Postharvest control of Rhizopus stolonifer on blackberry (Rubus fruticosus) by blackberry native crop bacteria

The potential of four native bacterial strains of blackberries cv. Brazos (Rubus fruticosus): Bacillus subtilis (BSS), Bacillus subtilis (BSL), Bacillus licheniformis (BLI) and Leifsonia aquatica (LAQ), was evaluated for the postharvest control of soft rot caused by Rhizopus stolonifer in blackberry fruits. The fruits were treated with cell suspensions (CS) and cell-free supernatants (CFE) from each bacterial strain and were infected with two strains of R. stolonifer (RSA and RSC). The severity and inhibition percentage of the disease were determined. Additionally, the inhibition by siderophores and the inhibition percentage of R. stolonifer spore germination were analyzed as possible control mechanisms. The CS of BSS inhibited RSA by 45.8%, followed by CFE of LAQ which controlled the same strain by 39.7%. The CS of BLI inhibited RSC by 37.7%, whereas the CFE of BSS and LAQ controlled it by 47.7 and 41.8%, respectively. All bacterial strains inhibited RSA and RSC by siderophores production (38.7 to 48.6 %) and the inhibition of spore germination of RSC was higher than 93% after 48 h. This work is one of the first to report R. stolonifer control by native bacteria CS and CFE, particularly LAQ in postharvested blackberry fruits. These results show the combination of mechanisms used by bacteria to control both R. stolonifer strains.The potential of four native bacterial strains of blackberries cv. Brazos (Rubus fruticosus): Bacillus subtilis (BSS), Bacillus subtilis (BSL), Bacillus licheniformis (BLI) and Leifsonia aquatica (LAQ), was evaluated for the postharvest control of soft rot caused by Rhizopus stolonifer in blackberry fruits. The fruits were treated with cell suspensions (CS) and cell-free supernatants (CFE) from each bacterial strain and were infected with two strains of R. stolonifer (RSA and RSC). The severity and inhibition percentage of the disease were determined. Additionally, the inhibition by siderophores and the inhibition percentage of R. stolonifer spore germination were analyzed as possible control mechanisms. The CS of BSS inhibited RSA by 45.8%, followed by CFE of LAQ which controlled the same strain by 39.7%. The CS of BLI inhibited RSC by 37.7%, whereas the CFE of BSS and LAQ controlled it by 47.7 and 41.8%, respectively. All bacterial strains inhibited RSA and RSC by siderophores production (38.7 to 48.6 %) and the inhibition of spore germination of RSC was higher than 93% after 48 h. This work is one of the first to report R. stolonifer control by native bacteria CS and CFE, particularly LAQ in postharvested blackberry fruits. These results show the combination of mechanisms used by bacteria to control both R. stolonifer strains

Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions

Background: In the wake of the SARS-CoV-2 pandemic, scientists have scrambled to collect and analyze SARS-CoV-2 genomic data to inform public health responses to COVID-19 in real time. Open source phylogenetic and data visualization platforms for monitoring SARS-CoV-2 genomic epidemiology have rapidly gained popularity for their ability to illuminate spatial-temporal transmission patterns worldwide. However, the utility of such tools to inform public health decision-making for COVID-19 in real time remains to be explored. Objective: The aim of this study is to convene experts in public health, infectious diseases, virology, and bioinformatics—many of whom were actively engaged in the COVID-19 response—to discuss and report on the application of phylodynamic tools to inform pandemic responses. Methods: In total, 4 focus groups (FGs) occurred between June 2020 and June 2021, covering both the pre- and postvariant strain emergence and vaccination eras of the ongoing COVID-19 crisis. Participants included national and international academic and government researchers, clinicians, public health practitioners, and other stakeholders recruited through purposive and convenience sampling by the study team. Open-ended questions were developed to prompt discussion. FGs I and II concentrated on phylodynamics for the public health practitioner, while FGs III and IV discussed the methodological nuances of phylodynamic inference. Two FGs per topic area to increase data saturation. An iterative, thematic qualitative framework was used for data analysis. Results: We invited 41 experts to the FGs, and 23 (56%) agreed to participate. Across all the FG sessions, 15 (65%) of the participants were female, 17 (74%) were White, and 5 (22%) were Black. Participants were described as molecular epidemiologists (MEs; n=9, 39%), clinician-researchers (n=3, 13%), infectious disease experts (IDs; n=4, 17%), and public health professionals at the local (PHs; n=4, 17%), state (n=2, 9%), and federal (n=1, 4%) levels. They represented multiple countries in Europe, the United States, and the Caribbean. Nine major themes arose from the discussions: (1) translational/implementation science, (2) precision public health, (3) fundamental unknowns, (4) proper scientific communication, (5) methods of epidemiological investigation, (6) sampling bias, (7) interoperability standards, (8) academic/public health partnerships, and (9) resources. Collectively, participants felt that successful uptake of phylodynamic tools to inform the public health response relies on the strength of academic and public health partnerships. They called for interoperability standards in sequence data sharing, urged careful reporting to prevent misinterpretations, imagined that public health responses could be tailored to specific variants, and cited resource issues that would need to be addressed by policy makers in future outbreaks. Conclusions: This study is the first to detail the viewpoints of public health practitioners and molecular epidemiology experts on the use of viral genomic data to inform the response to the COVID-19 pandemic. The data gathered during this study provide important information from experts to help streamline the functionality and use of phylodynamic tools for pandemic responses

Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota)

Compared to the higher fungi (Dikarya), taxonomic and evolutionary studies on the basal clades of fungi are fewer in number. Thus, the generic boundaries and higher ranks in the basal clades of fungi are poorly known. Recent DNA based taxonomic studies have provided reliable and accurate information. It is therefore necessary to compile all available information since basal clades genera lack updated checklists or outlines. Recently, Tedersoo et al. (MycoKeys 13:1--20, 2016) accepted Aphelidiomycota and Rozellomycota in Fungal clade. Thus, we regard both these phyla as members in Kingdom Fungi. We accept 16 phyla in basal clades viz. Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. Thus, 611 genera in 153 families, 43 orders and 18 classes are provided with details of classification, synonyms, life modes, distribution, recent literature and genomic data. Moreover, Catenariaceae Couch is proposed to be conserved, Cladochytriales Mozl.-Standr. is emended and the family Nephridiophagaceae is introduced

Structural forces and the production of TB-related stigma among Haitians in two contexts

In recent years renewed interest in health-related stigma has underscored the importance of better understanding the structural underpinnings of stigma processes. This study investigated the influence of sociocultural context on perceived components of tuberculosis-related stigma in non-affected persons by comparing Haitians living in South Florida, USA, with Haitians residing in Leogane Commune, Haiti. Using the methods of cultural epidemiology, a two-phase study based on fieldwork between 2004 and 2007 collected ethnographic data on the cultural context and components of tuberculosis (TB) stigma, and administered a stigma scale developed specifically for these populations. Thematic analysis of stigma components expressed in interviews, focus groups and observation revealed commonalities as well as distinctive emphases of TB stigma in the two comparison groups. Factor analyses of stigma scale scores confirmed the thematic differences revealed in ethnographic findings and highlight the influence of political and economic factors in shaping the meaning and experience of illness. Perceived components of TB stigma among Haitians in South Florida incorporated aspects of Haitian identity as a negatively stereotyped minority community within the larger society, while in Haiti, stigma was associated primarily with poverty, malnutrition, and HIV co-infection. Discussion of findings focuses on the social production of perceived and anticipated stigma as it is influenced by structural forces including the influences of politics, economics, institutional policies, and health service delivery structures. The findings also demonstrate the value of a transnational framework encompassing both sending and receiving countries for understanding TB-related stigma in immigrant communitie

Structural forces and the production of TB-related stigma among Haitians in two contexts

In recent years renewed interest in health-related stigma has underscored the importance of better understanding the structural underpinnings of stigma processes. This study investigated the influence of sociocultural context on perceived components of tuberculosis-related stigma in non-affected persons by comparing Haitians living in South Florida, USA, with Haitians residing in Léogane Commune, Haiti. Using the methods of cultural epidemiology, a two-phase study based on fieldwork between 2004 and 2007 collected ethnographic data on the cultural context and components of tuberculosis (TB) stigma, and administered a stigma scale developed specifically for these populations. Thematic analysis of stigma components expressed in interviews, focus groups and observation revealed commonalities as well as distinctive emphases of TB stigma in the two comparison groups. Factor analyses of stigma scale scores confirmed the thematic differences revealed in ethnographic findings and highlight the influence of political and economic factors in shaping the meaning and experience of illness. Perceived components of TB stigma among Haitians in South Florida incorporated aspects of Haitian identity as a negatively stereotyped minority community within the larger society, while in Haiti, stigma was associated primarily with poverty, malnutrition, and HIV co-infection. Discussion of findings focuses on the social production of perceived and anticipated stigma as it is influenced by structural forces including the influences of politics, economics, institutional policies, and health service delivery structures. The findings also demonstrate the value of a transnational framework encompassing both sending and receiving countries for understanding TB-related stigma in immigrant communities.Haiti USA Stigma Tuberculosis Haitians Cultural epidemiology Immigrant communities

Genomic investigation of a mycobacterium tuberculosis outbreak involving prison and community cases in Florida, United States

We used whole-genome sequencing to investigate a tuberculosis outbreak involving U.S.-born persons in the prison system and both U.S.- and foreign-born persons in the community in Florida over a 7-year period (2009-2015). Genotyping by spacer oligonucleotide typing and 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat suggested that the outbreak might be clonal in origin. However, contact tracing could not link the two populations. Through a multidisciplinary approach, we showed that the cluster involved distinct bacterial transmission networks segregated by country of birth. The source strain is of foreign origin and circulated in the local Florida community for more than 20 years before introduction into the prison system. We also identified novel transmission links involving foreign and U.S.-born cases not discovered during contact investigation. Our data highlight the potential for spread of strains originating from outside the United States into U.S. "high-risk" populations (such as prisoners), with subsequent movement back to the general community

Management and diagnosis of tuberculosis in solid organ transplant candidates and recipients: Expert survey and updated review,

Background: Optimal screening and management of latent tuberculosis infection (LTBI) and active tuberculosis (TB) in solid organ transplant (SOT) candidates and recipients is necessary to prevent morbidity and mortality.Methods: We conducted a cross-sectional survey of TB and transplant experts across the United States reviewing the clinical practice preferences on key management issues related to LTBI and TB in SOT candidates and recipients.Results: Thirty TB and 13 SOT experts were surveyed (response rate = 53.8%). Both groups agreed that tuberculin skin test (TST) and chest x-ray screening in SOT candidates was useful (78.6% and 84.6%, respectively). TST after SOT was not useful for most transplant experts and TB experts (0% vs. 32.1%, respectively), but both groups were split on usefulness of interferon gamma release assays (IGRA) in SOT recipients (42.9% TB experts vs. 46.2% SOT experts). Most experts recommend LTBI treatment prior to SOT if close monitoring is assured (82.1% TB experts vs. 76.9% transplant experts). LTBI treatment with isoniazid was preferred for patients on calcineurin inhibitors. Evaluation for suspected TB in SOT recipients varied, but most TB experts favored sputum testing (88.9%) whereas most transplant experts favored bronchoscopic testing (69.2%). Preferred TB treatment regimens in SOT recipients were similar to regimens recommended for immunocompetent patients.Conclusions: Most TB and transplant experts recommend evaluation and treatment for LTBI in SOT candidates. Liver transplant candidates, however, should only be treated if close monitoring can be assured and after consulting with a hepatologist. Practice preferences varied regarding the initial diagnostic approach for suspected TB in SOT recipients; however, most experts agreed that SOT recipients should receive similar treatments as immunocompetent patients. Keywords: Tuberculosis, Transplantation, Surve

Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness

Objective: To determine if viable virus could be isolated from the air within a car driven by a patient infected with SARS-CoV-2, and to assess the size range of the infectious particles. Methods: We used a Sioutas personal cascade impactor sampler (PCIS) to screen for SARS-CoV-2 in a car driven by a COVID-19 patient. The patient, who had only mild illness without fever or cough and was not wearing a mask, drove the car for 15 min with the air conditioning turned on and windows closed. The PCIS was clipped to the sun-visor above the front passenger seat and was retrieved from the car two hours after completion of the drive. Results: SARS-CoV-2 was detectable at all PCIS stages by PCR and was cultured from the section of the sampler collecting particles in the 0.25–0.50 μm size range. Conclusions: Our data highlight the potential risk of SARS-CoV-2 transmission by minimally symptomatic persons in the closed space inside of a car and suggest that a substantial component of that risk is via aerosolized virus