with capabilities to download publicly available isolates and assignments for use with external software. MGTdb is currently available for Salmonella enterica serovars Typhimurium and Enteritidis and Vibrio cholerae. We demonstrate the usability of MGTdb through three case studies — to study the long-term national surveillance of S. Typhimurium, the local epidemiology and outbreaks of S. Typhimurium, and the global epidemiology of V. cholerae. Thus, MGTdb enables epidemiological and microbiological investigations at multiple levels of resolution for all publicly available isolates of these pathogens.

Database URL: https://mgtdb.unsw.edu.au

Genomic Epidemiology of Vibrio cholerae O139, Zhejiang Province, China, 1994-2018

Cholera caused by Vibrio cholerae O139 was first reported in Bangladesh and India in 1992. To determine the genomic epidemiology and origins of O139 in China, we sequenced 104 O139 isolates collected from Zhejiang Province, China, during 1994-2018 and compared them with 57 O139 genomes from other countries in Asia. Most Zhejiang isolates fell into 3 clusters (C1-C3), which probably originated in India (C1) and Thailand (C2 and C3) during the early 1990s. Different clusters harbored different antimicrobial resistance genes and IncA/C plasmids. The integrative and conjugative elements carried by Zhejiang isolates were of a new type, differing from ICEVchInd4 and SXTMO10 by single-nucleotide polymorphisms and presence of genes. Quinolone resistance-conferring mutations S85L in parC and S83I in gyrA occurred in 71.2% of the Zhejiang isolates. The ctxB copy number differed among the 3 clusters. Our findings provided new insights for prevention and control of O139 cholera .

Detecting falsified oral contraceptives by visual assessment and diffuse reflectance spectroscopy (350–2500 nm): the need for supplementing traditional pharmacopeia techniques and the public health implications

Objectives

Substandard and falsified pharmaceuticals can present a major health risk, particularly for low- and middle-income countries. In a Sub-Saharan African market, United States Agency for International Development (USAID) staff found an oral contraceptive product (0.15 mg levonorgestrel/0.03 mg ethinyl estradiol) labeled with a logo (and brand name) visually matching one historically used by USAID but purportedly manufactured by an unauthorized source. Additional assessment was conducted to determine if more evidence of falsification was present to better understand the public health impact.

Study design

Relative to a control, the suspect sample was assessed visually for tablet features and with United States and International Pharmacopeia methods for levonorgestrel/ethinyl estradiol tablets. Diffuse reflectance spectra (350–2500 nm) were collected to further characterize the sample.

Results

Although the suspect sample aligned with pharmacopeia tests, visual examination of tablet characteristics and diffuse reflectance spectroscopy (350–2500 nm) assessments supported the tablets were not the same as control samples, confirming the suspect sample was falsified. These results raised concerns for the overall regulatory oversight available for the market with uncertainty regarding the true clinical bioequivalence levels (although adequate dissolution levels were observed).

Conclusions

Comprehensive characterization of suspect pharmaceuticals from the field can often be required depending on the nature of the sample and can have dramatic implications for understanding the public health risks to the end user within the local market. Simple visual assessment and spectroscopic techniques to screen a sample can help to supplement traditional pharmacopeia approaches.

Implications

Proper characterization of suspect pharmaceuticals is necessary to best understand their potential public health impact. Situations can occur where traditional pharmacopeial techniques may not adequately characterize a sample. Visual assessments and diffuse reflectance spectroscopy can be supplemented to provide a more holistic analysis.

Pyrogallate‐Based Metal‐Organic Framework with a Two‐Dimensional Secondary Building Unit

We report a metal-organic framework (MOF) with a rare two-dimensional (2D) secondary building unit (SBU). The SBU comprises mixed-valent Fe²⁺ and Fe³⁺ metal ions bridged by oxygen atoms pertaining to the polytopic ligand 3,3',4,4',5,5'-hexahydroxybiphenyl, which also define the iron-oxide 2D layers. Overall, the anionic framework exhibits rare topology and evidences strong electronic communication between the mixed-valence iron sites. These results highlight the importance of dimensionality control of MOF SBUs for discovering new topologies in reticular chemistry, and especially for improving electronic communication within the MOF skeleton.

Mass drug administration of ivermectin, diethylcarbamazine, plus albendazole compared with diethylcarbamazine plus albendazole for reduction of lymphatic filariasis endemicity in Papua New Guinea: a cluster-randomised trial

Background

Methods

Findings

Interpretation

Funding

COVID-19 vaccine booster dose needed to achieve Omicron-specific neutralisation in nursing home residents

BACKGROUND

Nursing home (NH) residents have borne a disproportionate share of SARS-CoV-2 morbidity and mortality. Vaccines have limited hospitalisation and death from earlier variants in this vulnerable population. With the rise of Omicron and future variants, it is vital to sustain and broaden vaccine-induced protection. We examined the effect of boosting with BNT162b2 mRNA vaccine on humoral immunity and Omicron-specific neutralising activity among NH residents and healthcare workers (HCWs).

METHODS

We longitudinally enrolled 85 NH residents (median age 77) and 48 HCWs (median age 51), and sampled them after the initial vaccination series; and just before and 2 weeks after booster vaccination. Anti-spike, anti-receptor binding domain (RBD) and neutralisation titres to the original Wuhan strain and neutralisation to the Omicron strain were obtained.

FINDINGS

Booster vaccination significantly increased vaccine-specific anti-spike, anti-RBD, and neutralisation levels above the pre-booster levels in NH residents and HCWs, both in those with and without prior SARS-CoV-2 infection. Omicron-specific neutralisation activity was low after the initial 2 dose series with only 28% of NH residents' and 28% HCWs' titres above the assay's lower limit of detection. Omicron neutralising activity following the booster lifted 86% of NH residents and 93% of HCWs to the detectable range.

INTERPRETATION

With boosting, the vast majority of HCWs and NH residents developed detectable Omicron-specific neutralising activity. These data provide immunologic evidence that strongly supports booster vaccination to broaden neutralising activity and counter waning immunity in the hope it will better protect this vulnerable, high-risk population against the Omicron variant.

FUNDING

NIH AI129709-03S1, U01 CA260539-01, CDC 200-2016-91773, and VA BX005507-01.

Self-reported health condition severity and ambulation status postmajor dysvascular limb loss

BACKGROUND

Individuals with dysvascular lower limb amputations (LLA) secondary to complications of peripheral arterial disease (PAD) and/or diabetes have high rates of co-morbidities.

OBJECTIVES

To describe self-reported health condition severity and their association with sociodemographic factors and ambulations status among individuals with major dysvascular LLA.

STUDY DESIGN

Cross sectional telephone and in person survey with adults with major dysvascular LLA living in the community setting in Ontario, Canada.

METHODS

Survey by phone/in person, and completion of the Dysvascular Conditions Scale and Special Interest in Amputee Medicine Mobility (SIGAM) Grade by each participant.

RESULTS

Two hundred thirty-one individuals with major dysvascular LLAs participated in the study. Most of them were male individuals (80.5%) and had undergone a transtibial amputation (74%). On average, participants were 3.4 years postlimb loss and had five identified Dysvascular Conditions Scale health conditions. The top five reported health conditions were diabetes, hypertension, phantom limb pain, musculoskeletal pain, and back pain. With the exclusion of hypertension, these conditions were also perceived by respondents to be quite severe for their impact. Vision impairment was also rated as being severe in nature. Lower mobility Special Interest Group in Amputee Medicine grades were associated with higher health condition severity scores.

CONCLUSIONS

Individuals with dysvascular limb loss experience high multimorbidity with perceived negative impact on their overall wellness and function. Rehabilitation and self-management strategies to help patients with dysvascular LLAs to manage chronic health conditions may improve outcomes.

Establishment of instrument operation qualification and routine performance qualification procedures for handheld near-infrared spectrometers used at different locations within a laboratory network

Quality assurance of finished pharmaceuticals is a necessity in ensuring the safety of consumers. There is a need for low-cost and portable rapid screening methods of pharmaceuticals in resource limited areas. Recent advances in technology have made handheld and low-cost diffuse reflectance spectrometers available to the public. While these handheld spectrometers offer advantages over benchtop spectrometers, the accuracy and repeatability must be assessed before these instruments can be used for quality assurance screening. Here, five handheld spectrometers of the same model were purchased, where an in-house installation qualification and operational qualification (IQOQ) was subsequently established for the instruments. Wavelength and photometric accuracy (and repeatability), spectroscopic noise, stray light, and bandpass were assessed between instruments. Results were found to be consistent between the spectrometers, passing IQOQ procedures, and were determined to be ready for field use. Once the handheld spectrometer's performance was verified, a practical and low-cost daily performance verification was established using common high density polyethylene vial caps on location in South Africa, Thailand, and the United States. A Mahalanobis distance-based classifier found the five spectrometers to be in agreement.

Relationship between sociodemographics, healthcare providers' competence and healthcare access among two-spirit, gay, bisexual, queer and other men who have sex with men in Manitoba: results from a community-based cross-sectional study

OBJECTIVE

Little is known about barriers to healthcare access for two-spirit, gay, bisexual and queer (2SGBQ+) men in Manitoba.

DESIGN

Data were drawn from a community-based, cross-sectional survey designed to examine health and healthcare access among 2SGBQ+ men.

SETTING

Community-based cross-sectional study in Manitoba, Canada.

PARTICIPANTS

Community-based sample of 368 2SGBQ+ men.

OUTCOMES

Logistic regression analyses assessed the relationship between sociodemographics, healthcare discrimination, perceived healthcare providers' 2SGBQ+ competence/knowledge and two indicators of healthcare access (analytic outcome variables): (1) having a regular healthcare provider and (2) having had a healthcare visit in the past 12 months.

RESULTS

In multivariate analyses, living in Brandon (adjusted OR (AOR)=0.08, 95% CI 0.03 to 0.22), small cities (AOR=0.20, 95% CI 0.04 to 0.98) and smaller towns (AOR=0.26, 95% CI 0.08 o 0.81) in Manitoba (compared with living in Winnipeg), as well as having a healthcare provider with poor (AOR=0.19, 95% CI 0.04 to 0.90) or very poor competence/knowledge (AOR=0.03, 95% CI 0.03 to 0.25) of 2SGBQ+ men's issues (compared with very good competence) was associated with lower odds of having a regular healthcare provider. Living in Brandon (AOR=0.05, 95% CI 0.02 to 0.17) and smaller towns (AOR=0.25, 95% CI 0.67 to 0.90) in Manitoba (compared with living in Winnipeg) was associated with lower odds of having a healthcare visit in the past 12 months, while identifying as a gay man compared with bisexual (AOR=12.57, 95% CI 1.88 to 83.97) was associated with higher odds of having a healthcare visit in the past 12 months.

CONCLUSIONS

These findings underscore the importance of reducing the gap between the healthcare access of rural and urban 2SGBQ+ men, improving healthcare providers' cultural competence and addressing their lack of knowledge of 2SGBQ+ men's issues.

Improved Genomic Identification, Clustering, and Serotyping of Shiga Toxin-Producing Escherichia coli Using Cluster/Serotype-Specific Gene Markers

Shiga toxin-producing Escherichia coli (STEC) have more than 470 serotypes. The well-known STEC O157:H7 serotype is a leading cause of STEC infections in humans. However, the incidence of non-O157:H7 STEC serotypes associated with foodborne outbreaks and human infections has increased in recent years. Current detection and serotyping assays are focusing on O157 and top six (“Big six”) non-O157 STEC serogroups. In this study, we performed phylogenetic analysis of nearly 41,000 publicly available STEC genomes representing 460 different STEC serotypes and identified 19 major and 229 minor STEC clusters. STEC cluster-specific gene markers were then identified through comparative genomic analysis. We further identified serotype-specific gene markers for the top 10 most frequent non-O157:H7 STEC serotypes. The cluster or serotype specific gene markers had 99.54% accuracy and more than 97.25% specificity when tested using 38,534 STEC and 14,216 non-STEC E. coli genomes, respectively. In addition, we developed a freely available in silico serotyping pipeline named STECFinder that combined these robust gene markers with established E. coli serotype specific O and H antigen genes and stx genes for accurate identification, cluster determination and serotyping of STEC. STECFinder can assign 99.85% and 99.83% of 38,534 STEC isolates to STEC clusters using assembled genomes and Illumina reads respectively and can simultaneously predict stx subtypes and STEC serotypes. Using shotgun metagenomic sequencing reads of STEC spiked food samples from a published study, we demonstrated that STECFinder can detect the spiked STEC serotypes, accurately. The cluster/serotype-specific gene markers could also be adapted for culture independent typing, facilitating rapid STEC typing. STECFinder is available as an installable package (https://github.com/LanLab/STECFinder) and will be useful for in silico STEC cluster identification and serotyping using genome data.

Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping

Shigella and enteroinvasive Escherichia coli (EIEC) cause human bacillary dysentery with similar invasion mechanisms and share similar physiological, biochemical and genetic characteristics. Differentiation of Shigella from EIEC is important for clinical diagnostic and epidemiological investigations. However, phylogenetically, Shigella and EIEC strains are composed of multiple clusters and are different forms of E. coli, making it difficult to find genetic markers to discriminate between Shigella and EIEC. In this study, we identified 10 Shigella clusters, seven EIEC clusters and 53 sporadic types of EIEC by examining over 17000 publicly available Shigella and EIEC genomes. We compared Shigella and EIEC accessory genomes to identify cluster-specific gene markers for the 17 clusters and 53 sporadic types. The cluster-specific gene markers showed 99.64% accuracy and more than 97.02% specificity. In addition, we developed a freely available in silico serotyping pipeline named Shigella EIEC Cluster Enhanced Serotype Finder (ShigEiFinder) by incorporating the cluster-specific gene markers and established Shigella and EIEC serotype-specific O antigen genes and modification genes into typing. ShigEiFinder can process either paired-end Illumina sequencing reads or assembled genomes and almost perfectly differentiated Shigella from EIEC with 99.70 and 99.74% cluster assignment accuracy for the assembled genomes and read mapping respectively. ShigEiFinder was able to serotype over 59 Shigella serotypes and 22 EIEC serotypes and provided a high specificity of 99.40% for assembled genomes and 99.38% for read mapping for serotyping. The cluster-specific gene markers and our new serotyping tool, ShigEiFinder (installable package: https://github.com/LanLab/ShigEiFinder, online tool: https://mgtdb.unsw.edu.au/ShigEiFinder/), will be useful for epidemiological and diagnostic investigations.

Significantly elevated antibody levels and neutralization titers in nursing home residents after SARS-CoV-2 BNT162b2 mRNA booster vaccination

Nursing home (NH) residents have experienced significant morbidity and mortality to SARS-CoV-2 throughout the pandemic. Vaccines initially curbed NH resident morbidity and mortality, but antibody levels and protection have declined with time since vaccination, prompting introduction of booster vaccination. This study assesses humoral immune response to booster vaccination in 85 NH residents and 44 health care workers (HCW) that we have followed longitudinally since initial SARS-CoV-2 BNT162b2 mRNA vaccination. The findings reveal that booster vaccination significantly increased anti-spike, anti-receptor binding domain, and neutralization titers above the pre-booster levels in almost all NH residents and HCW to significantly higher levels than shortly after the completion of the initial vaccine series. These data support the CDC recommendation to offer vaccine boosters to HCWs and NH residents on an immunological basis. Notably, even the older, more frail and more multi-morbid NH residents have sizable antibody increases with boosting.

Reduced BNT162b2 Messenger RNA Vaccine Response in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)-Naive Nursing Home Residents

After BNT162b2 messenger RNA vaccination, antibody levels to spike, receptor-binding domain, and virus neutralization were examined in 149 nursing home residents and 110 healthcare worker controls. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-naive nursing home residents' median post-second vaccine dose antibody neutralization titers are one-quarter that of SARS-CoV-2-naive healthcare workers.

422. Sustainability of Improvements to Hand Hygiene Performance Throughout the COVID-19 Pandemic

Background

Hand hygiene (HH) is a standard infection prevention and control precaution to be applied in healthcare settings to prevent transmission of COVID-19. Many healthcare institutions observed significant improvements in HH performance during wave one of the COVID-19 pandemic but the sustainability of this change is unknown. Our aim was to evaluate long-term HH performance throughout subsequent waves of the pandemic across acute care hospitals in Ontario, Canada.

Methods

HH adherence was measured using a previously validated group electronic monitoring system which was installed on all alcohol handrub and sink soap dispensers inside and outside each patient room across 56 inpatient units (35 wards and 21 critical care units) spanning 13 acute care hospitals (6 university and 7 community teaching hospitals) from 1 November 2019 to 31 May 2021. Daily HH adherence was compared with daily COVID-19 case count across Ontario. During this period, weekly performance continued to be reported to units but unit-based quality improvement discussions were inconsistent due to the COVID-19 response.

Results

Figure 1 depicts daily aggregate HH adherence plotted against the new daily COVID-19 case count across Ontario. An elevation in HH adherence was seen prior to the start of the first wave, rising almost to 80% and then remained above 70% for the peak of wave one. During waves two and three, peak COVID-19 case counts were associated with a maximum HH adherence of 51%, only marginally above the pre-pandemic baseline. After the end of wave one (from 1 July 2020 to 31 May 2021) the median HH performance was only 49% (interquartile range 47%-50%).

Figure 1. Hand hygiene adherence across 13 acute care hospitals in comparison to overall new daily COVID-19 cases in Ontario

Conclusion

Initial improvements in HH adherence preceding the start of the COVID-19 pandemic were not sustained, possibly due to increasing comfort and reduced anxiety associated with providing care to COVID-19 patients leading to a perception of reduced COVID-19 transmission risk. These findings highlight the need for HH monitoring to be tied to longitudinal unit-led quality improvement in order to achieve durable changes in practice.

Disclosures

Susy S. Hota, MSc MD FRCPC, Finch Therapeutics (Research Grant or Support) Susy S. Hota, MSc MD FRCPC, Finch Therapeutics (Individual(s) Involved: Self): Grant/Research Support

Significant Reduction in Vaccine-Induced Antibody Levels and Neutralization Activity Among Healthcare Workers and Nursing Home Residents 6 Months Following Coronavirus Disease 2019 BNT162b2 mRNA Vaccination

Antibody decline occurred from 2 weeks to 6 months post-BNT162b2 mRNA vaccination in nursing home (NH) residents and healthcare workers. Antispike, receptor-binding domain, and neutralization levels dropped >81% irrespective of prior infection. Notably, 69% of infection-naive NH residents had neutralizing antibodies at or below the assay's limit of detection.

A low-cost and portable near-infrared spectrometer using open-source multivariate data analysis software for rapid discriminatory quality assessment of medroxyprogesterone acetate injectables

Medroxyprogesterone acetate (MPA) injectable suspensions are used by millions of women for family planning and hormonal therapy. Falsified or substandard medications may result in a health risk for consumers. Near-infrared spectroscopy (NIR) has previously been applied as a means of non-destructive and rapid screening of product quality compliance. These methods offer advantages but can be logistically and cost prohibitive for field use in resource limited areas. Here, a handheld spectrometer (900-1700 nm) with open-sourced software is used to evaluate vials of MPA from three suppliers (N = 227 vials) and verified by a benchtop UV-VIS-NIR (350-2500 nm) with licensed software. Multivariate data analysis assesses the spectral signatures of samples and builds a discriminant classification method based on Mahalanobis distances calculated from a principal component analysis scores. The handheld device paired with open-source software resulted in a product discrimination accuracy of 100% (verified by benchtop UV-VIS-NIR and chemical testing data) as well indicating that the low-cost field portable device is suitable for rapidly assessing samples in resource limited areas for consistency of manufacturing and sourcing.

P14.29 The treatment of melanoma brain metastases with stereotactic radiosurgery concurrently with immune checkpoint inhibition is associated with improved extracranial disease control and overall survival compared to the overall metastatic melanoma cohort - a synergistic effect reaching beyond local control?

BACKGROUND

Melanoma brain metastases (MBM) are an increasingly common referral to the neuro-oncology MDT in the context of lengthening survivorship of metastatic melanoma (MM) patients in the immunotherapy era. Stereotactic radiosurgery (SRS) and immune checkpoint inhibition (ICI) are both effective in the management of MBM and, when combined, 12-month local control rates of &gt;85% and overall survival (OS) &gt;80% have been reported.[4,5] Recent local analysis of patients treated at our tertiary SRS referral centre has revealed even greater outcomes in this patient cohort. This study aimed to compare the outcomes of patients with MBM treated with concurrent SRS and ICI compared to the overall metastatic melanoma cohort, to elucidate whether the addition of SRS to ICI may improve disease control outside of the brain as well as within.

MATERIAL AND METHODS

A retrospective analysis of our local SRS database and an ARIA ePrescribing database search was performed to identify a cohort of patients treated with concurrent SRS and ICI for MBM, as well as a control cohort of MM patients who received ICI alone, over a 4 year period until February 2020. The primary endpoints were the extracranial progression free survival (PFS) and overall survival (OS) at 12 months. Secondary endpoints were the median PFS (mPFS) and OS (mOS). Kaplan-Meier curves and survival statistics were generated using SPSS v26.

RESULTS

A total of 34 MBM from 19 patients were identified in the SRS+ICI group and there were 200 patients in the control group. The minimum follow up was 12 months. The median patient age, duration of ICI and use of combination ICI favoured the SRS+ICI group. The number of sites of extracranial disease pre-ICI and overall anti-PD-1 usage was well matched. In the SRS+ICI group, there were no cases of extracranial progression and no deaths within 12 months. In the control group, the 12-month PFS and OS rates were 50.5% and 77.5% respectively. In terms of mPFS, this was not reached (estimated 37.6 months) in the SRS+ICI group, versus 13.4 months in the control group (log rank test, p=0.001). In terms of mOS, this was not reached in the SRS+ICI group, versus 55.8 months in the control group (log rank test, p=0.016).

CONCLUSION

We demonstrate improved extracranial disease control and survivorship amongst metastatic melanoma patients who develop brain metastases and are treated with concurrent SRS and ICI compared to those who do not. The outcomes of our control cohort are comparable to the 4-year follow up of the CheckMate 067 trial (n=945),[6] which strengthens the validity of the statistical comparisons made in this study. The improved extracranial disease control seen when SRS and ICI are combined in the treatment of MBM questions whether an abscopal effect may be at play, and therefore further accents the utility of SRS in MBM beyond that of local control alone. This could influence management in cases of borderline decisions for SRS.

P–539 The use of expanded carrier screening of gamete donors

Study question

What are the sperm and egg donor rejection rates after expanded carrier screening (ECS)?

Summary answer

Using an ECS panel looking at 46/47 genes, 17.6% of donors were rejected.

What is known already

The use of ECS is becoming commonplace in assisted reproductive technology, including testing of egg and sperm donors. Most national guidelines recommend rejection of donors if they are carriers of a genetic disease. If the use of ECS increases, there will be a decline in the number of donors available.

Study design, size, duration

A review of the current preconception ECS panels available to donors was carried out through an online search. The genetic testing results of donors from Cryos International were analysed to determine how many were rejected on the basis of the ECS.

Participants/materials, setting, methods

Data on gamete donors and their carrier status was provided by Cryos International, who screen donors using their own bespoke ECS panel. The ECS panels identified through the review were compared to the Cryos International panel and data.

Main results and the role of chance

A total of 16 companies and 42 associated ECS panels were reviewed. There were a total of 2673 unique disorders covered by the panels examined, with a mean of 329 disorders screened. None of these disorders were common to all panels. Cryos International screen 46 disorders in males and 47 in females. From 883 candidate donors, 17.6% (155/883) were rejected based on their ECS result. Carriers of alpha-thalassaemia represented the largest proportion of those rejected (19.4%, 30/155), then spinal muscular atrophy (15.5%, 24/155) and cystic fibrosis (14.8%, 23/155).

Limitations, reasons for caution

Panel information was found on company web sites and may not have been accurate.

Wider implications of the findings: This study highlights the need for consistent EU regulations and guidelines which allow genetic matching of gamete donors to recipients, preventing the need to reject donors who are known carriers. A larger ECS panel would be most beneficial, however, this would not be viable without matching of donors and recipients.

Trial registration number

Not applicable

Population Structure and Multidrug Resistance of Non-O1/Non-O139 Vibrio cholerae in Freshwater Rivers in Zhejiang, China

To understand the environmental reservoirs of Vibrio cholerae and their public health significance, we surveyed freshwater samples from rivers in two cities (Jiaxing [JX] and Jiande [JD]) in Zhejiang, China. A total of 26 sampling locations were selected, and river water was sampled 456 times from 2015 to 2016 yielding 200 V. cholerae isolates, all of which were non-O1/non-O139. The average isolation rate was 47.3% and 39.1% in JX and JD, respectively. Antibiotic resistance profiles of the V. cholerae isolates were examined with nonsusceptibility to cefazolin (68.70%, 79/115) being most common, followed by ampicillin (47.83%, 55/115) and imipenem (27.83%, 32/115). Forty-two isolates (36.52%, 42/115) were defined as multidrug resistant (MDR). The presence of virulence genes was also determined, and the majority of the isolates were positive for toxR (198/200, 99%) and hlyA (196/200, 98%) with few other virulence genes observed. The population structure of the V. cholerae non-O1/non-O139 sampled was examined using multilocus sequence typing (MLST) with 200 isolates assigned to 128 STs and 6 subpopulations. The non-O1/non-O139 V. cholerae population in JX was more varied than in JD. By clonal complexes (CCs), 31 CCs that contained isolates from this study were shared with other parts of China and/or other countries, suggesting widespread presence of some non-O1/non-O139 clones. Drug resistance profiles differed between subpopulations. The findings suggest that non-O1/non-O139 V. cholerae in the freshwater environment is a potential source of human infections. Routine surveillance of non-O1/non-O139 V. cholerae in freshwater rivers will be of importance to public health.

Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing

Salmonella enterica serovar Enteritidis is a major cause of foodborne Salmonella infections and outbreaks in humans. Effective surveillance and timely outbreak detection are essential for public health control. Multilevel genome typing (MGT) with multiple levels of resolution has been previously demonstrated as a promising tool for this purpose. In this study, we developed MGT with nine levels for S. Enteritidis and characterised the genomic epidemiology of S. Enteritidis in detail. We examined 26 670 publicly available S. Enteritidis genome sequences from isolates spanning 101 years from 86 countries to reveal their spatial and temporal distributions. Using the lower resolution MGT levels, globally prevalent and regionally restricted sequence types (STs) were identified; avian associated MGT4-STs were found that were common in human cases in the USA; temporal trends were observed in the UK with MGT5-STs from 2014 to 2018 revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified multidrug resistance (MDR) associated STs at various MGT levels, which improves precision of detection and global tracking of MDR clones. We also found that the majority of the global S. Enteritidis population fell within two predominant lineages, which had significantly different propensity of causing large scale outbreaks. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.

Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds

Salmonella enterica serovar Typhimurium is the leading cause of salmonellosis in Australia, and the ability to identify outbreaks and their sources is vital to public health. Here, we examined the utility of whole-genome sequencing (WGS), including complete genome sequencing with Oxford Nanopore technologies, in examining 105 isolates from an endemic multi-locus variable number tandem repeat analysis (MLVA) type over 5 years. The MLVA type was very homogeneous, with 90 % of the isolates falling into groups with a five SNP cut-off. We developed a new two-step approach for outbreak detection using WGS. The first clustering at a zero single nucleotide polymorphism (SNP) cut-off was used to detect outbreak clusters that each occurred within a 4 week window and then a second clustering with dynamically increased SNP cut-offs were used to generate outbreak investigation clusters capable of identifying all outbreak cases. This approach offered optimal specificity and sensitivity for outbreak detection and investigation, in particular of those caused by endemic MLVA types or clones with low genetic diversity. We further showed that inclusion of complete genome sequences detected no additional mutational events for genomic outbreak surveillance. Phylogenetic analysis found that the MLVA type was likely to have been derived recently from a single source that persisted over 5 years, and seeded numerous sporadic infections and outbreaks. Our findings suggest that SNP cut-offs for outbreak cluster detection and public-health surveillance should be based on the local diversity of the relevant strains over time. These findings have general applicability to outbreak detection of bacterial pathogens.

Association between distance from the radiation source and radiation exposure: A phantom-based study

OBJECTIVES

The study evaluated the association between distance from radiation source and radiation exposure.

BACKGROUND

Radiation exposure during medical procedures is associated with increased risk of cancer and other adverse effects.

METHODS

An American National Standards Institute phantom was used to study the relationship between measured entrance surface exposure (MESE) and distance from the X-ray source in postero-anterior, left anterior oblique, and right anterior oblique projections. Three distance settings for table height were evaluated with "low" defined as 52 cm, "mid" 66 cm, and "high" 80 cm from the focal point of the X-ray source. Air-kerma and dose-area product measurements were recorded. Operator exposure with each of these conditions was measured, in a short operator (150 cm) as well as in a tall operator (190 cm).

RESULTS

Aggregate results for the three projections were as follows. MESE (μGy/frame) significantly decreased as table-height increases (median, interquartile range, p-value) (low table-height 192.5 [122.4-201.2], mid table-height 105.8 [82.7-115.8], and high table-height 71.7 [58.4-75], p < .0005). The operator exposure (μGy/frame), significantly increased as the table-height increased (low table-height 0.0943 [0.0598-0.1157], medium table-height 0.1128 [0.0919-0.1397], and high table-height 0.158 [0.1339-0.2165], p < .0005). A shorter operator received higher radiation exposure compared to a taller operator (short operator 0.1405 [0.1155-0.1758] and tall operator 0.0995 [0.0798-0.1212], p < .0005).

CONCLUSIONS

Increasing table-height is associated with a significant decrease in MESE. Operator radiation exposure increases with increasing table-height and shorter operators receive greater radiation exposure compared to taller operators.

Reduced BNT162b2 mRNA vaccine response in SARS-CoV-2-naive nursing home residents

The SARS-CoV-2 pandemic impact on nursing home (NH) residents prompted their prioritization for early vaccination. To fill the data gap for vaccine immunogenicity in NH residents, we examined antibody levels after BNT162b2 mRNA vaccine to spike, receptor binding domain (RBD) and for virus neutralization in 149 NH residents and 111 health care worker controls. SARS-CoV-2-naive NH residents mount antibody responses with nearly 4-fold lower median neutralization titers and half the anti-spike level compared to SARS-CoV-2-naive healthcare workers. By contrast, SARS-CoV-2-recovered vaccinated NH residents had neutralization, anti-spike and anti-RBD titers similar to SARS-CoV-2-recovered vaccinated healthcare workers. NH residents' blunted antibody responses have important implications regarding the quality and durability of protection afforded by neoantigen vaccines. We urgently need better longitudinal evidence on vaccine effectiveness specific to NH resident populations to inform best practices for NH infection control measures, outbreak prevention and potential indication for a vaccine boost.

Phenotypic and Genotypic Correlates of Penicillin Susceptibility in Nontoxigenic Corynebacterium diphtheriae, British Columbia, Canada, 2015-2018

In 2015, the Clinical and Laboratory Standards Institute (CLSI) updated its breakpoints for penicillin susceptibility in Corynebacterium species from <1 mg/L to <0.12 mg/L. We assessed the effect of this change on C. diphtheriae susceptibility reported at an inner city, tertiary care center in Vancouver, British Columbia, Canada, during 2015–2018 and performed whole-genome sequencing to investigate phenotypic and genotypic resistance to penicillin. We identified 44/45 isolates that were intermediately susceptible to penicillin by the 2015 breakpoint, despite meeting previous CLSI criteria for susceptibility. Sequencing did not reveal β-lactam resistance genes. Multilocus sequence typing revealed a notable predominance of sequence type 76. Overall, we saw no evidence of penicillin nonsusceptibility at the phenotypic or genotypic level in C. diphtheriae isolates from our institution. The 2015 CLSI breakpoint change could cause misclassification of penicillin susceptibility in C. diphtheriae isolates, potentially leading to suboptimal antimicrobial treatment selection.

Development and comparison of novel multiple cross displacement amplification (MCDA) assays with other nucleic acid amplification methods for SARS-CoV-2 detection

The development of alternative isothermal amplification assays including multiple cross displacement amplification (MCDA) may address speed and portability limitations of real-time PCR (rt-PCR) methods for SARS-CoV-2 detection. We developed a novel SARS-CoV-2 MCDA assay and compared its speed and sensitivity to loop-mediated isothermal amplification (LAMP) and rt-PCR. Two MCDA assays targeting SARS-CoV-2 N gene and ORF1ab were designed. The fastest time to detection and sensitivity of MCDA was compared to LAMP and rt-PCR using DNA standards and transcribed RNA. For the N gene, MCDA was faster than LAMP and rt-PCR by 10 and 20 min, respectively with fastest time to detection at 5.2 min. rt-PCR had the highest sensitivity with the limit of detection at 10 copies/µl compared with MCDA (100 copies/µl) and LAMP (500 copies/µl). For ORF1ab, MCDA and LAMP had similar speed with fastest time to detection at 9.7 and 8.4 min, respectively. LAMP was more sensitive for ORF1ab detection with 50 copies/µl compared to MCDA (500 copies/µl). In conclusion, different nucleic acid amplification methods provide different advantages. MCDA is the fastest nucleic acid amplification method for SARS-CoV-2 while rt-PCR is the most sensitive. These advantages should be considered when determining the most suitable nucleic acid amplification methods for different applications.

The Effect of Dual-Task Testing on Balance and Gait Performance in Adults with Type 1 or Type 2 Diabetes Mellitus: A Systematic Review

BACKGROUND

Individuals with diabetes mellitus (DM) are susceptible to balance, gait and cognitive impairments. Importantly, diabetes affects executive function, a set of cognitive processes critical to everyday cortical function and mobility. Reduced executive function is a risk factor for falls in people with DM. Dual-task testing, the completion of two tasks at once, enables the examination of the cognitive-mobility relationship. A synthesis of the literature on the effects of dual- task testing on the balance and gait of individuals with DM has not been performed.

OBJECTIVE

To systematically review the literature on the effect of dual-task testing on balance and gait in people with DM.

METHODS

Databases EMBASE, CINAHL, MEDLINE, PsycINFO, Scopus and Web of Science were searched (inception-April 2020).

INCLUSION CRITERIA

participants were adults with a diagnosis of DM, instrumented dual-task balance and/or gait was assessed, and articles were published in English.

RESULTS

Ten articles met inclusion criteria- three examined dual-task balance and seven dual-task gait. In people with DM with or without peripheral neuropathy, dual-task resulted in larger sway velocities during standing tests. Individuals with DM and peripheral neuropathy had impaired dual-- task gait; specifically, and more consistently, reduced pace and rhythm compared to controls or people with DM without peripheral neuropathy.

CONCLUSION

The findings support a compromise in the cognitive-mobility relationship of people with DM, and especially in those with peripheral neuropathy. Future research should continue to examine the cognitive-mobility relationship in order to understand the increased prevalence of falls in this population.

Multilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens

Background

Both long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of strain relatedness. Previous typing efforts using these data have mainly focussed on outbreak detection.

Aim

We aimed to develop multilevel genome typing (MGT), using consecutive multilocus sequence typing (MLST) schemes of increasing sizes, stepping up from seven-gene MLST to core genome MLST, to allow examination of genetic relatedness at multiple resolution levels.

Methods

The system was applied to Salmonellaenterica serovar Typhimurium. The MLST scheme used at each step (MGT level), defined a given MGT-level specific sequence type (ST). The list of STs generated from all of these increasing MGT levels, was named a genome type (GT). Using MGT, we typed 9,096 previously characterised isolates with publicly available data.

Results

Our approach could identify previously described S. Typhimurium populations, such as the DT104 multidrug resistance lineage (GT 19-2-11) and two invasive lineages of African isolates (GT 313-2-3 and 313-2-752). Further, we showed that MGT-derived clusters can accurately distinguish five outbreaks from each other and five background isolates.

Conclusion

MGT provides a universal and stable nomenclature at multiple resolutions for S. Typhimurium strains and could be implemented as an internationally standardised strain identification system. While established so far only for S. Typhimurium, the results here suggest that MGT could form the basis for typing systems in other similar microorganisms.

Self-directed usage of an in-home exergame after a supervised telerehabilitation training program for older adults with lower-limb amputation

BACKGROUND

While home-based exergames help overcome accessibility barriers to rehabilitation, it is unclear what constitutes effective intervention design in using exergames to support self-efficacy and engagement.

OBJECTIVE

Examine usage of an in-home exergame, compared to control, unsupervised after supervised training by older persons with lower-limb amputation.

STUDY DESIGN

Secondary analysis of a multi-site parallel evaluator-masked randomized control trial.

METHODS

WiiNWalk uses the WiiFit and teleconferencing for in-home group-based exergame therapy with clinical supervision. Participants engaged in a 4-week supervised training phase followed by a 4-week unsupervised phase in experimental (WiiNWalk) and attention control groups. Usage between phases and between groups was compared using unsupervised/supervised ratio of session count (over 4 weeks) and session time (mean min/session over 4 weeks) for each phase.

RESULTS

Participants: n=36 experimental, n=28 control, unilateral lower-limb amputation, age > 50 years, prosthesis usage ≥ 2 hours/day. Session count ratio unsupervised/supervised, median and interquartile range (IQR), was less than parity (p<0.01) for experimental (0.25, IQR 0.00 -0.68) and control (0.18, IQR 0.00 -0.67) groups, with no different between groups (p=0.92). Experimental session time unsupervised/supervised showed consistency (1.12, IQR 0.80 -1.41) between phases (p=0.24); control showed lower (0.76, IQR 0.57 -1.08) ratios compared to experimental (p=0.027).

CONCLUSIONS

Unsupervised exercise duration remained consistent with supervised, but frequency was reduced. Social and clinical guidance features may remain necessary for sustained lower-limb amputation exergame engagement at home.

CLINICAL RELEVANCE

This study provides context regarding when prosthesis users are more likely to use exergames such as Wii Fit for exercise therapy. Clinicians may consider our results when applying exergames in their practice or when developing new exergame intervention strategies.

Impressions on Reliability and Students' Perceptions of Learning in a Peer-Based OSCE

BACKGROUND

Peer assessment of performance in the objective structured clinical examination (OSCE) is emerging as a learning instrument. While peers can provide reliable scores, there may be a trade-off with students' learning. The purpose of this study is to evaluate a peer-based OSCE as a viable assessment instrument and its potential to promote learning and explore the interplay between these two roles.

METHODS

A total of 334 medical students completed an 11-station OSCE from 2015 to 2016. Each station had 1-2 peer examiners (PE) and one faculty examiner (FE). Examinees were rated on a 7-point scale across 5 dimensions: Look, Feel, Move, Special Tests and Global Impression. Students participated in voluntary focus groups in 2016 to provide qualitative feedback on the OSCE. Authors analysed assessment data and transcripts of focus group discussions.

RESULTS

Overall, PE awarded higher ratings compared with FE, sources of variance were similar across 2 years with unique variance consistently being the largest source, and reliability (r _φ ) was generally low. Focus group analysis revealed four themes: Conferring with Faculty Examiners, Difficulty Rating Peers, Insider Knowledge, and Observing and Scoring.

CONCLUSIONS

While peer assessment was not reliable for evaluating OSCE performance, PE's perceived that it was beneficial for their learning. Insight gained into exam technique and self-appraisal of skills allows students to understand expectations in clinical situations and plan approaches to self-assessment of competence.