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Since the outbreak of the novel coronavirus disease 2019 (COVID-19) in Wuhan, China, many health care systems have been heavily engaged in treating and preventing the disease, and the year 2020 may be called as "historic COVID-19 vaccine breakthrough". Due to the COVID-19 pandemic, many companies have initiated investigations on developing an efficient and safe vaccine against the virus. From Moderna and Pfizer in the United States to PastocoVac in Pasteur Institute of Iran and the University of Oxford in the United Kingdom, different candidates have been introduced to the market. COVID-19 vaccine research has been facilitated based on genome and structural information, bioinformatics predictions, epitope mapping, and data obtained from the previous developments of severe acute respiratory syndrome coronavirus (SARS-CoV or SARS-CoV-1) and middle east respiratory syndrome coronavirus (MERS-CoV) vaccine candidates. SARS-CoV genome sequence is highly homologous to the one in COVID-19 and both viruses use the same receptor, angiotensin-converting enzyme 2 (ACE2). Moreover, the immune system responds to these viruses, partially in the same way. Considering the on-going COVID-19 pandemic and previous attempts to manufacture SARS-CoV vaccines, this paper is going to discuss clinical cases as well as vaccine challenges, including those related to infrastructures, transportation, possible adverse reactions, utilized delivery systems (e.g., nanotechnology and electroporation) and probable vaccine-induced mutations. [ABSTRACT FROM AUTHOR]

The diagnosis of hepatitis B virus (HBV) infection requires HBV DNA testing and serologic testing for detection of the surface antigen (HBsAg) and the hepatitis B core antibody (anti-HBc). There is a population of patients with occult HBV infection (OBI), which is not detected by HBsAg or HBV DNA quantification in blood, despite the presence of active replication in the liver. This document provides a definition of OBI and describes the diagnostic techniques currently used. It also addresses the detection of patients with risk factors and the need for screening for OBI in these patients. Correct diagnosis of OBI prevents HBV reactivation and transmission. Diagnosis of OBI is based on the detection of HBV DNA in patients with undetectable HBsAg in blood. A high number of patients with OBI may remain undiagnosed; therefore, screening for OBI in patients with factor risks is essential. For a correct diagnosis of OBI, it is necessary that new markers such as ultrasensitive HBsAg are incorporated, and a more comprehensive marker study is performed by including markers such as cccDNA. [ABSTRACT FROM AUTHOR]

Organic pollutants can alter the physicochemical properties and microbial communities of water bodies. In water contaminated with organic pollutants, the unique extracellular electron transfer mechanisms that promote sulfamethoxazole (SMX) degradation in tri-electrode microbial electrochemical systems (TE-MES) may be impacted. To simulate biodegradable organic matter contamination, glucose (GLU) was added. Metagenomics and metabolomics were used to analyze changes in microbial community structure, metabolism, and function on the electrodes. GLU addition accelerated water quality deterioration, and enhanced SMX degradation. Microbial taxa on the electrodes experienced selective enrichment. Notably, methanogens and SMX-degrading bacteria were enriched, while denitrifying bacteria and antibiotic-resistant bacteria were suppressed. Enriched metabolites were linked to 15 metabolic pathways and other functions like microbial signaling and genetics. Non-redundant genes also clustered in metabolic pathways, aligning with metabolite enrichment results. Additional pathways involved life cycle processes and protein interactions. Enzymes related to carbon metabolism, particularly glycoside hydrolases, increased significantly, indicating a shift in carbon metabolism on microbial electrodes after GLU addition. The abundance of intracellular electron transfer enzymes rose, while outer membrane proteins decreased. This contrasts with the typical TE-MES mechanism where outer membrane proteins facilitate SMX degradation. The presence of organic pollution may shift SMX degradation from an extracellular electrochemical process to an intracellular metabolic process, possibly involving co-metabolism with simple organic compounds. This study provides mechanistic insights and theoretical guidance for using TE-MES with embedded microbial electrodes to treat antibiotic-contaminated water affected by organic pollution. [Display omitted] • Deteriorated water quality and enhanced SMX degradation occurred upon GLU addition. • Microbial taxa on the electrodes underwent selective enrichment. • Significantly enriched metabolites were mainly associated with 15 metabolic pathways. • Variations in abundance of multiple enzymes revealed a new SMX degradation mechanism. [ABSTRACT FROM AUTHOR]

A correction is presented to the article "Genetics of Bacteria: a call for papers" published in a previous issue of the periodical.

A correction notice to the article "EG.5 (Eris) and BA.2.86 (Pirola) two new subvariants of SARS‑CoV‑2: a new face of old COVID‑19", which appeared in the previous issue of the periodical, is presented.

Rhizosphere is a dynamic and complex environment shaped by intricate interactions between plants and a diverse microbial community. The rhizosphere microbiome is crucial for plant growth, nutrition, and health in agro-ecosystems. Recent advancements in metagenomics, especially through shotgun sequencing, offer unprecedented opportunities to unravel the complexities of rhizosphere microbial dynamics. Sequence and function-based metagenomic approaches enhance our understanding of plant-microbe relationships and serve as transformative tools for sustainable agriculture. They offer insights into precision microbiome engineering and ecosystem management by capturing the genomic landscape of microbial communities, revealing their taxonomic composition and functional potential. The integration of computational tools and machine learning approaches provides a powerful analytical framework to interpret vast and intricate metagenomic datasets. This paper comprehensively explores the rhizosphere using cutting-edge shotgun sequencing techniques to capture a holistic view of microbial communities in this crucial zone. Additionally, it delves into the emerging domain of virus-rhizosphere interactions, elucidating the impact of viral dynamics on rhizosphere microbial composition. To date, significant achievements in rhizosphere biology through metagenomics include detailed characterizations of microbial diversity, functional profiling of microbial communities, and identification of key microbial players in plant health and nutrient cycling. These advances underscore the critical role of metagenomics in advancing our understanding of rhizosphere biology and its applications in sustainable agriculture. The novel application of these advanced metagenomic techniques presents both opportunities and challenges, offering deeper insights into the rhizosphere while highlighting the need for improved data integration and interpretation methods. [Display omitted] • Metagenomics is a tool for studying rhizosphere microbial community genetics. • Shotgun sequencing is a common high-throughput method in metagenomics. • Metagenomics explores plant-microbe ecological interactions, including viruses. • Computational tools process and analyze large metagenomic data sets. • Metagenomics reveals insights into metabolic pathways, nutrient cycling, and plant interactions. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) is a global health threat that has been referred to as the 'silent pandemic'. In this article the need for greater awareness and acknowledgement of the relationship between AMR and biofilms is explored. The natural link between AMR and biofilms creates an alarming threat in chronic infections. There is a significant need for new antimicrobial strategies to disrupt biofilm, enhancing the action of antimicrobial agents and reducing the opportunity for antibiotic resistance gene transfer within the biofilm. [ABSTRACT FROM AUTHOR]

Objective. We investigated the characteristics of vaginal microbiome in reproductive-age females with HPV infection in Xinjiang, China. Methods. A total of 135 females of reproductive age were enrolled. There were 43 healthy HPV-negative females in control group (N group), 58 HPV-positive females in nonlesion group (P1 group), and 34 HPV-positive females in low-grade squamous intraepithelial lesion group (P2 group). DNA was extracted from the vaginal secretions, and V3–V4 regions of bacterial 16S rDNA were amplified and sequenced by NovaSeq. QIIME2 and R software were used to perform diversity analysis of bacteria. PICRUSt2 was used to predict the function of the vaginal microbiota. Results. Lactobacillus was the main genus of vaginal microbiota in asymptomatic reproductive-age females with or without HPV in Xinjiang. The diversity of vaginal microbiota in the P1 group was significantly higher than that in the N group, and the proportion of Gardnerella increased significantly. The vaginal microbiota structure of the P2 group was different from the N group, characterized by the decrease of Lactobacillus crispatus and the increase of Shuttleworthia. The function of the inordinate microbiome may play a role in accelerating HPV replication and integration. Conclusion. The structure of vaginal microbiota alters under persistent HPV infection in asymptomatic females of reproductive age in Xinjiang. The Gardnerella increase is associated with increased susceptibility to HPV infection, and Lactobacillus iners predominance and Shuttleworthia presence may be a signature of HPV infection with low-grade squamous intraepithelial lesion. [ABSTRACT FROM AUTHOR]

Background and Aim: Pseudomonas aeruginosa (P. aeruginosa) is an important causative organism of burn infection. Several virulence factors are implicated in P. aeruginosa colonization and invasion, making P. aeruginosa infection's outcome worse. Type III secretion system (T3SS) effector proteins are among these virulence factors. The present study evaluated the frequency of genes encoding T3SS effectors as a virulence determinant in P. aeruginosa isolates from burn patients. Materials and Methods: Wound swabs were collected from burn patients admitted to the Plastic and Reconstructive Surgery Center, Mansoura University, Egypt, and identified by different microbiological testing methods. The modified Kirby Bauer's disc diffusion method was used to test the antibiotic susceptibility of P. aeruginosa isolates against different antibiotics. Prevalence and the presence of exo genes that encode type T3SS proteins (exoS, exoT, exoU, and exoY) in P. aeruginosa isolates were evaluated by the multiplex PCR. Chi-square and Fisher's test were used for statistical analysis. Results: A total of 45 P. aeruginosa isolates were identified from 101 burn patients, including 27 males and 18 females, with a mean age of 15.78±2.65 years old. P. aeruginosa isolates were mostly susceptible to piperacillin/tazobactam and imipenem (73.33 and 62.22%), respectively; while the lowest susceptibility rates were in ceftazidime (4.44%), Tobramycin (4.44%), and ceftriaxone (6.67%). The exoY and exoT genes were detected in 100% of the P. aeruginosa isolates, while 62.22% and 42.22% of clinical isolates harbored exoS and exoU genes, respectively. Conclusion: This study established a correlation between T3SS proteins, particularly exoS and exoU genes and antimicrobial resistance in P. aeruginosa isolates from burn infection. [ABSTRACT FROM AUTHOR]

Objectives: This paper presents a meta-analytical review of research on antimicrobial resistance in animals and environment, with a goal of providing additional data on the current status of AMR in Kenya. Data sources: The data was collected from a desktop search on studies carried out on antimicrobial susceptibility or resistance in Kenya, with respect to bacteria isolated from animals and environment. Study selection: A total of fifteen data sources were consulted. Out of these, 13 specifically covered AMR in bacteria isolated from Kenyan animals and 2 from environment. Studies undertaken included phenotypic and/or genotypic profiling of one or many bacteria against varying combinations of antimicrobials. Data extraction and synthesis: The study involved a meta-analytical review of the data sources; noting the respective antimicrobial susceptibility profiles of the isolates. Results: The studies show that most bacterial isolates manifested varying susceptibility profiles to a variety of antimicrobials and were mostly resistant to antimicrobials commonly used in Kenya, and more susceptible to the least commonly used ones. Some studies alluded to the possibility of gene transfer between bacteria. Eleven out of the 13 animal studies (84.6%) and the two studies on environmental isolates indicated presence of multi-drug resistant strains –up to 7 antimicrobials. Where the antimicrobial combinations were given, the one included most was Sulphamethoxazole at 85.7%; the least was Gentamycin (at 1/14; 7.1%). Conclusion: Antimicrobial-resistant bacteria are common in all types of Kenyan animals and environment. They pose a danger of being transferred to humans and complicate treatment of human bacterial diseases. [ABSTRACT FROM AUTHOR]

Objective : To investigate the longitudinal influence of alveolar bone grafting on the oral microbiota of children with cleft lip and palate (CLP). Materials and methods : Twenty-eight children with nonsyndromic CLP were recruited and underwent secondary alveolar bone grafting at the first time. Unstimulated saliva and plaque samples were collected from the subjects preoperatively and at 2 days, 1 month, and 3 months postoperatively. The v3–v4 hypervariable regions of the 16S rRNA gene from bacterial DNA were sequenced using the Illumina MiSeq sequencing platform. Results : The alpha diversity of the saliva and plaque microbiota was significantly decreased at 2 days postoperatively and then increased at 1 and 3 months postoperatively. The saliva and plaque microbiota compositions at 2 days postoperatively differed from those at the other time points, and the microbiota compositions at 1 and 3 months postoperatively showed a gradual shift toward the preoperative composition. The saliva, but not plaque, microbiota composition 3 months postoperatively was similar to that preoperatively. Conclusion : The effect of secondary alveolar bone grafting on the plaque microbiota in children with CLP lasted longer than the saliva microbiota. Alveolar bone grafting altered the saliva microbiota in children with CLP within 3 months postoperatively. [ABSTRACT FROM AUTHOR]

Objectives: It has been generally believed that women who exposed to Toxoplasma gondii before pregnancy and have anti‐T. gondii IgG antibody are immunized and their newborns will be protected from congenital infection. This study is aimed to investigate the role of T. gondii infection in spontaneous abortion through serological and molecular methods in southern Iran. Study design: Blood samples were taken from 50 spontaneously aborted mothers and anti‐T. gondii antibodies were assessed using conventional enzyme‐linked immunosorbent assay (ELISA) and avidity ELISA methods. The placenta and blood samples of aborted women were used for detection of the parasite's DNA by polymerase chain reaction (PCR) method targeting the RE gene. The parasite genotypes were determined by PCR‐restriction fragment length polymorphism (RFLP) method using SAG3 and GRA6 genes. Results: IgG antibody was detected in 28% (14/50) of mothers, but all samples were negative for IgM antibody. In the avidity ELISA test, 26% (13/50) of the samples had a high avidity index, suggesting chronic infection, while a low avidity index was detected in one case (2%), which suggests acute infection. The parasite's DNA was detected in 18% (9/50) and 14% (7/50) of blood and placenta samples, respectively. All DNA positive samples were IgG positive. All isolates were belonged to the T. gondii type III genotype. Conclusion: The results suggest that T. gondii seropositive women are not protected from congenital transmission. However, the results should be interpreted cautiously until further studies will be confirmed these results. [ABSTRACT FROM AUTHOR]

Background: The highly contagious SARS-COV-2 virus spread rapidly from China and formed a global pandemic. The virus has infected over 509 million people worldwide and killed about 6.32 million up to date. Up on invasion, the Receptor Binding Domain (RBD) of Spike protein plays a crucial role in the entry of the virus into the host cell. The virus N protein is another protein that has a critical role for genome packaging. Methods: As bioinformatics approaches, the cassette design, codon adaptation, and protein stability were investigated in this study. Synthetic genes of RBD and N were cloned separately in pET28a + expression vector. They were transferred into Escherichia coli ( E. coli) BL21 DE3 host cell, and expression of recombinant proteins was induced with IPTG. The recombinant proteins were purified by column chromatography and approved by Western blotting. Animal immunization was performed with each of the recombinant proteins individually and in combination of the two. The antibody titer of the blood serum from control and immunized mice groups was determined by ELISA technique. Finally, the anti-spike neutralization test was performed. Results: The expression and purification of RBD protein were monitored on SDSPAGE, two bands of about 28 and 45 kDa for RBD and N appeared on gel distinctly, which were further validated by Western blotting. According to ELISA results, related antibodies were traced to a dilution of 1/64000 in immunized sera. The neutralization test exhibited produced antibodies' potency to bind the virus proteins. Using SPSS software, statistical analysis was performed by Duncan's test and T-test. Conclusion: According to the present study, recombinant proteins, either RBD alone or in combination with N adequately stimulated the immune response, and the raised antibodies could neutralize the virus in in vitro test. [ABSTRACT FROM AUTHOR]

Salmonella is estimated to cause over a million infections and ~400 deaths annually in the U.S. Salmonella enterica serotype Javiana strains (n = 409) that predominantly originated from the State of Arkansas over a six-year period (2003 to 2008) were studied. This period coincided with a rapid rise in the incidence of S. Javiana infections in the U.S. Children under the age of 10 displayed the highest prevalence of S. Javiana infections, regardless of sex or year of detection. Antimicrobial susceptibility to 15 different antimicrobials was assessed and 92% (n = 375) were resistant to at least one of the antimicrobials. Approximately 89% of the isolates were resistant to sulfisoxazole alone and 3% (n = 11) were resistant to different antimicrobials, including gentamicin, ciprofloxacin or ceftiofur. The pulsed-field gel electrophoresis (PFGE) analyses assessed the genotypic diversity and distribution of S. Javiana strains using XbaI restriction. Nine major clusters were identified and isolates from each group were digested with the restriction enzyme AvrII. Isolates with identical profiles of XbaI and AvrII were found to be disseminated in human populations. These distinct "types" of S. Javiana were persistent in human populations for multiple years. A subset of isolates (n = 19) with unique resistance phenotypes underwent plasmid and incompatibility (Inc) type analyses and the isolates resistant to more than one antimicrobial harbored multiple plasmids (<3 to 165 kb). Furthermore, these strains possessed 14 virulence genes, including pagC, cdtB, and iroN. The whole genome sequences (WGS) of 18 isolates that mostly originated from Arkansas from 2003 to 2011 were compared with isolates collected from different areas in the U.S. in 1999, indicating the perseverance of S. Javiana in disseminating antimicrobial resistance and virulence genes. [ABSTRACT FROM AUTHOR]

Today, the spread of vancomycin-resistant strains isolated from Enterococcus faecalis (E. faecalis) has become a major health concern worldwide. Therefore, it is essential to provide a rapid and sensitive assay for identifying vanA gene for timely and appropriate antimicrobial control of resistant enterococcal infections. For this purpose, a cross-sectional study was performed on different clinical specimens of enterococci from Imam Reza hospital, Kermanshah, Iran. The antimicrobial susceptibility testing was determined by disk diffusion and MIC methods. Triplex-PCR and duplex-LAMP assays were also used to identify vanA E. faecalis resistance gene isolates. The results of this study shown that out of 108 Enterococcus isolates, 86, 18, 2, 1, and one isolates of E. faecalis, E. faecium, E. avium, E. psudoavium, and E. raffinosus were identified, respectively. On the other hand, E. faecalis was confirmed in 87 and 88 isolates using duplex-LAMP and triplex PCR, respectively. The LAMP primer set designed in this study can reliably identify seven distinct regions of the vanA gene, and finally the sensitivity, specificity, and the positive and negative predictive values of LAMP assay were shown to be 94.19%, 72.73%, 76.19%, and 93.10%, respectively. In general, sample processing, isothermal reaction and result reporting were completed using the LAMP assay in 75 minutes. Our findings suggest that LAMP assay has been approved as an alternative to the vancomycin resistance Enterococcus genotype (vanA and vanB) compared to other methods and has the advantage of being rapid, time-consuming, and easy for diagnosis. [ABSTRACT FROM AUTHOR]

Microbial population genetics models often assume that all lineages are constrained by the same population size dynamics over time. However, many neutral and selective events can invalidate this assumption and can contribute to the clonal expansion of a specific lineage relative to the rest of the population. Such differential phylodynamic properties between lineages result in asymmetries and imbalances in phylogenetic trees that are sometimes described informally but which are difficult to analyze formally. To this end, we developed a model of how clonal expansions occur and affect the branching patterns of a phylogeny. We show how the parameters of this model can be inferred from a given dated phylogeny using Bayesian statistics, which allows us to assess the probability that one or more clonal expansion events occurred. For each putative clonal expansion event, we estimate its date of emergence and subsequent phylodynamic trajectory, including its long-term evolutionary potential which is important to determine how much effort should be placed on specific control measures. We demonstrate the applicability of our methodology on simulated and real data sets. Inference under our clonal expansion model can reveal important features in the evolution and epidemiology of infectious disease pathogens. [Clonal expansion; genomic epidemiology; microbial population genomics; phylodynamics.] [ABSTRACT FROM AUTHOR]

The coronavirus disease is a respiratory tract disorder which causes pneumonia-like symptoms in severe patients and mild flu-like symptoms in mild symptomatic cases first noticed in Wuhan, China. DNA sequencing and further analysis shows it to be 79% like the 2002 SARS-CoV and 50% like the 2012 MERS-CoV. It was also observed that the novel coronavirus's spike protein was larger and very different from its previously known strains. For diagnosis, multiple strategies were developed and real time reverse-transcriptase-polymerase chain reaction (RT-PCR) technique was determined to be the best technique. The CT scan was also found effective majorly for the continuous assessment of the disease. Treatment strategies used in previous outbreaks were looked into and put to trial like convalescent plasma therapy. Vaccine development using various genetic engineering strategies are going on across the world. To contain the spread of the disease, countries with positive cases were put under lockdown to break the chain of spread. These lockdowns forced industries, offices, schools, religious places, stadiums, travel, and many more to close which impacted the economies of all the major countries. Lesser human interaction and more use of social media has impacted the social aspects of human life. Cases of domestic violence and mental stress increased among households. Economic stimulus package was announced by various countries to curb the socio-economic impact of the COVID-19 pandemic. [ABSTRACT FROM AUTHOR]

Objective: Chronic rhinosinusitis (CRS) is characterized by a persistent inflammation of the nasal and paranasal sinus mucosa that could be potentially linked to a dysregulation between the microbiota and the immune system. We aim to explore general, methodological, and microbiological aspects of microbiota research in CRS compared to disease-free individuals., Data Sources: Embase, Ovid MEDLINE, PubMed, Scopus, and Web of Science., Review Methods: All studies comparing the composition of the resident microbiota of the sinonasal cavities in 2 groups: CRS and normal participants. We conducted systematic study selection, data extraction, and analysis first using the title and abstract, and then the full texts based on predefined inclusion and exclusion criteria. Compiled and presented findings include sampling site and technique, and microbiological results such as the relative abundance and the variability of the composition of the microbiota in both groups., Results: Twenty-seven studies, using genomic identification with 16s RNA were analyzed. Case definitions primarily followed EPOS or AAO-HNS guidelines, with endoscopic swabs (82%), and middle meatus sampling (74%) being prevalent techniques. Despite relative abundance variability, patterns emerged across studies, indicating an increase in Haemophilus (19%) and Pseudomonas (11%), and decrease in Propionibacterium (15%) and Anaerococcus (11%). Another pattern was observed, showing a decreased alpha diversity (6/19; 22%) in CRS compared to normal individuals., Conclusion: While variations exist among studies, analysis of CRS microbiota suggests an association with dysbiosis, potentially contributing to chronic inflammation. Future research must prioritize standardized criteria for diagnostics and patient selection, fostering a more comprehensive understanding of CRS microbiota., Competing Interests: None., (© 2024 The Author(s). OTO Open published by Wiley Periodicals LLC on behalf of American Academy of Otolaryngology–Head and Neck Surgery Foundation.)

The precision health era is likely to reduce and respond to antimicrobial resistance (AMR). Our stewardship and precision efforts share terminology, seeking to deliver the "right drug, at the right dose, at the right time." Already, rapid diagnostic testing, phylogenetic surveillance, and real-time outbreak response provide just a few examples of molecular advances we dub "precision stewardship." However, the AMR causal factors range from the molecular to that of global health policy. Mirroring the cross-sectoral nature of AMR science, the research addressing the ethical, legal and social implications (ELSI) of AMR ranges across academic scholarship. As the rise of AMR is accompanied by an escalating sense of its moral and social significance, what is needed is a parallel field of study. In this paper, we offer a gap analysis of this terrain, or an agenda for "the ELSI of precision stewardship." In the first section, we discuss the accomplishments of a multi-decade U.S. national investment in ELSI research attending to the advances in human genetics. In the next section, we provide an overview of distinct ELSI topics pertinent to AMR. The distinctiveness of an ELSI agenda for precision stewardship suggests new opportunities for collaboration to build the stewardship teams of the future. [ABSTRACT FROM AUTHOR]

Background: Complete SARS-CoV-2 genome sequencing in the early phase of the outbreak in Iran showed two independent viral entries. Subsequently, as part of a genome surveillance project, we aimed to characterize the genetic diversity of SARS-CoV-2 in Iran over one year after emerging. Methods: We provided 319 SARS-CoV-2 whole-genome sequences used to monitor circulating lineages in March 2020-May 2021 time interval. Results: The temporal dynamics of major SARS-CoV-2 clades/lineages circulating in Iran is comparable to the global perspective and represent the 19A clade (B.4) dominating the first disease wave, followed by 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7), leading the second, third and fourth waves, respectively. We observed a mixture of circulating B.1.36, B.1.1.413, B.1.1.7 lineages in winter 2021, paralleled in a fading manner for B.1.36/B.1.1.413 and a growing rise for B.1.1.7, prompting the fourth outbreak. Entry of the Delta variant, leading to the fifth disease wave in summer 2021, was detected in April 2021. This study highlights three lineages as hallmarks of the SARS-CoV-2 outbreak in Iran; B4, dominating early periods of the epidemic, B.1.1.413 (B.1.1 with the combination of [D138Y-S477N-D614G] spike mutations) as a characterizing lineage in Iran, and the co-occurrence of [I100T-L699I] spike mutations in half of B.1.1.7 sequences mediating the fourth peak. It also designates the renowned combination of G and GR clades' mutations as the top recurrent mutations. Conclusion: In brief, we provided a real-time and comprehensive picture of the SARS-CoV-2 genetic diversity in Iran and shed light on the SARS-CoV-2 transmission and circulation on the regional scale. [ABSTRACT FROM AUTHOR]

The demand for renewable energy is increasing. Klebsiella pneumoniae is one of the most promising strains to produce 2,3-butanediol (2,3-BD). Compared with chemical methods, the biological production of 2,3-BD has the characteristics of substrate safety, low cost, and low energy consumption. However, excessive glucose concentrations can cause damage to cells. Therefore, this study investigated the effect of sRNA-SgrS as a sugar transport regulator on the fermentative production of 2,3-BD by K. pneumoniae in response to sugar stress. We designed multiple mutants of K. pneumoniae HD79 to redistribute its carbon flux to produce 2,3-BD. It was found that the 2,3-BD yield of sgrS overexpressed strain decreased by 44% compared with the original strain. The results showed that a high concentration of sRNA-SgrS could accelerate the degradation of ptsG mRNA (encoding the glucose transporter EIICBGlc) and downregulate the expression levels of the budA gene (encoding the α-acetyllactate decarboxylase) and the budB gene (encoding the α-acetyllactate synthase) and budC gene (encoding the 2,3-BD dehydrogenase) but had no effect on the ack gene (encoding the acetate kinase) and the ldh gene (encoding the lactate dehydrogenase). It provides a theoretical basis and a technical reference for understanding the complex regulation mechanism of sRNA in microorganisms and the genetics and breeding in industrial fermentation engineering. [ABSTRACT FROM AUTHOR]

Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 Arabidopsis thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes. [ABSTRACT FROM AUTHOR]

Aims: Klebsiella pneumoniae is an important cause of nosocomial infections. The present study sought to detect resistance status and the frequency of multidrug-resistant (MDR), extensively drug-resistant (XDR), and pandrug-resistant (PDR) K. pneumoniae strains isolated from hospitalized patients. Materials and Methods: Confirmation of K. pneumoniae isolates was performed by polymerase chain reaction (PCR) for rpoB fragment. Drug susceptibility was done by disk diffusion method based on the Clinical and Laboratory Standards Institute. According to the susceptibility pattern, the strains were categorized as MDR, XDR, and PDR. Results: On the basis of PCR results, rpoB gene was identified in all 100 K. pneumoniae isolates. Most K. pneumoniae strains showed a high percentage of resistance against ampicillin-sulbactam (93%). On the other hand, tigecycline and fosfomycin were active against 100% and 90% isolates, respectively. The multiple resistance analysis of the strains showed that 58% and 13% of isolates were identified as MDR and XDR, respectively. Overall, no PDR isolate was detected in any tested strains. Conclusion: Our results demonstrated that the vast majority of K. pneumoniae strains indicated the MDR phenotype including a high resistance rate to common antibiotics. Therefore, it is suggested to implement antimicrobial susceptibility testing before prescribing, to assist in selecting the most effective agents within the antimicrobial categories for the treatment of infections with multiple antibiotic-resistant K. pneumoniae strains in hospitalized patients. [ABSTRACT FROM AUTHOR]

Aim: The current study aimed to investigate sequence variations in the C-terminus of latent membrane protein 1 (LMP1) in Epstein- Barr virus (EBV) isolates from Iranian patients with chronic gastritis or gastric cancer (GC). Background: LMP1, an essential viral oncoprotein, is the critical element in the immortalization of B cells. It contains a small twenty-four amino acid cytoplasmic N-terminal region, six transmembrane segments, and a two hundred amino acid cytoplasmic Cterminal domain. Most LMP1-mediated signal transduction events are moderated by some functional parts of the cytoplasmic Cterminal domain. Methods: Thirty-two EBV-positive biopsy tissues were obtained from patients with gastric cancer and patients with chronic gastritis. The C-terminal nucleotide sequences of LMP1 were amplified using nested-PCR and analyzed by DNA sequencing. Results Four to eight copies of the 11 repeat elements (codon 254--302) were observed in the carboxyl-terminal site of patients, but no relationship was found between the number of repeat sequences and disease status. The 30-bp deletion corresponding to codon 345--354 of the B95-8 strain was observed in 34% of isolates, and the remaining samples were non-deleted. In the gastric cancer group, a higher number of 33-bp repeats (≥5 repeats) was observed in 30-bp-deletion (100%) than in non-deleted (42%) isolates, and the difference was statistically significant. Analysis revealed that a gastritis isolate may be the result of recombination between Alaskan and China1 strains. Conclusion: Overall, the current results showed no association between C-terminal sequence variations of LMP1 and malignant or non-malignant isolate origin. [ABSTRACT FROM AUTHOR]

We assessed public perspectives of microbiome research privacy risks before and after a nationwide emergency was declared in the United States regarding the Covid‐19 pandemic. From January to July of 2020, we conducted an online survey of perceived privacy risks of microbiome research among U.S. adults. Among 3,106 participants (the preemergency group), most expressed that the microbiome posed privacy risks similar to those associated with DNA (60.3%) or medical records (50.6%) and that they would prefer detailed explanations (70.2%) of risk in consent materials. Only 8.9% reported moderate to high familiarity with microbiome privacy risks. In adjusted analyses, individuals who participated in the study after the Covid‐19 emergency was declared (the Covid‐19 emergency group) were less likely to express that microbiome privacy risks were similar to those of DNA or medical records and more likely to report familiarity with the privacy risks of microbiomes. There was a trend toward increased concern after the Covid‐19 emergency was declared (p = 0.053). Overall, the study revealed that many U.S. adults believe that microbiome privacy risks are similar to those associated with DNA or medical records, and they prefer detailed explanations in consent documents. Individuals who participated after the Covid‐19 emergency was declared reported greater knowledge of microbiome privacy risks but had more concern. [ABSTRACT FROM AUTHOR]

Background: The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota. Results: Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects. Conclusions: This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage. [ABSTRACT FROM AUTHOR]