Effects of vaccination on the two-strain transmission dynamics of COVID-19: Dougherty County, Georgia, USA, as a case study

The emergence of multiple strains of SARS-COV-2 has made it complicated to predict and control the COVID-19 pandemic. Although some vaccines have been effective in reducing the severity of the disease, these vaccines are designed for a specific strain of the virus and are usually less effective for other strains. In addition, the waning of vaccine-induced immunity, reinfection of recovered people, and incomplete vaccination are challenging to the vaccination program. In this study, we developed a detailed model to describe the multi-strain transmission dynamics of COVID-19 under vaccination. We implemented our model to examine the impact of inter-strain transmission competition under vaccination on the critical outbreak indicators: hospitalized cases, undiagnosed cases, basic reproduction numbers, and the overtake-time by a new strain to the existing strain. In particular, our results on the dependence of the overtake-time on vaccination rates, progression-to-infectious rate, and relative transmission rates provide helpful information for managing a pandemic with circulating two strains. Furthermore, our results suggest that a reduction in the relative transmission rates and a decrease in vaccination dropout rates or an increase in vaccination rates help keep the reproduction number of both strains below unity and keep the number of hospitalized cases and undiagnosed cases at their lowest levels. Moreover, our analysis shows that the second and booster-dose vaccinations are useful for further reducing the reproduction number.

Efficacy and safety of human gut-derived multi-strain probiotics in patients with irritable bowel syndrome: A prospective open-label observation study

This study aimed to investigate the efficacy and safety of human gut-derived multi-strain probiotics in patients with irritable bowel syndrome (IBS). This was an open-label, prospective, observational study. Patients with IBS were administered human gut-derived multi-strain probiotics for 4 weeks. The primary and secondary outcomes were based on the overall responder rate of the total IBS severity scoring system (IBS-SSS) score (>50-point decrease) and the IBS quality of life (IBS-QOL) score and IBS-SSS1 subscore (>10-point decrease in both scores), respectively. The estimated response rate is 55%. Of 44 patients, the total IBS-SSS score responder rate was 18.2% and 63.6% of patients at 2 and 4 weeks, respectively (P = .018). Compared with baseline, a significant improvement in the IBS-QOL score was observed in 27.3% and 63.6% of patients at 2 and 4 weeks, respectively (P = .001). Overall improvement rates in the IBS-SSS1 subscore were observed in 29.5% and 61.4% of patients at 2 and 4 weeks, respectively (P < .001). Primary and secondary outcomes were higher at 4 weeks (total IBS-SSS score, 63.6%; IBS-QOL score, 63.6%; IBS-SSS1 subscore, 61.4%) than the estimated responder rate (55%). Human gut-derived multi-strain probiotics have the potential to become an effective and safe treatment option for IBS patients.

Reconstructing multi-strain pathogen interactions from cross-sectional survey data via statistical network inference

Infectious diseases often involve multiple pathogen species or multiple strains of the same pathogen. As such, knowledge of how different pathogens interact is key to understand and predict the outcome of interventions targeting only a subset of species or strains involved in disease. Population-level data may be useful to infer pathogen strain interactions, but most previously used inference methods only consider uniform interactions between all strains or focus on marginal pairwise interactions. As such, these methods are prone to bias induced by indirect interactions through other strains. Here, we evaluated statistical network inference for reconstructing heterogeneous interactions from cross-sectional surveys detecting joint presence/absence patterns of pathogen strains within hosts. We applied various network models to simulated survey data, representing endemic infection states of multiple pathogen strains with potential interactions in acquisition or clearance of infection. Satisfactory performance was demonstrated by the estimators converging to the true interactions. Accurate reconstruction of interaction networks was achieved by regularization or penalization for sample size. Although performance deteriorated in the presence of host heterogeneity, this was overcome by correcting for individual-level risk factors. Our work demonstrates how statistical network inference could prove useful for detecting multi-strain pathogen interactions and may have applications beyond epidemiology.

The Multi-Strain Probiotic OMNi-BiOTiC® Active Reduces the Duration of Acute Upper Respiratory Disease in Older People: A Double-Blind, Randomised, Controlled Clinical Trial

Immunosenescence is the adverse change in the human immune function during aging, leaving older people more prone to an increased risk of infections and morbidity. Acute upper respiratory tract infections (URTIs) are very common among older people, often resulting in continued morbidity and mortality. Therefore, approaches, such as consuming probiotics, that shorten the duration or even reduce the incidence of URTIs in older people are being studied. The aim of this study was to determine the effects of a multi-strain probiotic OMNi-BiOTiC^® Active, which contains 11 live probiotic strains, on the incidence, duration, and severity of URTIs in older people. In this randomized double-blinded placebo-controlled study, 95 participants, with an average age of 70.9 years in the probiotic group and 69.6 years in the placebo group, were randomly allocated to two groups: 10¹⁰ cfu per day of the multi-strain probiotic intervention OMNi-BiOTiC^® Active (49) or placebo (46). The incidence of URTIs in older people after 12 weeks supplementation with OMNi-BiOTiC^® showed no statistically significant difference between the two groups (p = 0.5244). However, the duration of the URTI infections was statistically significantly different between the groups (p = 0.011). The participants that consumed the probiotic had an average duration of illness of 3.1 ± 1.6 days, whilst participants that received the placebo had symptoms for an average of 6.0 ± 3.8 days (p = 0.011). Statistically significant differences in lymphocyte counts in both groups after supplementation (p = 0.035 for the probiotic group and p = 0.029 for the placebo group) and between both groups were found (p = 0.009). Statistically significant differences in eosinophil (p = 0.002) and basophil counts (p = 0.001) in the probiotic groups before and after supplementation with probiotics were also found. Supplementation with the multi-strain probiotic OMNi-BiOTiC^® Active may benefit older people with URTIs. Larger randomised controlled clinical trials are warranted. Clinical Trial Registration; identifier NCT05879393.

Dynamics of a multi-strain malaria model with diffusion in a periodic environment

This paper mainly explores the complex impacts of spatial heterogeneity, vector-bias effect, multiple strains, temperature-dependent extrinsic incubation period (EIP) and seasonality on malaria transmission. We propose a multi-strain malaria transmission model with diffusion and periodic delays and define the reproduction numbers Ri and R^i (i = 1, 2). Quantitative analysis indicates that the disease-free ω-periodic solution is globally attractive when Ri<1, while if Ri>1>Rj (i≠j,i,j=1,2), then strain i persists and strain j dies out. More interestingly, when R1 and R2 are greater than 1, the competitive exclusion of the two strains also occurs. Additionally, in a heterogeneous environment, the coexistence conditions of the two strains are R^1>1 and R^2>1. Numerical simulations verify the analytical results and reveal that ignoring vector-bias effect or seasonality when studying malaria transmission will underestimate the risk of disease transmission.

Novel mono- and multi-strain probiotics supplementation modulates growth, intestinal microflora composition and haemato-biochemical parameters in broiler chickens

Background

The reduction of antimicrobial usage in food‐producing animals necessitates the intense search for novel alternatives, including new probiotic strains with more effective properties in improving growth performance and curtailing diseases in animals.

Objective

This study evaluated the effects of novel mono‐ and multi‐strain probiotics on the growth performance, intestinal microbiota and haemato‐biochemical parameters of broilers.

Methods

A total of 160 one‐day‐old Cobb 500 broilers were divided into eight treatment groups with two replicates consisting of (1) basal diet (negative control), (2) basal diet with antibiotic, colistin sulphate, (3) basal diet with commercial probiotic, PROMAX® (positive control), (4) basal diet with Pediococcus acidilactici I5, (5) basal diet with P. pentosaceus I13, (6) basal diet with Enterococcus faecium C14, (7) basal diet with Lactobacillus plantarum C16 and (8) basal diet with the combination of all the four probiotic strains. Birds were kept for 35 days and through oral gavage, 1 ml of 108 study probiotic strains administered on days 3–6, 14 and 18.

Results

Supplementation with P. pentosaceus I13, L. plantarum C16 or multi‐strain probiotics significantly (p < 0.05) improved the body weight gain and feed conversion ratio with decrease in feed intake and intestinal Enterobacteria counts. There was a significant (p < 0.05) increase in haemoglobin, mean corpuscular volume, total white blood cells, platelets counts and a lowered (p < 0.05) total cholesterol and glucose levels in multi‐strains probiotic supplemented birds.

Conclusion

The supplementation with novel multi‐strain probiotics improved growth, intestinal health and haemato‐biochemical parameters in broilers and could be used as suitable antibiotic alternatives.

A critical evaluation of the factors affecting the survival and persistence of beneficial bacteria in healthy adults

The efficacy of a probiotic depends on its ability to survive and persist in the digestive tract. Regulatory agencies around the world recommend minimum dosages in order for a product to be termed a probiotic. However, the effect of dosage on the survival of the bacteria in the gut - the primary objective of probiotic administration - has not been critically evaluated. We performed a systematic literature review to assess the available data on the survival rate, during gastrointestinal transit, of probiotic bacteria that were orally administered to healthy adults. We also evaluated the persistence of the administered strain(s) after discontinuation of treatment and the potential role played by the food matrix in which probiotics have been administered. From a regulatory perspective, the profile of the target population is key to establishing the efficacy of probiotics. Therefore, we focussed on subjects without disease conditions. We evaluated 17 studies of single strains and 13 studies of multi-strain products, which reported survival and persistence outcomes. Persistence in the gut and recovery from stool were strain dependent. When the administered dose was higher than 10¹⁰ cfu/day, the probiotic could be recovered from stool regardless of the strain used. Treatment duration did not affect faecal recovery. Thus, dosage recommendations for probiotics by regulatory agencies are lower than that required for a strain to survive, persist and be efficacious in the gut.

Differences in Immune Response and Biochemical Parameters of Mice Fed by Kefir Milk and Lacticaseibacillus paracasei Isolated from the Kefir Grains

The health benefits of kefir consumption have been well-known for hundreds of years. The objective of this study was to investigate the effect of kefir milk and the probiotic strain Lacticaseibacillus paracasei Ž2 isolated from kefir grains on the immune response and selected parameters of the lipid and liver enzymatic profiles of mice. Mice fed with kefir milk showed significantly increased phagocytic activity and percentages of B cells in the blood and increased gene expression for mucins and percentages of CD8+ lymphocytes in the gut. By applying kefir, we achieved a significant reduction in serum LDL cholesterol and an LDL/HDL ratio that favored an increase in HDL cholesterol. Regarding the hepatic enzymes, in particular a significant reduction in ALT activity was observed. L. paracasei Ž2 alone stimulated the immune response more markedly compared with kefir milk. Regarding the systemic level, we observed increases in the proportion of all T cells (CD3⁺), CD4⁺ lymphocytes and the ratio of CD4+:CD8+ cells, and regarding the local intestinal level we noted a significant increase in gene expression for mucins (MUC-1 and MUC-2) and IgA. Moreover, we confirmed the formation of a biofilm on the surface of the forestomach only after the application of L. paracasei Ž2 alone, but not after kefir administration. The results confirmed the hypothesis that the final effect of the probiotic does not correspond with the effect of the individual strain but is the result of mutual interactions of the microorganisms presented in a preparation, and therefore in the case of multi-strain probiotics, in vivo testing of the complex preparation is necessary.

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Genome-scale models (GEMs) of bacterial strains' metabolism have been formulated and used over the past 20 years. Recently, with the number of genome sequences exponentially increasing, multi-strain GEMs have proved valuable to define the properties of a species. Here, through four major stages, we extend the original Protocol used to generate a GEM for a single strain to enable multi-strain GEMs: (i) obtain or generate a high-quality model of a reference strain; (ii) compare the genome sequence between a reference strain and target strains to generate a homology matrix; (iii) generate draft strain-specific models from the homology matrix; and (iv) manually curate draft models. These multi-strain GEMs can be used to study pan-metabolic capabilities and strain-specific differences across a species, thus providing insights into its range of lifestyles. Unlike the original Protocol, this procedure is scalable and can be partly automated with the Supplementary Jupyter notebook Tutorial. This Protocol Extension joins the ranks of other comparable methods for generating models such as CarveMe and KBase. This extension of the original Protocol takes on the order of weeks to multiple months to complete depending on the availability of a suitable reference model.

Challenges in the management of HIV infection: update on the role of probiotic supplementation as a possible complementary therapeutic strategy for cART treated people living with HIV/AIDS

Introduction: Recent insights show that gut-mucosal immunity and intestinal microbiota play a key role in the pathogenesis of HIV infection. Alterations in the composition of intestinal flora (dysbiosis) could be associated with an impaired intestinal epithelium barrier activity and an impaired mucosal immunity function, significantly contributing to microbial translocation which is considered a major driver of chronic immune activation. Areas covered: This article provides an overview on the novel trends in probiotic therapy application. A particular emphasis is addressed to the importance of probiotics as a novel strategy to attenuate or prevent gastrointestinal involvement and to improve gut-mucosal immunity in HIV-infected subjects. Therefore, opportunities, limits and methodological criticalities of supplementation with probiotic therapy are considered and analyzed. Expert opinion: Use of probiotics is emerging as a novel strategy to manage dysbiosis and gut-mucosal impairment, to reduce immune activation and to limit a number of non-AIDS-related disorders. However, despite the growing use of probiotic therapy, mechanisms by which oral bacteria intake exhibits its effects are strain-related and disease-specific, hence clinicians need to take these two factors into consideration when suggesting probiotic supplementation to HIV-infected patients.

Impact of High-Dose Multi-Strain Probiotic Supplementation on Neurocognitive Performance and Central Nervous System Immune Activation of HIV-1 Infected Individuals

Background: Gut microbiota has metabolic activity which influences mucosal homeostasis, local and systemic immune responses, and other anatomical systems (i.e., brain). The effects of dysbiosis are still poorly studied in Human Immunodeficiency Virus-1 (HIV-1) positive subjects and insufficient data are available on the impairment of the gut-brain axis, despite neurocognitive disorders being commonly diagnosed in these patients. This study evaluated the impact of a probiotic supplementation strategy on intrathecal immune activation and cognitive performance in combined antiretroviral therapy (cART) treated HIV-1 infected subjects. Methods: Thirty-five HIV-1 infected individuals were included in this study. At baseline (T0) a battery of tests was administered, to evaluate neurocognitive function and a lumbar puncture was performed to determine neopterin concentration in cerebrospinal fluid (CSF), as a marker of Central Nervous System (CNS) immune activation. Subsequently, a subgroup of participants underwent a 6-month course of multi-strain probiotics supplementation; this intervention group was evaluated, after probiotic treatment, with a second lumbar puncture and with repeated neurocognitive tests. Results: At T0, all participants showed impaired results in at least one neurocognitive test and elevated neopterin concentrations in CSF. After supplementation with probiotics (T6), the interventional group presented a significant decrease in neopterin concentration and a significant improvement in several neurocognitive tests. In contrast, no significant modifications were observed in the neurocognitive performance of controls between T0 and T6. The CNS Penetration Effectiveness Score of antiretroviral therapy did not show an influence from any of the investigated variables. Conclusions: Multi-strain probiotic supplementation seems to exert a positive effect on neuroinflammation and neurocognitive impairment in HIV-1 infected subjects, but large trials are needed to support the concept that modulation of the gut microbiota can provide specific neurological benefits in these patients.

Competitive exclusion in a multi-strain immuno-epidemiological influenza model with environmental transmission

In this paper, a multi-strain model that links immunological and epidemiological dynamics across scales is formulated. On the within-host scale, the n strains eliminate each other with the strain having the largest immunological reproduction number persisting. However, on the population scale, we extend the competitive exclusion principle to a multi-strain model of SI-type for the dynamics of highly pathogenic flu in poultry that incorporates both the infection age of infectious individuals and biological age of pathogen in the environment. The two models are linked through the age-since-infection structure of the epidemiological variables. In addition the between-host transmission rate, the shedding rate of individuals infected by strain j and the disease-induced death rate depend on the within-host viral load. The immunological reproduction numbers [Formula: see text] and the epidemiological reproduction numbers [Formula: see text] are computed. By constructing a suitable Lyapunov function, the global stability of the infection-free equilibrium in the system is obtained if all reproduction numbers are smaller or equal to one. If [Formula: see text], the reproduction number of strain j is larger than one, then a single-strain equilibrium, corresponding to strain j exists. This single-strain equilibrium is globally stable whenever [Formula: see text] and [Formula: see text] is the unique maximal reproduction number and all of the reproduction numbers are distinct. That is, the strain with the maximal basic reproduction number competitively excludes all other strains.

Linking immunological and epidemiological dynamics of HIV: the case of super-infection

In this paper, a two-strain model that links immunological and epidemiological dynamics across scales is formulated. On the within-host scale, the two strains eliminate each other with the strain with the larger immunological reproduction persisting. However, on the population scale superinfection is possible, with the strain with larger immunological reproduction number super-infecting the strain with the smaller immunological reproduction number. The two models are linked through the age-since-infection structure of the epidemiological variables. In addition, the between-host transmission and the disease-induced death rate depend on the within-host viral load. The immunological reproduction numbers, the epidemiological reproduction numbers and invasion reproduction numbers are computed. Besides the disease-free equilibrium, there are two population-level strain one and strain two isolated equilibria, as well as a population-level coexistence equilibrium when both invasion reproduction numbers are greater than one. The single-strain population-level equilibria are locally asymptotically stable suggesting that in the absence of superinfection oscillations do not occur, a result contrasting previous studies of HIV age-since-infection structured models. Simulations suggest that the epidemiological reproduction number and HIV population prevalence are monotone functions of the within-host parameters with reciprocal trends. In particular, HIV medications that decrease within-host viral load also increase overall population prevalence. The effect of the immunological parameters on the population reproduction number and prevalence is more pronounced when the initial viral load is lower.