Salivary polyreactive antibodies and Haemophilus influenzae are associated with respiratory infection severity in young children with recurrent respiratory infections.

BACKGROUND: Recurrent respiratory tract infections (rRTIs) are a common reason for immunodiagnostic testing in children, which relies on serum antibody level measurements. However, because RTIs predominantly affect the respiratory mucosa, serum antibodies may inaccurately reflect local immune defences. We investigated antibody responses in saliva and their interplay with the respiratory microbiota in relation to RTI severity and burden in young children with rRTIs. METHODS: We conducted a prospective cohort study including 100 children aged <10 years with rRTIs, their family members and healthy healthcare professionals. Total and polyreactive antibody concentrations were determined in serum and saliva (ELISA); respiratory microbiota composition (16S rRNA sequencing) and respiratory viruses (quantitative PCR) were characterised in nasopharyngeal swabs. Proteomic analysis (Olink) was performed on saliva and serum samples. RTI symptoms were monitored with a daily mobile phone application and assessed using latent class analysis and negative binomial mixed models. RESULTS: Serum antibody levels were not associated with RTI severity. Strikingly, 28% of salivary antibodies and only 2% of serum antibodies displayed polyreactivity (p<0.001). Salivary polyreactive IgA was negatively associated with recurrent lower RTIs (adjusted OR 0.80, 95% CI 0.67-0.94) and detection of multiple respiratory viruses (adjusted OR 0.76, 95% CI 0.61-0.96). Haemophilus influenzae abundance was positively associated with RTI symptom burden (regression coefficient 0.05, 95% CI 0.02-0.08). CONCLUSION: These results highlight the importance of mucosal immunity in RTI severity and burden, and suggest that the level of salivary polyreactive IgA and H. influenzae abundance may serve as indicators of infection severity and burden in young children with rRTIs.

Respiratory adenovirus infections in children: a focus on Africa.

PURPOSE OF REVIEW: Lower respiratory tract infections (LRTIs) are an important cause of child morbidity and mortality globally, especially in children under the age of 5 years in Africa. Respiratory viruses, including human adenoviruses (HAdVs), are common causes of LRTIs in children. This review aims to shed light on the epidemiology, clinical manifestations, sequelae, and treatment options specific to adenovirus respiratory infections in African children. RECENT FINDINGS: Recent evidence has challenged the perception that adenovirus is a negligible cause of LRTIs. Studies show HAdV emerging as the third most common viral pathogen in fatal pneumonias among under-5 children in low-income and middle-income African countries, contributing to 5.5% of all pneumonia deaths and ranking second in hospital-associated viral pneumonia deaths. Predominant HAdV serotypes associated with disease differ by country and region, and have changed over time. Risk factors for increased disease severity and long-term respiratory sequelae in previously healthy African children with HAdV LRTIs are not well established. SUMMARY: Although respiratory viruses, including HAdV, are recognized contributors to LRTIs, the prevalence and impact of adenovirus infections have been under-recognized and understated. Available data suggests that African children, particularly those under 5 years old, are at risk of severe sequelae from respiratory HAdV infections. Long-term sequelae, including bronchiectasis and postinfectious bronchiolitis obliterans, further underscore the significant impact of HAdV infections. However, the scarcity of comprehensive data hampers our understanding of the extent of the impact of HAdV infections on child lung health in Africa. We recommend scaled-up HAdV surveillance, ensuring its consistent inclusion in population-level LRTI assessments, and expanded and equitable access to diagnostics for early recognition of African children at risk of developing chronic sequelae and death. Enhanced understanding of adenovirus epidemiology and clinical outcomes and the availability of therapeutic options are essential for informed public health strategies and clinical care.

PHB Production by Bacillus megaterium LSRB 0103 Using Cornstarch and Urea.

Polyhydroxybutyrates (PHBs) are biopolymers that are good green alternative for synthetic carbon-based polymers, and are also one of the most researched members of the Polyhydroxyalkanoates (PHA) family. In this study, a gram-positive bacterial strain Bacillus megaterium LSRB 0103 was isolated from Pallikaranai Marshland, Chennai, India. Primary screening using Sudan Black dye revealed the presence of intracellular PHB granules. Minimal Davis Media (MDM) which was used or PHB production gave a yield of 0.7107 g/L. Subsequently, using response surface methodology (RSM), a central composite design (CCD) model was designed for media optimization having cornstarch, urea, and pH as independent variables. The findings of the CCD model were fitted into a second-order polynomial equation. The RSM model predicted the maximum PHB yield of 0.93 g/L, at these independent variable levels, cornstarch, 5 g/L; urea, 2.1 g/L; and pH 7.0; while the experimental PHB yield was 0.94 g/L, with a percentage error of 1.1%. This study is the first-time report of production of PHB by Bacillus megaterium using cornstarch and urea as substrate.

Associations between restrictive feeding practices and children's dietary intake: Systematic review and meta-analyses.

BACKGROUND: Parents' attempt to limit or restrict children's intake of 'unhealthy' or discretionary foods has been widely considered as a counterproductive feeding practice associated with poorer dietary outcomes, but empirical evidence is varied. AIM: The present systematic literature review aimed to investigate the association between parental restriction and children's dietary intake. METHOD: Studies were identified through PsycInfo, MEDLINE, CINAHL, Web of Science, and Scopus databases on April 29th, 2022. Included were peer-reviewed, English-language articles published between 2001 and 2022, with an effect size between restriction and children's intake of foods that are 'healthy' (i.e., fruit, vegetables, other general healthy foods) or 'discretionary' (i.e., sweet or savoury energy-dense/nutrient poor foods, high-sugar foods, high-salt/fat foods, and high-energy/sugar-sweetened beverages), or overall diet quality. Risk of bias was assessed using a quality assessment checklist designed to evaluate survey studies. RESULTS: Included studies (n = 44) were most often conducted in the USA, cross-sectional, and participants were mothers. Effect sizes (k = 59) from 21 studies were used in nine meta-analyses investigating various healthy and discretionary dietary intake variables. No meta-analytic effects were statistically significant. Qualitative synthesis of effect sizes ineligible for meta-analysis (k = 91) identified patterns of associations between restriction and increased intake of healthy foods, and decreased intake of discretionary foods. CONCLUSIONS: Studies used a diverse selection of measures of restriction and dietary intake, limiting the ability of this review to make accurate cross-study comparisons. However, results suggest that instead of restriction being detrimental for children's dietary outcomes, it may be unrelated, or associated with more beneficial dietary outcomes. Research that utilises validated measures of restriction and dietary outcomes and a longitudinal design is needed to clarify this association.

A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data.

Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data.

CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine.

Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. When viruses infect bacteria, a small portion of the viral DNA is inserted into the bacterial DNA in a specific pattern to produce segments known as CRISPR arrays. Metagenome assembled genomes (MAGs) were used in our study to identify the CRISPR sequence for determining the interacted phage. Metagenomic data from a coal mine was used to perform a computational study. From raw reads, 206151 contigs were assembled. Then contigs were clustered into 150 Metagenome assembled genomes from which 78 non-redundant MAGs were selected. Using the CHECKM standard, seven MAGs were found to have >80 completeness and <20 contaminations. Those MAGs were analyzed for the presence of CRISPR elements. Out of seven MAGs, four MAGs have the CRISPR elements and are searched against the VIROblast database. CRISPR arrays have 4, 1, 3, and 7 spacer sequences in the MAGs of Burkholderia, Acinetobacter, Oxalobacteraceae, and Burkholderia multivorans respectively. The uncultured Caudovirales phage genomic regions were present in the genomes of Burkholderia, Oxalobacteriaceae, and Burkholderia multivorans. This study follows the unconventional metagenomics workflow to provide a better understanding of bacteria and phage interactions.

Clinical and biochemical footprints of inherited metabolic diseases. XII. Immunological defects.

Immunological problems are increasingly acknowledged manifestations in many inherited metabolic diseases (IMDs), ranging from exaggerated inflammation, autoimmunity and abnormal cell counts to recurrent microbial infections. A subgroup of IMDs, the congenital disorders of glycosylation (CDG), includes CDG types that are even classified as primary immunodeficiencies. Here, we reviewed the list of metabolic disorders reported to be associated with various immunological defects and identified 171 IMDs accompanied by immunological manifestations. Most IMDs are accompanied by immune dysfunctions of which immunodeficiency and infections, innate immune defects, and autoimmunity are the most common abnormalities reported in 144/171 (84%), 44/171 (26%) and 33/171 (19%) of IMDs with immune system involvement, respectively, followed by autoinflammation 17/171 (10%). This article belongs to a series aiming at creating and maintaining a comprehensive list of clinical and metabolic differential diagnoses according to organ system involvement.

Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: a metagenomic approach.

Pichavaram mangrove forest was established as a wetland of International Importance by Article 2.1 in April 2022 by the Ministry of Environment, Forest and Climate Change, India. Even though it is a conserved site, xenobiotic agrochemical leaching on the forest land during monsoon is inevitable. These threaten the microbial diversity in the environment. Xenobiotic degradation is achieved using bacterial consortia already acclimatised to this environment. This study aims to identify the indigenous microbial consortia able to degrade xenobiotic compounds such as fluorobenzoate, furfural, and steroids. Pichavaram mangrove metagenomic dataset was obtained by shotgun sequencing of soil DNA and processed using the automated tool SqueezeMeta. Further, the DIAMOND database provided the taxonomical classification of the microbes in each contig. With reference to the KEGG database, the selected xenobiotic degradation pathways were confirmed in the dataset. Of 1,253,029 total contigs, 1332, 72 and 1262 were involved in fluorobenzoate, furfural and steroid degradation, respectively. This study identified that microbial consortia comprising Marinobacter, Methyloceanibacter and Vibrio natriegens/Gramella sp. can degrade fluorobenzoate. While Afipia, Nitrosopumilus sp., and Phototrophicus methaneseepsis favour the degradation of furfural compound. The steroid degradation pathway possessed a plethora of bacteria belonging to the phylum Proteobacteria.

Antibody deficiencies in children are associated with prematurity and a family history of infections.

BACKGROUND: Recurrent respiratory tract infections (rRTIs) frequently affect young children and are associated with antibody deficiencies. We investigated the prevalence of and epidemiological risk factors associated with antibody deficiencies in young children with rRTIs and their progression over time, and linked these to prospectively measured RTI symptoms. METHODS: We included children <7 years with rRTIs in a prospective cohort study. Patient characteristics associated with antibody deficiencies were identified using multivariable logistic regression analysis. RESULTS: We included 146 children with a median age of 3.1 years. Daily RTI symptoms were monitored in winter in n = 73 children and repeated immunoglobulin level measurements were performed in n = 45 children. Antibody deficiency was diagnosed in 56% and associated with prematurity (OR 3.17 [1.15-10.29]) and a family history of rRTIs (OR 2.37 [1.11-5.15]). Respiratory symptoms did not differ between children with and without antibody deficiencies. During follow-up, antibody deficiency diagnosis remained unchanged in 67%, while 18% of children progressed to a more severe phenotype. CONCLUSION: Immune maturation and genetic predisposition may lie at the basis of antibody deficiencies commonly observed in early life. Because disease severity did not differ between children with and without antibody deficiency, we suggest symptom management can be similar for all children with rRTIs. IMPACT: An antibody deficiency was present in 56% of children <7 years with recurrent respiratory tract infections (rRTIs) in a Dutch tertiary hospital setting. Prematurity and a family history of rRTIs were associated with antibody deficiencies, suggesting that immune maturation and genetic predisposition may lie at the basis of antibody deficiencies in early life. RTI symptoms did not differ between children with and without antibody deficiency, suggesting that symptom management can be similar for all children with rRTIs, irrespective of humoral immunological deficiencies. During follow-up, 18% of children progressed to a more severe phenotype, emphasizing that early diagnosis is warranted to prevent long-term morbidity and increase quality of life.

Concordance in pathogen identification at the upper and lower respiratory tract of children with severe pneumonia.

BACKGROUND: Nasopharyngeal swabs are taken to determine the causative agent of community acquired pneumonia (CAP), while the reliability of upper respiratory tract sampling as a proxy for lower respiratory tract infections is still unclear. METHODS: Nasopharyngeal (NP) swabs, bronchoalveolar lavage (BAL) fluid samples and clinical data were collected from 153 hospitalized children between 3 months and 14 years of age with severe CAP, enrolled from March to June 2019. Written informed consent for the storage and use of the samples for further studies was obtained from the parents or caregivers. Putative pathogens were detected using a sensitive, high-throughput GeXP-based multiplex PCR and qPCR. RESULTS: The same bacterial species in paired samples were found in 29 (23.4%) and the same viral species in 52 (27.5%) of the patients. moderate concordance was found for Mycoplasma pneumoniae (ĸ=0.64), followed by Haemophilus influenzae (ĸ=0.42). The strongest discordance was observed for human adenovirus and also for Pseudomonas aeruginosa, the latter was exclusively detected in BAL samples. In the adenovirus cases strong concordance was associated with high viral loads in the NP swabs. CONCLUSION: The variation in concordance in pathogen detection in the upper and lower respiratory tract of children with severe pneumonia is generally high but varies depending on the species. Novel and impactful insights are the concordance between NP and BAL detection for M. pneumoniae and H. influenzae and the strong correlation between high adenoviral loads in NP swabs and detection in BAL fluid.

Development of novel composite data quality scores to evaluate facility-level data quality in electronic data in Kenya: a nationwide retrospective cohort study.

BACKGROUND: In this evaluation, we aim to strengthen Routine Health Information Systems (RHIS) through the digitization of data quality assessment (DQA) processes. We leverage electronic data from the Kenya Health Information System (KHIS) which is based on the District Health Information System version 2 (DHIS2) to perform DQAs at scale. We provide a systematic guide to developing composite data quality scores and use these scores to assess data quality in Kenya. METHODS: We evaluated 187 HIV care facilities with electronic medical records across Kenya. Using quarterly, longitudinal KHIS data from January 2011 to June 2018 (total N = 30 quarters), we extracted indicators encompassing general HIV services including services to prevent mother-to-child transmission (PMTCT). We assessed the accuracy (the extent to which data were correct and free of error) of these data using three data-driven composite scores: 1) completeness score; 2) consistency score; and 3) discrepancy score. Completeness refers to the presence of the appropriate amount of data. Consistency refers to uniformity of data across multiple indicators. Discrepancy (measured on a Z-scale) refers to the degree of alignment (or lack thereof) of data with rules that defined the possible valid values for the data. RESULTS: A total of 5,610 unique facility-quarters were extracted from KHIS. The mean completeness score was 61.1% [standard deviation (SD) = 27%]. The mean consistency score was 80% (SD = 16.4%). The mean discrepancy score was 0.07 (SD = 0.22). A strong and positive correlation was identified between the consistency score and discrepancy score (correlation coefficient = 0.77), whereas the correlation of either score with the completeness score was low with a correlation coefficient of -0.12 (with consistency score) and -0.36 (with discrepancy score). General HIV indicators were more complete, but less consistent, and less plausible than PMTCT indicators. CONCLUSION: We observed a lack of correlation between the completeness score and the other two scores. As such, for a holistic DQA, completeness assessment should be paired with the measurement of either consistency or discrepancy to reflect distinct dimensions of data quality. Given the complexity of the discrepancy score, we recommend the simpler consistency score, since they were highly correlated. Routine use of composite scores on KHIS data could enhance efficiencies in DQA at scale as digitization of health information expands and could be applied to other health sectors beyondHIV clinics.

Genetic testing of dogs predicts problem behaviors in clinical and nonclinical samples.

BACKGROUND: Very little is known about the etiology of personality and psychiatric disorders. Because the core neurobiology of many such traits is evolutionarily conserved, dogs present a powerful model. We previously reported genome scans of breed averages of ten traits related to fear, anxiety, aggression and social behavior in multiple cohorts of pedigree dogs. As a second phase of that discovery, here we tested the ability of markers at 13 of those loci to predict canine behavior in a community sample of 397 pedigree and mixed-breed dogs with individual-level genotype and phenotype data. RESULTS: We found support for all markers and loci. By including 122 dogs with veterinary behavioral diagnoses in our cohort, we were able to identify eight loci associated with those diagnoses. Logistic regression models showed subsets of those loci could predict behavioral diagnoses. We corroborated our previous findings that small body size is associated with many problem behaviors and large body size is associated with increased trainability. Children in the home were associated with anxiety traits; illness and other animals in the home with coprophagia; working-dog status with increased energy and separation-related problems; and competitive dogs with increased aggression directed at familiar dogs, but reduced fear directed at humans and unfamiliar dogs. Compared to other dogs, Pit Bull-type dogs were not defined by a set of our markers and were not more aggressive; but they were strongly associated with pulling on the leash. Using severity-threshold models, Pit Bull-type dogs showed reduced risk of owner-directed aggression (75th quantile) and increased risk of dog-directed fear (95th quantile). CONCLUSIONS: Our association analysis in a community sample of pedigree and mixed-breed dogs supports the interbreed mapping. The modeling shows some markers are predictive of behavioral diagnoses. Our findings have broad utility, including for clinical and breeding purposes, but we caution that thorough understanding is necessary for their interpretation and use.

The microbiota in respiratory tract infections: from association to intervention.

PURPOSE OF REVIEW: The respiratory microbiota has a role in respiratory tract infection (RTI) pathogenesis. On the mucosa, the respiratory microbiota interacts with potential pathogenic viruses, bacteria and the host immune system, including secretory IgA (sIgA). This review discusses the role of the respiratory microbiota and its interaction with the (mucosal) immune system in RTI susceptibility, as well as the potential to exploit the microbiota to promote health and prevent RTIs. RECENT FINDINGS: Recent studies confirm that specific microbiota profiles are associated with RTI susceptibility and during susceptibility and found accompanying RTIs, although clear associations have not yet been found for SARS-CoV-2 infection. sIgA plays a central role in RTI pathogenesis: it stands under control of the local microbiota, while at the same time influencing bacterial gene expression, metabolism and defense mechanisms. Respiratory microbiota interventions are still newly emerging but promising candidates for probiotics to prevent RTIs, such as Corynebacterium and Dolosigranulum species, have been identified. SUMMARY: Improved understanding of the respiratory microbiota in RTIs and its interplay with the immune system is of importance for early identification and follow-up of individuals at risk of infection. It also opens doors for future microbiota interventions by altering the microbiota towards a healthier state to prevent and/or adjunctively treat RTIs.

Analysing the protection from respiratory tract infections and allergic diseases early in life by human milk components: the PRIMA birth cohort.

BACKGROUND: Many studies support the protective effect of breastfeeding on respiratory tract infections. Although infant formulas have been developed to provide adequate nutritional solutions, many components in human milk contributing to the protection of newborns and aiding immune development still need to be identified. In this paper we present the methodology of the "Protecting against Respiratory tract lnfections through human Milk Analysis" (PRIMA) cohort, which is an observational, prospective and multi-centre birth cohort aiming to identify novel functions of components in human milk that are protective against respiratory tract infections and allergic diseases early in life. METHODS: For the PRIMA human milk cohort we aim to recruit 1000 mother-child pairs in the first month postpartum. At one week, one, three, and six months after birth, fresh human milk samples will be collected and processed. In order to identify protective components, the level of pathogen specific antibodies, T cell composition, Human milk oligosaccharides, as well as extracellular vesicles (EVs) will be analysed, in the milk samples in relation to clinical data which are collected using two-weekly parental questionnaires. The primary outcome of this study is the number of parent-reported medically attended respiratory infections. Secondary outcomes that will be measured are physician diagnosed (respiratory) infections and allergies during the first year of life. DISCUSSION: The PRIMA human milk cohort will be a large prospective healthy birth cohort in which we will use an integrated, multidisciplinary approach to identify the longitudinal effect human milk components that play a role in preventing (respiratory) infections and allergies during the first year of life. Ultimately, we believe that this study will provide novel insights into immunomodulatory components in human milk. This may allow for optimizing formula feeding for all non-breastfed infants.

All-cause and cause-specific mortality rates for Kisumu County: a comparison with Kenya, low-and middle-income countries.

BACKGROUND: Understanding the magnitude and causes of mortality at national and sub-national levels for countries is critical in facilitating evidence-based prioritization of public health response. We provide comparable cause of death data from Kisumu County, a high HIV and malaria-endemic county in Kenya, and compared them with Kenya and low-and-middle income countries (LMICs). METHODS: We analyzed data from a mortuary-based study at two of the largest hospital mortuaries in Kisumu. Mortality data through 2019 for Kenya and all LMICs were downloaded from the Global Health Data Exchange. We provided age-standardized rates for comparisons of all-cause and cause-specific mortality rates, and distribution of deaths by demographics and Global Burden of Disease (GBD) classifications. RESULTS: The all-cause age-standardized mortality rate (SMR) was significantly higher in Kisumu compared to Kenya and LMICs (1118 vs. 659 vs. 547 per 100,000 population, respectively). Among women, the all-cause SMR in Kisumu was almost twice that of Kenya and double the LMICs rate (1150 vs. 606 vs. 518 per 100,000 population respectively). Among men, the all-cause SMR in Kisumu was approximately one and a half times higher than in Kenya and nearly double that of LMICs (1089 vs. 713 vs. 574 per 100,000 population). In Kisumu and LMICs non-communicable diseases accounted for most (48.0 and 58.1% respectively) deaths, while in Kenya infectious diseases accounted for the majority (49.9%) of deaths. From age 10, mortality rates increased with age across all geographies. The age-specific mortality rate among those under 1 in Kisumu was nearly twice that of Kenya and LMICs (6058 vs. 3157 and 3485 per 100,000 population, respectively). Mortality from injuries among men was at least one and half times that of women in all geographies. CONCLUSION: There is a notable difference in the patterns of mortality rates across the three geographical areas. The double burden of mortality from GBD Group I and Group II diseases with high infant mortality in Kisumu can guide prioritization of public health interventions in the county. This study demonstrates the importance of establishing reliable vital registry systems at sub-national levels as the mortality dynamics and trends are not homogeneous.

Parental and physician's point-of-view towards antibiotic prescriptions and discharge conversations in the pediatric emergency department.

BACKGROUND: Within Europe, the Netherlands has one of the lowest antibiotic consumption rates. We aimed to gain insight into attitudes of Dutch physicians and parents towards information provided during discharge conversations in the emergency department (ED) and towards antibiotic use in children, in order to obtain information on the assumptions and beliefs that underlie a practice of low prescription rates. METHODS: Discharge conversations of 70 children presenting with an infectious disease at the ED were observed. After 7-10 days, 55 parents were called for a semi-structured interview. In addition, 29 pediatricians and pediatric residents completed a questionnaire on their prescription behaviour. RESULTS: Concerns about (recognizing) the severity of their child's infection was parents' main motivation to seek help. Both pediatricians and parents reported a general reluctance towards antibiotic use. While pediatricians took appropriateness based on indication and the risk of antimicrobial resistance development into account when considering antibiotic treatment, a thorough medical assessment was deemed more important for Dutch parents than any type of therapeutic treatment, including antibiotics. The topic most often discussed during the discharge conversations was safety netting instructions (in 86%), which were discussed more often during discharge conversations with parents of children that did not receive antibiotic treatment (91% versus 69%). CONCLUSION: Dutch pediatricians and parents are both reluctant to use antibiotics for uncomplicated infections in children, but for different reasons. The emphasis of discharge conversations was on safety netting instructions, which seems to be an alternative for (early) antibiotic use in our setting and may guide overuse prevention strategies in settings where antibiotic overuse is more common.

Nasopharyngeal Microbiota Profiles in Rural Venezuelan Children Are Associated With Respiratory and Gastrointestinal Infections.

BACKGROUND: Recent research suggests that the microbiota affects susceptibility to both respiratory tract infections (RTIs) and gastrointestinal infections (GIIs). In order to optimize global treatment options, it is important to characterize microbiota profiles across different niches and geographic/socioeconomic areas where RTI and GII prevalences are high. METHODS: We performed 16S sequencing of nasopharyngeal swabs from 209 Venezuelan Amerindian children aged 6 weeks-59 months who were participating in a 13-valent pneumococcal conjugate vaccine (PCV13) study. Using random forest models, differential abundance testing, and regression analysis, we determined whether specific bacteria were associated with RTIs or GIIs and variation in PCV13 response. RESULTS: Microbiota compositions differed between children with or without RTIs (P = .018) or GIIs (P = .001). Several species were associated with the absence of infections. Some of these health-associated bacteria are also observed in developed regions, such as Corynebacterium (log2(fold change [FC]) = 3.30 for RTIs and log2(FC) = 1.71 for GIIs), while others are not commonly observed in developed regions, such as Acinetobacter (log2(FC) = 2.82 and log2(FC) = 5.06, respectively). Klebsiella spp. presence was associated with both RTIs (log2(FC) = 5.48) and GIIs (log2(FC) = 7.20). CONCLUSIONS: The nasopharyngeal microbiota of rural Venezuelan children included several bacteria that thrive in tropical humid climates. Interestingly, nasopharyngeal microbiota composition not only differed in children with an RTI but also in those with a GII, which suggests a reciprocal interplay between the 2 environments. Knowledge of region-specific microbiota patterns enables tailoring of preventive and therapeutic approaches.

Clinical Experience With Severe Acute Respiratory Syndrome Coronavirus 2-Related Illness in Children: Hospital Experience in Cape Town, South Africa.

BACKGROUND: Children seem relatively protected from serious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related disease, but little is known about children living in settings with high tuberculosis and human immunodeficiency virus (HIV) burden. This study reflects clinical data on South African children with SARS-CoV-2. METHODS: We collected clinical data of children aged <13 years with laboratory-confirmed SARS-CoV-2 presenting to Tygerberg Hospital, Cape Town, between 17 April and 24 July 2020. RESULTS: One hundred fifty-nine children (median age, 48.0 months [interquartile range {IQR}, 12.0-106.0 months]) were included. Hospitalized children (n = 62), with a median age of 13.5 months (IQR, 1.8-43.5 months) were younger than children not admitted (n = 97; median age, 81.0 months [IQR, 34.5-120.5 months]; P < .01.). Thirty-three of 159 (20.8%) children had preexisting medical conditions. Fifty-one of 62 (82.3%) hospitalized children were symptomatic; lower respiratory tract infection was diagnosed in 21 of 51 (41.2%) children, and in 11 of 16 (68.8%) children <3 months of age. Respiratory support was required in 25 of 51 (49.0%) children; 13 of these (52.0%) were <3 months of age. One child was HIV infected and 11 of 51 (21.2%) were HIV exposed but uninfected, and 7 of 51 (13.7%) children had a recent or new diagnosis of tuberculosis. CONCLUSIONS: Children <1 year of age hospitalized with SARS-CoV-2 in Cape Town frequently required respiratory support. Access to oxygen may be limited in some low- and middle-income countries, which could potentially drive morbidity and mortality. HIV infection was uncommon but a relationship between HIV exposure, tuberculosis, and SARS-CoV-2 should be explored.

IND-enzymes: a repository for hydrolytic enzymes derived from thermophilic and psychrophilic bacterial species with potential industrial usage.

Biocatalysts provide many advantages over the traditional chemically assisted processes prevalent in industries. Consequently, the search for novel enzymes has increased over the years with a renewed interest in thermophilic and psychrophilic bacterial species. Enzymes or extremozymes extracted from such species have exhibited an affinity to extreme temperatures which is a prerequisite for many industrial applications. However, utilisation of these enzymes faces a major bottleneck. The distribution of sequence data associated with thermophiles and psychrophiles is overwhelming, spanning various databases and scientific literature. Based on more than 100 publications and genomes from over 300 thermophilic and psychrophilic bacterial species, we have constructed the database IND-Enzymes (indenzymes.srmist.edu.in). This database consists of over 20,120 nucleotide and protein sequences belonging to the hydrolytic enzyme class lipase, protease, esterase and amylase. Users can access over 100 published enzymes, 200 PDB structural data. Enzymes derived from genomes can be directly downloaded and users can also access the entire annotation data derived from species individually. Along with an alignment tool and python based pipelines, IND-Enzymes serves as the largest sequence repository for hydrolytic enzymes from thermophilic and psychrophilic bacterial species. This database showcases resources that are essential for protein engineering of hot-cold stable enzymes.

Compost Samples from Different Temperature Zones as a Model to Study Co-occurrence of Thermophilic and Psychrophilic Bacterial Population: a Metagenomics Approach.

In this study, using a metagenomic approach, we explore the bacterial diversity of compost sites categorized based on their ambient temperatures. The two sites were Reckong Peo in the lower Himalayas and Tambaram in the southern region of the country, namely, CPR and CT. Following assembly of the raw reads from shotgun metagenomics, similarity hits were generated using NCBI BLAST + and SILVA database. A total of 1463 and 1483 species were annotated from CPR and CT. A species-level annotation was performed using a python-based literature search pipeline revealing their growth characteristics. Thermophiles Thermomonospora curvata and Thermus scotoductus were among the prominent species in CT. CPR too was seen abundant with Acidothermus cellulolyticus and Moorella thermoacetica, constituting 10% of the population. Nearly 3% of the identified species in the site CPR were psychrophilic. Although found higher in CPR, psychrophilic species were identified in CT too. Flavobacterium and Psychrobacter spp. were present in both sites without any significant changes in their relative distribution contrary to the thermophilic species abundance (z = - 4.3). Akin to the sequenced samples, database-derived metagenomes also showed similar distribution of thermophiles and psychrophiles. Identifying such peculiar prevalence of extremophiles can be central to understanding extended growth temperatures.