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The gold standard for coronavirus disease 2019 diagnostic testing relies on RNA extraction from naso/oropharyngeal swab followed by amplification through reverse transcription-polymerase chain reaction (RT-PCR) with fluorogenic probes. While the test is extremely sensitive and specific, its high cost and the potential discomfort associated with specimen collection made it suboptimal for public health screening purposes. In this study, we developed an equally reliable, but cheaper and less invasive alternative test based on a one-step RT-PCR with the DNA-intercalating dye SYBR Green, which enables the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from saliva samples or RNA isolated from nasopharyngeal (NP) swabs. Importantly, we found that this type of testing can be fine-tuned to discriminate SARS-CoV-2 variants of concern. The saliva RT-PCR SYBR Green test was successfully used in a mass-screening initiative targeting nearly 4500 asymptomatic children under the age of 12. Testing was performed at a reasonable cost, and in some cases, the saliva test outperformed NP rapid antigen tests in identifying infected children. Whole genome sequencing revealed that the antigen testing failure could not be attributed to a specific lineage of SARS-CoV-2. Overall, this work strongly supports the view that RT-PCR saliva tests based on DNA-intercalating dyes represent a powerful strategy for community screening of SARS-CoV-2. The tests can be easily applied to other infectious agents and, therefore, constitute a powerful resource for an effective response to future pandemics., (© The Author(s) 2024. Published by Oxford University Press.)

Some members of the Firmicutes phylum, including many members of the human gut microbiota, are able to differentiate a dormant and highly resistant cell type, the endospore (hereinafter spore for simplicity). Spore-formers can colonize virtually any habitat and, because of their resistance to a wide variety of physical and chemical insults, spores can remain viable in the environment for long periods of time. In the anaerobic enteric pathogen Clostridioides difficile the aetiologic agent is the oxygen-resistant spore, while the toxins produced by actively growing cells are the main cause of the disease symptoms. Here, we review the regulatory circuits that govern entry into sporulation. We also cover the role of spores in the infectious cycle of C. difficile in relation to spore structure and function and the main control points along spore morphogenesis., (© 2024. The Author(s), under exclusive license to Springer Nature Switzerland AG.)

Oral vaccines are highly demanded by the aquaculture sector, to allow mass delivery of antigens without using the expensive and labor-intensive injectable vaccines. These later require individual handling of fish, provoking stress-related mortalities. One possible strategy to create injection-free vaccine delivery vehicles is the use of bacterial spores, extremely resistant structures with wide biotechnological applications, including as probiotics, display systems, or adjuvants. Bacterial spores, in particular those of Bacillus subtilis , have been shown to behave as mucosal vaccine adjuvants in mice models. However, such technology has not been extensively explored against fish bacterial disease. In this study, we used a laboratory strain of B. subtilis , for which a variety of genetic manipulation tools are available, to display at its spores surface either a Vibrio antigenic protein, OmpK, or the green fluorescence protein, GFP. When previously vaccinated by immersion with the OmpK- carrying spores, zebrafish survival upon a bacterial challenge with V. anguillarum and V. parahaemolyticus , increased up to 50 - 90% depending on the pathogen targeted. Further, we were able to detect anti-GFP-antibodies in the serum of European seabass juveniles fed diets containing the GFP-carrying spores and anti- V. anguillarum antibodies in the serum of European seabass juveniles fed the OmpK-carrying spores containing diet. More important, seabass survival was increased from 60 to 86% when previously orally vaccinated with in-feed OmpK- carrying spores. Our results indicate that B. subtilis spores can effectively be used as antigen-carriers for oral vaccine delivery in fish., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Gonçalves, Santos, Coutinho, Pedrosa, Curado, Machado, Costas, Bonneville, Serrano, Carvalho, Díaz-Rosales, Oliva-Teles, Couto and Serra.)

Introduction: Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates., Material and Methods: Ten CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated., Results: Clinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides., Discussion: WGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time., Conclusion: In Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.

Purpose: To study weight loss, comorbidity remission, complications, and nutritional deficits after duodenal switch (DS) and single-anastomosis DS with sleeve gastrectomy (SADI-S)., Material and Methods: Retrospective review of patients submitted to DS or SADI-S for morbid obesity in a single university hospital., Results: Four hundred forty patients underwent DS (n = 259) or SADI-S (n = 181). Mean preoperative body mass index (BMI) was 50.8 ± 6.4Kg/m 2 . Mean follow-up was 56.1 ± 37.2 months for DS and 27.2 ± 18.9 months for SADI-S. Global mean excess weight loss was 77.4% at 2 years similar for SADI-S and DS, and 72.1% at 10 years after DS. Although early complications were similar in SADI-S and DS (13.3% vs. 18.9%, p = n.s.), long-term complications and vitamin and micronutrient deficiencies were superior after DS. Rate of comorbidities remission was 85.2% for diabetes, 63.9% for hypertension, 77.6% for dyslipidemia, and 82.1% for sleep apnea, with no differences between both techniques. In patients with initial BMI > 55 kg/m 2 (n = 91), DS achieved higher percentage of BMI < 35 kg/m 2 (80% vs. 50%, p = 0.025) and higher rate of diabetes remission (100% vs. 75%, p = 0050)., Conclusions: DS and SADI-S showed similar weight loss and comorbidity remission rates at 2 years. In patients with initial BMI > 55 kg/m 2 , DS obtained better BMI control at 2 years and better diabetes remission, but more long-term complications and supplementation needs.

Study Design: Multicenter, prospective, cohort study., Objective: To estimate the Minimal Clinically Important Difference (MCID) for the physical (PCS) and mental (MCS) component summaries of Short Form SF-12 (SF-12), in patients with low back pain (LBP)., Summary of Background Data: Quality of life is one of the core domains recommended to be assessed in patients with LBP. SF-12 is the most widely used instrument for this purpose, but its MCID was unknown., Methods: A total of 458 patients with subacute and chronic LBP were consecutively recruited across 21 practices. LBP, referred pain, disability, PCS, and MCS were assessed upon recruitment and 12 months later. Self-reported health status change between baseline and 12 month-assessment, was used as the external criterion. The MCID for SF-12 was estimated following four anchor-based methods; minimal detectable change (MDC); average change (AC); change difference (CD); and receiver operating characteristic curve (ROC), for which the area under the curve (AUC) was calculated. The effect on MCID values of pain duration and baseline scores was assessed., Results: Values for PCS were: MDC: 0.56, AC: 2.71, CD: 3.29, and ROC: 1.14. Values for MCS were: MDC: 3.77, AC: 3.54, CD: 1.13, and ROC: 4.23. AUC values were <0.7; MCID values were smaller among chronic patients and those with better baseline quality of life., Conclusion: Different methods for MCID calculation lead to different results. In patients with subacute and chronic LBP, improvements >3.77 in MCS and >3.29 in PCS, can be considered clinically relevant. MCID is smaller in patients with longer pain duration and better baseline quality of life., Level of Evidence: 2.

Genetically identical cells growing under homogeneous growth conditions often display cell-cell variation in gene expression. This variation stems from noise in gene expression and can be adaptive allowing for division of labor and bet-hedging strategies. In particular, for bacterial pathogens, the expression of phenotypes related to virulence can show cell-cell variation. Therefore, understanding virulence-related gene expression requires knowledge of gene expression patterns at the single cell level. We describe protocols for the use of fluorescence reporters for single cell analysis of gene expression in the human enteric pathogen Clostridium difficile, a strict anaerobe. The reporters are based on modified versions of the human DNA repair enzyme O ( 6)-alkylguanine-DNA alkyltransferase, called SNAP-tag and CLIP-tag. SNAP becomes covalently labeled upon reaction with O ( 6)-benzylguanine conjugated to a fluorophore, whereas CLIP is labeled by O ( 6)-benzylcytosine conjugates. SNAP and CLIP labeling is orthogonal allowing for dual labeling in the same cells. SNAP and CLIP cassettes optimized for C. difficile can be used for quantitative studies of gene expression at the single cell level. Both the SNAP and CLIP reporters can also be used for studies of protein subcellular localization in C. difficile.

Public health action on a territory is complex and requires the involvement of multiple actors, who do not always act coordinately. Networks of organizations structures including the whole of the local actors facilitate the generation of synergies and enable greater effectiveness and efficiency of the joint action from the different actors on a same landscape. We present 3 years experience of four Public Health Committees in a region of Catalonia (Spain), composed by the main actors in public health planning. Each of the committees is organized on a plenary and working groups on issues arising from the regional health diagnosis, and coincident with the Health Plan of the Region. Coordination in no case implies the loss or dilution of the firm of the actor generator of intervention initiative in public health, but their empowerment and collaboration by the other actors. In conclusion welcomes the creation of a culture of collaboration and synergies between the different organizations concerned. Lack of specificity is observed in establishing operational objectives, and the need for greater coordination and involvement of the components of the various working groups., (Copyright © 2012 SESPAS. Published by Elsevier Espana. All rights reserved.)

Temporal and compartment-specific control of gene expression during sporulation in Bacillus subtilis is governed by a cascade of four RNA polymerase subunits. sigmaF in the prespore and sigmaE in the mother cell control early stages of development, and are replaced at later stages by sigmaG and sigmaK, respectively. Ultimately, a comprehensive description of the molecular mechanisms underlying spore morphogenesis requires the knowledge of all the intervening genes and their assignment to specific regulons. Here, in an extension of earlier work, DNA macroarrays have been used, and members of the four compartment-specific sporulation regulons have been identified. Genes were identified and grouped based on: i) their temporal expression profile and ii) the use of mutants for each of the four sigma factors and a bofA allele, which allows sigmaK activation in the absence of sigmaG. As a further test, artificial production of active alleles of the sigma factors in non-sporulating cells was employed. A total of 439 genes were found, including previously characterized genes whose transcription is induced during sporulation: 55 in the sigmaF regulon, 154 sigmaE-governed genes, 113 sigmaG-dependent genes, and 132 genes under sigmaK control. The results strengthen the view that the activities of sigmaF, sigmaE, sigmaG and sigmaK are largely compartmentalized, both temporally as well as spatially, and that the major vegetative sigma factor (sigmaA) is active throughout sporulation. The results provide a dynamic picture of the changes in the overall pattern of gene expression in the two compartments of the sporulating cell, and offer insight into the roles of the prespore and the mother cell at different times of spore morphogenesis.

RNA polymerase sigma factor sigma(F) initiates the prespore-specific program of gene expression during Bacillus subtilis sporulation. sigma(F) governs transcription of spoIIIG, encoding the late prespore-specific regulator sigma(G). However, transcription of spoIIIG is delayed relative to other genes under the control of sigma(F), and after synthesis, sigma(G) is initially kept in an inactive form. Activation of sigma(G) requires the complete engulfment of the prespore by the mother cell and expression of the spoIIIA and spoIIIJ loci. We screened for random mutations in spoIIIG that bypassed the requirement for spoIIIA for the activation of sigma(G). We found a mutation (spoIIIGE156K) that resulted in an amino acid substitution at position 156, which is adjacent to the position of a mutation (E155K) previously shown to prevent interaction of SpoIIAB with sigma(G). Comparative modelling techniques and in vivo studies suggested that the spoIIIGE156K mutation interferes with the interaction of SpoIIAB with sigma(G). The sigma(GE156K) isoform restored sigma(G)-directed gene expression to spoIIIA mutant cells. However, expression of sspE-lacZ in the spoIIIA spoIIIGE156K double mutant was delayed relative to completion of the engulfment process and was not confined to the prespore. Rather, beta-galactosidase accumulated throughout the entire cell at late times in development. This suggests that the activity of sigma(GE156K) is still regulated in the prespore of a spoIIIA mutant, but not by SpoIIAB. In agreement with this suggestion, we also found that expression of spoIIIGE156K from the promoter for the early prespore-specific gene spoIIQ still resulted in sspE-lacZ induction at the normal time during sporulation, coincidently with completion of the engulfment process. In contrast, transcription of spoIIIGE156K, but not of the wild-type spoIIIG gene, from the mother cell-specific spoIID promoter permitted the rapid induction of sspE-lacZ expression. Together, the results suggest that SpoIIAB is either redundant or has no role in the regulation of sigma(G) in the prespore.

Spores formed by wild-type Bacillus subtilis are encased in a multilayered protein structure (called the coat) formed by the ordered assembly of over 30 polypeptides. One polypeptide (CotB) is a surface-exposed coat component that has been used as a vehicle for the display of heterologous antigens at the spore surface. The cotB gene was initially identified by reverse genetics as encoding an abundant coat component. cotB is predicted to code for a 43-kDa polypeptide, but the form that prevails in the spore coat has a molecular mass of about 66 kDa (herein designated CotB-66). Here we show that in good agreement with its predicted size, expression of cotB in Escherichia coli results in the accumulation of a 46-kDa protein (CotB-46). Expression of cotB in sporulating cells of B. subtilis also results in a 46-kDa polypeptide which appears to be rapidly converted into CotB-66. These results suggest that soon after synthesis, CotB undergoes a posttranslational modification. Assembly of CotB-66 has been shown to depend on expression of both the cotH and cotG loci. We found that CotB-46 is the predominant form found in extracts prepared from sporulating cells or in spore coat preparations of cotH or cotG mutants. Therefore, both cotH and cotG are required for the efficient conversion of CotB-46 into CotB-66 but are dispensable for the association of CotB-46 with the spore coat. We also show that CotG does not accumulate in sporulating cells of a cotH mutant, suggesting that CotH (or a CotH-controlled factor) stabilizes the otherwise unstable CotG. Thus, the need for CotH for formation of CotB-66 results in part from its role in the stabilization of CotG. We also found that CotB-46 is present in complexes with CotG at the time when formation of CotB-66 is detected. Moreover, using a yeast two-hybrid system, we found evidence that CotB directly interacts with CotG and that both CotB and CotG self-interact. We suggest that an interaction between CotG and CotB is required for the formation of CotB-66, which may represent a multimeric form of CotB.

During sporulation in Bacillus subtilis, the prespore-specific developmental program is initiated soon after asymmetric division of the sporangium by the compartment-specific activation of RNA polymerase sigma factor sigma(F). sigma(F) directs transcription of spoIIIG, encoding the late forespore-specific regulator sigma(G). Following synthesis, sigma(G) is initially kept in an inactive form, presumably because it is bound to the SpoIIAB anti-sigma factor. Activation of sigma(G) occurs only after the complete engulfment of the prespore by the mother cell. Mutations in spoIIIJ arrest sporulation soon after conclusion of the engulfment process and prevent activation of sigma(G). Here we show that sigma(G) accumulates but is mostly inactive in a spoIIIJ mutant. We also show that expression of the spoIIIGE155K allele, encoding a form of sigma(G) that is not efficiently bound by SpoIIAB in vitro, restores sigma(G)-directed gene expression to a spoIIIJ mutant. Expression of spoIIIJ occurs during vegetative growth. However, we show that expression of spoIIIJ in the prespore is sufficient for sigma(G) activation and for sporulation. Mutations in the mother cell-specific spoIIIA locus are known to arrest sporulation just after completion of the engulfment process. Previous work has also shown that sigma(G) accumulates in an inactive form in spoIIIA mutants and that the need for spoIIIA expression for sigma(G) activation can be circumvented by the spoIIIGE155K allele. However, in contrast to the case for spoIIIJ, we show that expression of spoIIIA in the prespore does not support efficient sporulation. The results suggest that the activation of sigma(G) at the end of the engulfment process involves the action of spoIIIA from the mother cell and of spoIIIJ from the prespore.